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Prediction program of secondary structure from sequence of proteins according to the method of Chou and… Pham, Anne-Marie 1981

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PREDICTION PROGRAM OF SECONDARY STRUCTURE FROM SEQUENCE OF PROTEINS ACCORDING TO THE METHOD OF CHOU AND FASMAN by ANNE-MARIE PHAM B . S c , The U n i v e r s i t y of M o n t p e l l i e r , 1978 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE i n THE FACULTY OF GRADUATE SUDIES (Department of Food S c i e n c e ) We a c c e p t t h i s t h e s i s as co n f o r m i n g t o the r e q u i r e d s t a n d a r d THE UNIVERSITY OF BRITISH COLUMBIA J u l y 1981 (c) Anne-Marie Pham, 1981 I n p r e s e n t i n g t h i s t h e s i s i n p a r t i a l f u l f i l m e n t o f t h e r e q u i r e m e n t s f o r an advanced degree a t t h e U n i v e r s i t y o f B r i t i s h C o l u m b i a , I a g r e e t h a t t h e L i b r a r y s h a l l make i t f r e e l y a v a i l a b l e f o r r e f e r e n c e and s t u d y . I f u r t h e r agree t h a t p e r m i s s i o n f o r e x t e n s i v e c o p y i n g o f t h i s t h e s i s f o r s c h o l a r l y p u r p o s e s may be g r a n t e d by t h e head o f my department o r by h i s o r h e r r e p r e s e n t a t i v e s . I t i s u n d e r s t o o d t h a t c o p y i n g o r p u b l i c a t i o n o f t h i s t h e s i s f o r f i n a n c i a l g a i n s h a l l n o t be a l l o w e d w i t h o u t my w r i t t e n p e r m i s s i o n . Food S c i e n c e Department o f The U n i v e r s i t y o f B r i t i s h C o l u m b i a 2075 Wesbrook P l a c e V ancouver, Canada V6T 1W5 Date July 7, 1981 DE-6 (2/79) ABSTRACT S e v e r a l methods have been proposed f o r p r e d i c t i n g the secondary s t r u c t u r e o f p r o t e i n s . The method of Chou and Fasman (1974a, 1974b, 1978a, 1978b) i s r e l a t i v e l y s i m p l e i n t h e o r y and r e a s o n a b l y a c c u r a t e . U n f o r t u n a t e l y , the r u l e s o f Chou and Fasman are sometimes ambiguous and can be i n t e r -p r e t e d d i f f e r e n t l y by r e s e a r c h e r s . S e v e r a l attempts have been made f o r c o m p u t e r i z a -t i o n o f the r u l e s o f Chou and Fasman (Argos e_t al_. , 1976; Chou and Fasman, 1978b; D z i o n a r a e_t al_. , 1977). However, they are f o r c o m p u t a t i o n o f o n l y a p o r t i o n o f the p r o t e i n secondary s t r u c t u r e . The f i n a l assignment of the e n t i r e s t r u c t u r e has t o r e l y on the i n d i v i d u a l ' s m a n i p u l a t i o n . In a d d i t i o n to t h r e e s e p a r a t e computer programs f o r p r e d i c t i o n o f the a - h e l i x , g-sheet and g - t u r n s t r u c t u r e s , a f o u r t h program was w r i t t e n f o r c l a r i f y i n g o v e r l a p p i n g areas between a - h e l i x and g-sheet. A l t h o u g h the p r e d i c t e d s t r u c t u r e s o f 24 p r o t e i n s w i t h known c o n f o r m a t i o n were i n g e n e r a l s a t i s f a c t o r y , t h e r e were a number o f m i s s i n g areas and boundary v a l u e s d i f f e r e n t from X-ray d i f f r a c t i o n p a t t e r n s . In an attempt to improve the a c c u r a c y o f the p r e d i c t i o n , the n u c l e a t i o n r u l e s were m o d i f i e d to emphasize i i \ importance o f the type and p o s i t i o n s o f amino a c i d r e s i d u e s i n the r e g i o n . F u r t h e r m o r e , an e x t r a s t e p f o r boundary adjustment was added to the s e a r c h f o r a - h e l i x and 3-sheet r e g i o n s . T h i s s t e p compared the importance o f the boundary c o n f o r m a t i o n a l parameters and the p o s s i b l e i n t e r f e r e n c e o f the d i f f e r e n t c o n f o r m a t i o n s at the b o u n d a r i e s o f the p r e d i c t e d r e g i o n s . These m o d i f i c a t i o n s produced p r e d i c t e d secondary s t r u c t u r e s w hich were i n good agreement w i t h the X-ray d i f f r a c t i o n p a t t e r n s and the p r e d i c t e d p a t t e r n s o f Chou and Fasman '(1974b, 1978b) . The Matthews': c o e f f i c i e n t (C) c a l c u l a t e d f o r a - h e l i x and B-sheet were 0.39 or above, meaning t h a t the p r e d i c t i o n would be q u i t e u s e f u l a l t h o u g h t h e r e might be one or two h e l i c a l r e g i o n s missed or o v e r p r e d i c t e d . The p a i r e d -sample t - t e s t r e v e a l e d t h a t the v a l u e s o f (P < 0.01) and C D (E < 0.05) c a l c u l a t e d f o r the p r e s e n t p r e d i c t i o n were p — s i g n i f i c a n t l y improved from the v a l u e s o f Chou and Fasman. The c o m p u t e r - a s s i s t e d t e c h n i q u e d e s c r i b e d i n t h i s t h e s i s , t h e r e f o r e , would decrease the d i s c r e p a n c y between the ; p r e d i c t e d d a t a from d i f f e r e n t r e s e a r c h e r s due to the ambiguous i n t e r p r e t a t i o n s o f the r u l e s o f Chou and Fasman. The second p a r t o f t h i s s tudy i n v o l v e d the a p p l i c a t i o n o f the program to s e v e r a l f o o d r e l a t e d p r o t e i n s i i i (bovine serum a l b u m i n , a ^ - c a s e i n , 3 - c a s e i n , K - c a s e i n , chymosin, a - l a c t a l b u m i n , a - l a c t o g l o b u l i n , o v a l b u m i n , p e p s i n and t r y p s i n o g e n ) . A l t h o u g h r e f e r e n c e s c o u l d not be found f o r a l l p r o t e i n s t e s t e d , the r e s u l t s o b t a i n e d f o r K - c a s e i n and a - l a c t a l b u m i n were comparable to those r e p o r t e d by o t h e r r e s e a r c h e r s . S i n c e c o n f o r m a t i o n a l d a t a have l o n g be'en r e c o g n i z e d as c o n t r i b u t i n g to the i n f o r m a t i o n on p r o t e i n and enzyme f u n c t i o n a l i t y , the c o m p u t e r i z a t i o n o f the p r e d i c t i v e method of Chou and Fasman w i l l d e f i n i t e l y be a t o o l f o r e x p l a i n i n g the p r o t e i n f u n c t i o n a l i t y i n food p r o c e s s i n g . i v TABLE OF CONTENTS PAGE A b s t r a c t i i T a b l e o f C o n t e n t s v L i s t o f T a b l e s v i L i s t o f F i g u r e s i x Acknowledgements x i I n t r o d u c t i o n 1 L i t e r a t u r e Review 6 D e f i n i t i o n o f the d i f f e r e n t c o n f o r m a t i o n a l r e g i o n s : A. A l p h a - h e l i x 6 B. B e t a - s h e e t 8 C. C o i l r e g i o n 11 D. B e t a - t u r n 11 Review o f the v a r i o u s p r e d i c t i v e methods. 13 M a t e r i a l s and Methods 26 The Chou and Fasman p r e d i c t i v e method 26 A. Search f o r h e l i c a l r e g i o n s . 28 B. Search f o r 3-sheet r e g i o n s . 32 C. O v e r l a p p i n g a- and 3 - r e g i o n s . 34 D. Search f o r 3 - t u r n s . 36 E. E v a l u a t i o n o f the p r e d i c t i v e 37 a c c u r a c y v PAGE Amino a c i d sequence o f p r o t e i n s , 39 Programming. 4 0 R e s u l t s and D i s c u s s i o n , 41 Programming o f the method 41 A. Scheme f o r the s e a r c h o f h e l i x 42 and sheet r e g i o n s . B. Scheme f o r the s e a r c h o f 3 - t u r n s . 43 C. Scheme f o r s o l v i n g o v e r l a p p i n g 43 a- and 3-areas. E f f i c i e n c y o f the a - h e l i x p r e d i c t i o n . 47 E f f i c i e n c y o f the 3-sheet p r e d i c t i o n 128 E f f i c i e n c y o f the 3-t u r n p r e d i c t i o n 168 E f f i c i e n c y o f the r e s o l u t i o n o f o v e r l a p p i n g a - 172 and 3-areas. Comparison o f the p r e d i c t i v e a c c u r a c y 185 C o n f o r m a t i o n o f some food r e l a t e d p r o t e i n s 211 C o n c l u s i o n s 226 L i t e r a t u r e c i t e d 231 Appendix 241 v i LIST OF TABLES TABLE PAGE .1 C o n f o r m a t i o n a l parameters f o r 27 a - h e l i c a l and 8-sheet r e s i d u e s based on 29 p r o t e i n s 2 C o n f o r m a t i o n a l parameters o f h e l i c a l 29 boundary r e s i d u e s i n 29 p r o t e i n s C o n f o r m a t i o n a l parameters o f g-sheet 30 boundary r e s i d u e s i n 29 p r o t e i n s Frequency h i e r a r c h i e s o f amino a c i d s 37 i n t h e 8-turns o f 29 p r o t e i n s Comparison o f e x p e r i m e n t a l (X-ray) 189 and p r e d i c t e d h e l i c a l r e g i o n s o b t a i n e d by Chou and Fasman and by our program b e f o r e and a f t e r i t s r e f i n e m e n t Comparison of e x p e r i m e n t a l (X-ray) 198 and p r e d i c t e d 8-sheet r e g i o n s o b t a i n e d by Chou and Fasman and by our program b e f o r e and a f t e r i t s r e f i n e m e n t Agreement f a c t o r s Q a, C a o b t a i n e d 207 by Chou and Fasman (1974b), Argos e_t aJL. (1976) and our program Agreement f a c t o r s Qg, Cg o b t a i n e d by Chou and Fasman, Argos e_t a_l. , and our program 209 v i i TABLE 9 10 PAGE Pe r c e n t a g e s o f h e l i x , s h e e t , and 215 t u r n o f some f o o d r e l a t e d p r o t e i n s o b t a i n e d w i t h our program H e l i x , s h e e t , and t u r n r e g i o n s o f 216 some food r e l a t e d p r o t e i n s as p r e d i c t e d by our program v i i i LIST OF FIGURES Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f b o v i n e serum albumin Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f a g ^ - c a s e i n (bovine) Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f 3 - c a s e i n (bovine) Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f K - c a s e i n ( b o v i n e ) Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f chymosin (bovine) Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f a - l a c t a l b u m i n (bovine) Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f $ - l a c t o g l o b u l i n ( bovine) i x LIST OF FIGURES (cont'd) Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f ovalbumin Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f p e p s i n ( p o r c i n e ) Schematic diagram o f the p r e d i c t e d secondary s t r u c t u r e o f t r y p s i n o g e n ( b o v i n e ) ACKNOWLEDGEMENTS The a u t h o r wishes t o expr e s s her s i n c e r e a p p r e c i a -t i o n t o her s u p e r v i s o r , Dr. S. N a k a i , P r o f e s s o r , Department o f Food S c i e n c e , f o r h i s c o n s t a n t a d v i s e , h e l p and encour-agement thro u g h o u t the co u r s e o f t h i s s t u d y , and i n the p r e p a r a t i o n o f the t h e s i s . She i s a l s o t h a n k f u l t o the members o f her graduate committee: Dr. R. C. F i t z s i m m o n s , A s s o c i a t e P r o f e s s o r , Department o f P o u l t r y S c i e n c e Dr. W.D. P o w r i e , P r o f e s s o r and Head, Department o f Food S c i e n c e Dr. B.J. Sk u r a , A s s i s t a n t P r o f e s s o r , Department o f Food S c i e n c e f o r t h e i r i n t e r e s t i n t h i s r e s e a r c h and f o r the r e v i e w o f t h i s t h e s i s . x i -1 INTRODUCTION B r o a d l y , t h e f u n c t i o n a l p r o p e r t i e s o f p r o t e i n s de-note a n y p h y s i c o - c h e m i c a l p r o p e r t y t h a t a f f e c t s the p r o c e s s i n g and b e h a v i o r o f p r o t e i n s i n food systems,as judged by the quaT-i t y a t t r i b u t e s o f the f i n a l p r o d u c t . The f u n c t i o n a l p r o p e r -t i e s are i n f l u e n c e d by and v a r y a c c o r d i n g t o : a) the source o f p r o t e i n s , b) the method o f i s o l a t i o n and p u r i f i c a t i o n , c) the c o n c e n t r a t i o n o f p r o t e i n s , d) the type o f m o d i f i c a t i o n s ( e n z y m a t i c , a c i d , o r a l k a l i n e h y d r o l y s i s ) , a n d e) e n v i r o n m e n t a l c o n d i t i o n s (pH,temperature,and i o n i c s t r e n g t h ) . An e x t e n s i v e r e v i e w o f the v a r i o u s s t u d i e s on p r o -t e i n f u n c t i o n a l i t y was p u b l i s h e d by K i n s e l l a (1976). In gener-' a l most of the changes i n p r o t e i n f u n c t i o n a l i t y have been found to be r e l a t e d t o the degree o f d e n a t u r a t i o n t h a t pro-t e i n s undergo. For exa m p l e , i n g e l a t i o n a heat t r e a t m e n t i s u-/. sually r e q u i r e d t o cause a t l e a s t p a r t i a l d e n a t u r a t i o n or un-f o l d i n g of. the p o l y p e p t i d e c h a i n s . Those u n f o l d e d c h a i n s w i l l t h en g r a d u a l l y a s s o c i a t e to form a g e l m a t r i x i f a t t r a c t i v e f o r c e s and thermodynamic c o n d t i o n s are s u i t a b l e . I t i s n e c e s s a r y t o c o n s i d e r the h y d r o p h o b i c , e l e c t r o n -i c and s t e r i c parameters o f m o l e c u l e s t o u n d e r s t a n d the mech-anism o f f o l d i n g and u n f o l d i n g o f p r o t e i n s , t h e i r b i o l o g i c a l a c t i v i t y , a n d t o p r e d i c t t h e i r b e h a v i o r upon c e r t a i n t r e a t m e n t s 1 ( i . e . , possible areas o f d e n a t u r a t i o n , e x t e n t o f u n f o l d i n g , ex-p o s i n g o f the h y d r o p h o b i c c o r e ) . The e l e c t r o n i c parameters can be e v a l u a t e d by e l e c t r o p h o r e s i s , w h i l e a f l u o r o m e t r i c method has been dev e l o p e d by Kato and N a k a i (1980) f o r e v a l u a t i o n o f h y d r o p h o b i c p a r a m e t e r s . X-ray d i f f r a c t i o n has been used to study the s t e r i c parameters o f more than s i x t y p r o t e i n s . In a d d i t i o n , X-ray d i f f r a c t i o n has c o n t r i b u t e d a g r e a t d e a l to our knowledge o f p r o t e i n - p r o t e i n , p r o t e i n - m e t a l , p r o t e i n - s o l v e n t i n t e r a c t i o n s ( L i l j a s and Rossman, 1974^ ; Matthews, 1975b). However , t h e s e c r y s t a l l o g r a p h i c a n a l y s e s cannot be a p p l i e d to most food p r o -t e i n s , or to many membrane and r i b o s o m a l p r o t e i n s due to problems o f c r y s t a l l i z a t i o n . F u r t h e r m o r e , the X-ray t e c h n i q u e i s q u i t e l a b o r i o u s , e x p e n s i v e and time-consuming. A r i f i n s e n e_t a^ L. (1961) , s t u d y i n g the r e f o r m a t i o n o f reduced b o v i n e r i b o n u c l e a s e , observed t h a t the n a t i v e s t r u c -t u r e o f a p r o t e i n i s c o n t r o l l e d by i t s amino a c i d sequence. T h i s f i n d i n g has become the m o t i v a t i o n f o r many attempts to o b t a i n p a t t e r n s o f p r o t e i n s t r u c t u r e from sequence d a t a . A l t h o u g h p r o t e i n f u n c t i o n a l i t y depends on - i t s 1 unique t h r e e - d i m e n s i o n a l t o p o l o g y , one can s t i l l l e a r n much from the p r e d i c t i o n o f i t s secondary s t r u c t u r e . N i s h i k a w a and Ooi (1972, 1973), i n a s t u d y o f p r o t e i n t e r t i a r y s t r u c t u r e , based t h e i r energy c a l c u l a t i o n s on the c o n f o r m a t i o n d e r i v e d from the 2 (computation of s e t s o f d i h e d r a l a n g l e s <j) and . To f i t the-polv- . ypreptide .; c h a i n o f the tobacco mosaic v i r u s p r o t e i n (TMV) to a low r e s o l u t i o n F o u r i e r map,some i n f o r m a t i o n on the secondary s t r u c t u r e was found to be d e s i r a b l e (Leberman,1971). Secondary s t r u c t u r e p r e d i c t i o n s w i l l p r o v i d e u s e f u l i n f o r m a t i o n on areas o f p r o t e i n m o l e c u l e s where the X-ray p a t -t e r n i s not y e t c l e a r l y r e s o l v e d , e s p e c i a l l y a t the N - t e r m i n a l . For i n s t a n c e , areas p r e d i c t e d as h e l i c a l by Chou and Fasman (1974b) f o r cytochrome b^ and f e r r i c y t o c h r o m e c had not been o d e t e c t e d by X-ray d i f f r a c t i o n a t 2.8A r e s o l u t i o n . T h e i r r e s u l t s o o were l a t e r c o n f i r m e d by X-ray a t 2.45A and 2.OA r e s o l u t i o n ( D i c k e r s o n ejt a^ L. ,1971; Mathews e t al_. , 1972; Takano ejt a l . , 1973). C o n f o r m a t i o n a l i n f o r m a t i o n may a l s o be used to de-s i g n e x p e r i m e n t a l models f o r c h e c k i n g the e f f e c t s o f conforma-t i o n a l changes on hormonal or enzymatic a c t i v i t y (Dunn and Chaiken,1975; F i n k and Bodanszky,1976; Perta et a l . , 1 9 7 5 ) . Some r e s e a r c h e r s (Deber e_t al_. , 1976 ; Kopple ejt al_. , ] 975) con-s i d e r e d s t u d y o f the g- t u r n a good s t a r t i n g p o i n t f o r e l u c i - : d a t i n g the i n f l u e n c e o f sequence and s u r r o u n d i n g s ,on p r o t e i n c o n f o r m a t i o n . The g - t u r n s t r u c t u r e i s p o t e n t i a l l y i d e n t i f i a -b l e and i s s i m p l e enough to be c h a r a c t e r i z e d by e x p e r i m e n t a l 13 and p r e d i c t i v e t e c h n i q u e s ( C NMR, c i r c u l a r d i c h r o i s m , c o n f o r -3 m a t i o n a l energy c a l c u l a t i o n s ) . I t a l s o h e l p s t o e x p l a i n the mode of a c t i v a t i o n o f b i o l o g i c a l l y a c t i v e p e p t i d e s (Bradbury et a l . , 1 9 7 6 ) . ' Another a p p l i c a t i o n o f the secondary s t r u c t u r e p r e d i c t i o n i s the comparison o f p r o t e i n s o f the same f a m i l y which may m a i n t a i n some c o n f o r m a t i o n a l homology d e s p i t e v a r i a -t i o n s i n sequence d a t a , s u c h as the case o f p r o i n s u l i n s and p r o t e i n a s e i n h i b i t o r s (Chou and Fasman,1978b). The method o f Chou and Fasman (Chou and Fasman, 1978a,1978b) has been f r e q u e n t l y c o n s i d e r e d the l e a s t c o m p l i -c a t e d i n use f o r the p r e d i c t i o n o f the secondary s t r u c t u r e o f p r o t e i n s . Y e t , i t p o s s e s s e s an o v e r a l l a c c u r a c y h i g h e r than random g u e s s i n g f o r a t h r e e - s t a t e model ( a - h e l i x , 8 - s h e e t • a n d c o i l s t a t e ) . The p e r c e n t o f t o t a l r e s i d u e s c o r r e c t l y i d e n t i -f i e d i n a p r o t e i n i s 75 f o r t h i s method v e r s u s 33 f o r random g u e s s i n g . Furthermore,Chou and Fasman's work has improved on the e a r l i e r s t u d i e s (Davies,1964; Havsteen,1966; G o l d s a c k , 1969) s i n c e i t t a k e s i n t o account c o m b i n a t i o n s o f r e s i d u e s t h a t are a - h e l i x , 8 - s h e e t and B-t u r n formers and b r e a k e r s . The computed p e r c e n t a g e o f secondary s t r u c t u r e o b t a i n e d by t h e i r method agrees q u i t e w e l l w i t h e s t i m a t e s based on CD s t u d i e s (Kawauchi and L i , 1974; G a r e l e_t a J . ,1975 ; G a r n i e r et a J . ,1975; Green,1975; Matthews , 197 5a ; Scanu e_t a l . , 1975 ; H o l l a d a y and Pue t t , 1 9 7 6 ; Munoz e t a l . , 1 9 7 6 ; W a l l a c e , 1 9 7 6 ) . 4 With the e x c e p t i o n of Argos ejt a l _ . (1976) , most of the l a b o r a t o r i e s t h a t have a p p l i e d the method of Chou and Fasman f o r s p e c i f i c i n v e s t i g a t i o n s on p r o t e i n s t r u c t u r e have not y e t r e p o r t e d a common c o m p u t e r i z e d t e c h n i q u e which can be used f o r o t h e r p r o t e i n s . The o b j e c t i v e s o f t h i s s tudy were as f o l l o w s : a) d e s i g n a program which would p r o v i d e s i m i l a r r e s u l t s to those p u b l i s h e d by Chou and Fasman (1974b, 1978b) and b) i f s u c c e s s f u l , e x t e n d ' t h i s program to food r e l a t e d p r o t e i n s so t h a t p o s s i b l e c o r r e l a t i o n between p r o t e i n f u n c t i o n a l i t y and c o n f o r m a t i o n a l changes may be b e t t e r u n d e r s t o o d . 5 LITERATURE REVIEW D e f i n i t i o n o f the D i f f e r e n t C o n f o r m a t i o n a l Regions A c c o r d i n g t o the TUPAC - IUB Commission on b i o -c h e m i c a l nomenclature(1970) the secondary s t r u c t u r e o f a segment o f a p o l y p e p t i d e c h a i n i s the l o c a l s p a t i a l a r r a n g e -ment o f i t s main .chain atoms w i t h o u t r e g a r d t o the conforma-- t i o n o f i t s s i d e c h a i n o r i t s r e l a t i o n s h i p w i t h o t h e r segments. The f o u r t y p i c a l c o n f o r m a t i o n s e n c ountered i n the secondary s t r u c t u r e a re the a - h e l i x , the 8-sheet, the 6-turn (bend), and the random c o i l . A. A l p h a - H e l i x The a - h e l i x c o n t a i n s 3.6 amino a c i d r e s i d u e s per t u r n o f the p r o t e i n backbone, w i t h the R groups o f the amino a c i d s e x t e n d i n g outward from the a x i s o f the h e l i c a l s t r u c t u r e . Hydrogen bonding can oc c u r between the hydrogen o f the NH group o f one p e p t i d e bond and the oxygen o f the CO group o f another p e p t i d e bond f o u r r e s i d u e s a l o n g t h e p r o t e i n c h a i n . The hydrogen bonds are n e a r l y p a r a l l e l t o the a x i s o f the h e l i x , l e n d i n g s t r e n g t h t o the h e l i c a l s t r u c t u r e . S i n c e n a t u r a l amino a c i d s e x i s t i n L c o n f i g - , u r a t i o n , a r i g h t - h a n d e d h e l i x i s more s t a b l e than a 6 l e f t - h a n d e d h e l i x . T h e r e f o r e , i f h e l i c a l s t r u c t u r e s e x i s t i n p r o t e i n s they are i n v a r i a b l y r i g h t - h a n d e d h e l i c e s (Anglemier and Montgomery, 1976). S i n c e the a - h e l i x has the l o w e s t f e a s i b l e f r e e e n e r g y , f o r m a t i o n o f t h i s s t r u c t u r e i s spontaneous, p r o v i d e d t h e r e are no i n t e r a c t i o n s between charged R groups or s t e r i c h i n d r a n c e by r e s i d u e s on the l a r g e r amino a c i d s . Examples o f p r o t e i n t y p e s i n which the a - h e l i x predominates are enzymes and r e s p i r a t o r y p r o t e i n s . T a k i n g i n t o account the s t r u c t u r a l r e q u i r e m e n t s t h a t are s p e c i f i c to g l o b u l a r p r o t e i n s , Lim (1974a) proposed a number o f c o n d i t i o n s n e c e s s a r y f o r a h e l i x to e x i s t a l o n g the p e p t i d e c h a i n . E a c h s e p a r a t e b e l i e a 1 reg ion ..must have "a.'". . h y d r o p h o b i c s i d e group or a group which would p e r m i t the h e l i x t o a t t a c h i t s e l f t o the h y d r o p h o b i c c o r e o f the g l o b u l e . From the a n a l y s i s o f immersion o f the h y d r o p h o b i c s i d e c h a i n s i t u a t e d on the a - h e l i x s u r f a c e , L i m (1974a) emphasized the r o l e o f h y d r o p h o b i c p a i r s , ( 1 - 5 ) , a n d hydro-p h o b i c t r i p l e t s , (1-2 - 5) or ( 1 - 4 - 5 ) , i n the attachment o f the a - h e l i x t o the h y d r o p h o b i c core. H y d r o p h o b i c - h y d r o -p h i l i c t r i p l e t s , (1-2 - 5) and ( 1 - 4 - 5 ) , a r e a l s o i m p o r t a n t f o r h e l i x s t a b i l i z a t i o n . A n other way to d e s c r i b e the c o n f o r m a t i o n o f a p r o t e i n c h a i n i s t o measure the d i h e d r a l a n g l e s <J> and $ which c o r r e s p o n d to r o t a t i o n s about the N-C?1 and C a-C bonds. 7 The <J>, I[J a n g l e s f o r r e s i d u e s i n a r e g u l a r r i g h t - h a n d e d h e l i x are g i v e n by (-57, -47°) (IUPAC-IUB, 1970). S i n c e 3.6 r e s i d u e s are r e q u i r e d t o form a hydrogen bond i n a s i n g l e t u r n o f the a - h e l i x , a l l c o n s e c u t i v e sequences o f f o u r o r more r e s i d u e s h a v i n g cj), i|> a n g l e s w i t h i n 40° o f (-60 , - 50") are c o n s i d e r e d t o be h e l i c a l . Some r e s i d u e s at the h e l i c a l ends may have d i h e d r a l a n g l e s t h a t f a l l o ut-s i d e the range -100° < * < -20° and -90° < i> <_-10° but are i n c l u d e d as h e l i c a l i f they show hydrogen bo n d i n g . Based on the above c r i t e r i a a t o t a l o f 152 h e l i c a l r e g i o n s were i d e n t i f i e d i n 29 p r o t e i n s (Chou and Fasman, 1978a, 1978b). B. Beta-Sheet In t h i s c o n f o r m a t i o n , the p e p t i d e backbone forms a z i g - z a g p a t t e r n w i t h the R groups o f the amino a c i d s e x t e n d i n g above and below the p e p t i d e c h a i n . S i n c e a l l p e p t i d e bonds are a v a i l a b l e f o r hydrogen b o n d i n g , t h i s c o n f o r m a t i o n a l l o w s maximum c r o s s - l i n k i n g between a d j a c e n t p e p t i d e c h a i n s and,thus, good s t a b i l i t y . Both p a r a l l e l and a n t i - p a r a l l e l p l e a t e d s h e e t s are p o s s i b l e . T h i s conforma-t i o n p redominates i n many f i b r o u s p r o t e i n s such as s i l k and i n s e c t f i b r e s . A c c o r d i n g t o Lim (1974a), 8 - s t r u c t u r a l r e g i o n s can be d i v i d e d i n t o t h r e e t y p e s by t h e i r r e l a t i v e p o s i t i o n 8 to the s u r f a c e o f the g l o b u l e : the i n t e r n a l , t h e s u r f a c e , a n d the s e m i - s u r f a c e t y p e . In o r d e r to e x i s t w i t h o u t v i o l a t i n g s t r u c t u r a l r e q u i r e m e n t s f o r g l o b u l a r p r o t e i n s , e a c h type s h o u l d be formed from a c e r t a i n number of h y d r o p h o b i c / h y d r o p h i l i c r e s -i d u e s . For i n s t a n c e , e n t i r e l y h y d r o p h o b i c r e g i o n s or hydropho-b i c r e g i o n s w i t h one or two h y d r o p h i l i c r e s i d u e s i n the f i r s t two and/or l a s t two p o s i t i o n s on the N- and C - t e r m i n a l w i l l f a v o r the i n t e r n a l t y p e . The c o n d i t i o n f o r a B-chain to be l o c a t e d on the s u r f a c e o f the g l o b u l e r e q u i r e s t h a t one s i d e o f the band have o n l y h y d r o p h o b i c groups and the o t h e r s i d e o n l y h y d r o p h i l i c groups. The s e m i - s u r f a c e type may e x i s t i n p e r i p h e r a l r e g i o n s o f the B-sheets. These r e g i o n s must have o n l y h y d r o p h i l i c s i -de groups or m a i n l y r e s i d u e s o f G l y . The p o s i t i o n o f c e r t a i n amino a c i d r e s i d u e s can a l -so be v e r y c r i t i c a l . Pro cannot be i n c l u d e d i n the B - s t r u c t u -re because o f the s t e r e o c h e m i s t r y o f i t s s i d e group. The s u r -f a c e type must not have G l y on the h y d r o p h o b i c s i d e or Gly and A l a on the h y d r o p h i l i c s i d e . T h i s i s s t i p u l a t e d by the f a c t t h a t the p r e s ence of G l y on the h y d r o p h o b i c s i d e w i l l impede the t i g h t p a c k i n g f o r m a t i o n i n the h y d r o p h o b i c c o r e . Water m o l e c u l e s can l o o s e n hydrogen bonds of the p e p t i d e groups neigh-b o u r i n g w i t h the C a atoms of Gly or A l a when thes e two ami-no a c i d s o c c u r on the h y d r o p h i l i c s i d e . 9 The <j) J T) a n g l e s f o r r e s i d u e s i n a p a r a l l e l - c h a i n 8-sheet and an a n t i p a r a l l e l 8-sheet have v a l u e s o f (-119°,113°) and (-139°, 135°) , r e s p e c t i v e l y (IUPAC-IUB',1970) . A- c o n s e c u t i v e sequence o f t h r e e or more r e s i d u e s h a v i n g <J>JTJ a n g l e s w i t h i n 40° o f (-120°,110°) or (-140°,135°) are c o n s i d e r e d t o be i n the 8-conformation,even i f these r e s i d u e s are not i n v o l v e d i n hydrogen bo n d i n g . However,residues a t the 8-ends t h a t have d i -h e d r a l a n g l e s o u t s i d e the range -180 u < cj) < -8.0 and 175 u~< i\> £ 70° are i n c l u d e d i n the 8 - r e g i o n i f they p a r t i c i p a t e i n a t l e a s t one hydrogen bond. The two end r e s i d u e s t h a t are not hy-drogen bonded i n a n t i p a r a l l e l B - s h e e t s are not counted as B-r e s i d u e s but i n s t e a d a re a s s i g n e d t o the c o i l c o n f o r m a t i o n and /or the B - t u r n c o n f o r m a t i o n . Chou and Fasman ( 1 9 7 8 a , 1 9 7 8 b ) , a n a l y z i n g 137 B - r e -g i o n s , o b s e r v e d 3 t w o - r e s i d u e B-segments ( p a p a i n 111-112", 130-131, and f e r r o d o x i n 50-51), 10 t h r e e - r e s i d u e . B - s e g m e n t s , and 9 f o u r - r e s i d u e 8-segments. T h i s number i n c r e a s e s t o 28 and 24 f o r the f i v e - r e s i d u e and s i x - r e s i d u e B - s e g m e n t s , r e s p e c t i v e l y . The t h r e e l o n g e s t . B - r e g i o n s c o n t a i n 17 r e s i d u e s ( t h e r m o l y s i n 16-32), 16 r e s i d u e s ( r i b o n u c l e a s e 96-111), and 15 r e s i d u e s ( l a c t a t e dehydrogenase 280-294). In c o n t r a s t , Chou and Fasman (1978a,1978b) i d e n t i f i e d 24 h e l i c a l segments l o n g e r than 17 r e s i d u e s i n 29 p r o t e i n s . The r e a s o n t h a t h e l i c e s a r e l o n g e r 10 than 3-sheets may be because o f the g r e a t e r ease o f h e l i c a l i n t r a c h a i n hydrogen bond f o r m a t i o n compared to 3 -sheet i n t e r c h a i n hydrogen bond f o r m a t i o n . C. C o i l Regions Residues i n the p r o t e i n t h a t a re not c l a s s i f i e d to be i n the h e l i x or 3-regions are a s s i g n e d t o the c o i l c o n f o r m a t i o n , i r r e s p e c t i v e l y o f the cj>, a n g l e s o f the r e s i d u e . Hence, t h r e e c o n s e c u t i v e r e s i d u e s h a v i n g the a -c o n f o r m a t i o n or two c o n s e c u t i v e r e s i d u e s h a v i n g the 3-c o n f o r m a t i o n but w i t h o u t hydrogen bonding are c o n s i d e r e d to be i n the c o i l s t a t e (Chou and Fasman, 1978b). The f o u r l o n g e s t c o i l s r e g i o n s found among 29 p r o t e i n s c o n t a i n e d 54 r e s i d u e s ( t h e r m o l y s i n 181-234) , 51 r e s i d u e s (carboxypep-t i d a s e 123-173), 46 r e s i d u e s ( f e r r o d o x i n 4-49) and 41 r e s i d u e s ( r u b r e d o x i n 14-54). These c o i l r e g i o n s cannot be c o n s i d e r e d . c o m p l e t e l y s t r u c t u r e l e s s s i n c e they may c o n t a i n many 3 - t u r n s . In the case o f f e r r e d o x i n and r u b r e d o x i n , the f l e x i b i l i t y o f these c o i l r e g i o n s i s s e v e r e l y r e s t r i c t e d by the i r o n - s u l f u r c o o r d i n a t i o n s . D. 3-Turn Regions The 3-turn i n v o l v e s f o u r c o n s e c u t i v e r e s i d u e s i n 11 a p r o t e i n where the p o l y p e p t i d e c h a i n f o l d s back on i t s e l f by n e a r l y 180°. I t i s t h e s e r e g i o n s o f c h a i n r e v e r s a l t h a t g i v e a p r o t e i n i t s g l o b u l a r i t y r a t h e r than l i n e a r i t y . Lewis ejt a l . (1971) proposed t h a t c h a i n r e v e r s a l s p l a y the i m p o r t a n t r o l e o f b r i n g i n g d i s t a n t p a r t s o f the p e p t i d e c h a i n t o g e t h e r , e n a b l i n g i n t e r a c t i o n s between h e l i x - h e l i x , a n t i p a r a l l e l -p a r a l l e l 3 - p l e a t e d s h e e t , or h e l i x - 3 - s h e e t . Venkatachalam (1968) was the f i r s t t o c h a r a c t e r i z e t h r e e types of t u r n s i n a t e t r a p e p t i d e where t h e r e i s a hydrogen bond between the CO group of r e s i d u e i and the NH group o f r e s i d u e ( i + 3 ) . Most bends ( 80%) from 8 p r o t e i n s c o n t a i n a t l e a s t one o r more o f the f o l l o w i n g r e s i d u e s : S e r , Thr, Asp, Asn and P r o . T h i s s u p p o r t s the i d e a t h a t t h e s e r e s i d u e s are r e s p o n s i b l e f o r bend s t a b i l i t y and perhaps f o r bend f o r m a t i o n . With the e x c e p t i o n o f Pro which can occupy o n l y a few backbone c o n f o r m a t i o n s , these r e s i d u e s have been shown to be c a p a b l e o f f o r m i n g s i d e chain-backbone hydrogen bonds w i t h t h e i r own backbone (Lewis ejt a J . , 1973) . U s i n g the X-ray atomic c o o r d i n a t e s from 29 p r o t e i n s , Chou and Fasman (1977) computed the C^ - C^ +^ d i s t a n c e s o f 4651 t e t r a p e p t i d e s . Those whose d i s t a n c e s were below and not i n a h e l i c a l r e g i o n were c o n s i d e r e d as 3 - t u r n s . Of the 457 3 - t u r n s e l u c i d a t e d , 243 o f them a l s o have 0^ - N^ +^ 12 d i s t a n c e s < 3. and were c o n s i d e r e d to have hydrogen bonding. Chou and Fasman (1977) a l s o a s s i g n e d 8-turns to 11 types s i m i l a r t o those o f Lewis e_t a J . (1973) based on the <f>, d i h e d r a l a n g l e s o f the second and t h i r d r e s i d u e s o f the bend. Review o f the V a r i o u s P r e d i c t i v e Methods S e v e r a l r e s e a r c h e r s have attempted to p r e d i c t the secondary s t r u c t u r e o f p r o t e i n s from t h e i r sequence d a t a . S z e n t - G y o r g y i and Cohen (1957) t h r o u g h t h e i r s t u d y w i t h the KMEF p r o t e i n s ( k e r a t i n , myosin, e p i d e r m i n and f i b r i n o g e n ) and w i t h c o l l a g e n , demonstrated t h a t the h e l i x c o n t e n t d e t e r m i n e d by o p t i c a l r o t a t o r y d i s p e r s i o n (ORD) i s i n v e r s e l y p r o p o r t i o n a l to the p e r c e n t a g e o f Pro r e s i d u e s d i s t r i b u t e d t hroughout the sequence. They c o n c l u d e d t h a t l e s s t han 3 p e r c e n t Pro d i s t r i b u t e d randomly i n a c h a i n p e r m i t s more than 50 p e r c e n t a - h e l i x . About 8 p e r c e n t Pro deforms the backbone i n t o a rancom c o i l . V e r y h i g h Pro c o n t e n t may f a v o r a p o l y - L - p r o l i n e h e l i x t y p e . D a v i e s (1964) u s i n g the b Q v a l u e o f ORD, found a s t r o n g c o r r e l a t i o n between the h e l i x c o n t e n t o f f i f t e e n p r o-t e i n s and the mole p e r c e n t a g e o f (Ser + Thr + V a l + l i e + C y s ) , r e s i d u e s c l a s s i f i e d as " n o n h e l i c a l - f o r m e r s " by B l o u t 13 et a l . (1960) and B l o u t (1962). No s t r o n g c o r r e l a t i o n between the h e l i x c o n t e n t and the mole p e r c e n t a g e o f any p a r t i c u l a r amino a c i d was o b s e r v e d ( D a v i e s , 1964). F u r t h e r m o r e , the c o r -r e l a t i o n r e p o r t e d by S z e n t - G y o r g y i and Cohen (1957) was not s u s t a i n e d when the number of p r o t e i n s was i n c r e a s e d to t h a t used by Davies (1964). T h e r e f o r e , the c o r r e l a t i o n s p r e v i o u s l y mentioned s h o u l d be a p p l i e d w i t h c a u t i o n u n t i l they are sup-p o r t e d by a d d i t i o n a l d a t a . Havsteen (1966) c a r r i e d out a s t a t i s t i c a l a n a l y -s i s o f the c o r r e l a t i o n between the c o n t e n t o f c e r t a i n amino a c i d s i n 40 p r o t e i n s and t h e i r ORD parameter b . A l i n e a r r e l a t i o n s h i p was o b s e r v e d between -1/b and the p e r c e n t a g e c o n t e n t o f (Ser + Thr + P r o ) ; t h u s , s u p p o r t i n g the p r e v i o u s f i n d i n g s on the i n t e r a c t i o n s between h y d r o x y l groups o f S e r , Thr and p e p t i d e l i n k a g e s which may i n t e r f e r e w i t h the forma-t i o n o f a - h e l i c e s . Pro r e s i d u e s t e n d t o d e s t a b i l i z e h e l i c e s by r e q u i r i n g a 90° bend o f the p e p t i d e c h a i n . The p r e s ence of a B-form of l e f t - h a n d e d h e l i c e s a l s o seems to markedly i n -f l u e n c e b . The i n f l u e n c e o f the amino a c i d s i d e c h a i n s on o b Q j u s t i f y t h e i r c l a s s i f i c a t i o n as h e l i x - f a v o r i n g , h e l i x - i n -d i f f e r e n t , and h e l i x - i n h i b i t i n g groups. Goldsack (1969), u s i n g the d a t a o f 107 p r o t e i n s , demonstrated t h a t the parameter b Q can be c o r r e l a t e d to the t o t a l c o n t e n-t J o f . t h e s o.'- c a l l e d he 1 i x - f o r m i n g am i n o a c i d s 14 ('Ala + A r g + Asp + Cys + Glu+ Leu + Lys) , as w e l l a s , to t h a t o f the n o n h e l i x - f o r m i n g group o f amino a c i d s ( G l y + Phe.+ Pro + Ser + Thr + Trp + T y r ) . Gn the o t h e r hand, u s i n g the a Q parameter, i t seemed t h a t no p a r t i c u l a r amino a c i d s i d e c h a i n g r o s s l y c o n t r o l s the amount o f £-structure i n a p r o t e i n . N e v e r t h e l e s s , f u r t h e r ORD c h a r a c t e r i z a t i o n o f the d i f f e r e n t 8 - s t r u c t u r e s ( i n t r a m o l e c u l a r p a r a l l e l and a n t i p a r a l l e l , as w e l l a s, i n t e r m o l e c u l a r c r o s s - 3 s t r u c t u r e ) w i l l be u s e f u l to e l u c i d a t e the r e l a t i o n s h i p between a Q and the amino a c i d c o m p o s i t i o n . These p r e l i m i n a r y e f f o r t s i n p r e d i c t i n g p r o t e i n c o n f o r m a t i o n r e l i e d h e a v i l y on ORD d a t a and amino a c i d c o m p o s i t i o n . The X-ray a n a l y s i s o f p r o t e i n s t r u c t u r e was a t an e a r l y s tage o f development and the amino a c i d sequence was s t i l l unknown f o r many p r o t e i n s . Scheraga (1960) attempted to c o n s t r u c t a t h r e e -d i m e n s i o n a l model of r i b o n u c l e a s e on the b a s i s o f a v a i l a b l e d a t a on the p r i m a r y , secondary and t e r t i a r y s t r u c t u r e s . I t s importance l i e s i n the f a c t t h a t i t p r o v i d e s a b a s i s t o p l a n e x p e r i m e n t s f o r the i n v e s t i g a t i o n o f s i d e c h a i n group i n t e r a c t i o n s and i t may a l s o be o f h e l p i n F o u r i e r a n a l y s i s o f X-ray d a t a on r i b o n u c l e a s e c r y s t a l s . On the b a s i s o f known sequence and s t r u c t u r e o f m y o g l o b i n , a l p h a - and b e t a - h e m o g l o b i n , Guzzo (1965) 15 suggested t h a t the presence o f the f o u r c r i t i c a l groups; P r o , Asp, G l u and H i s may be a n e c e s s a r y c o n d i t i o n f o r a s e c t i o n o f p r o t e i n s t o be n o n - h e l i c a l . A n a l y s e s o f Pro replacement by Asp and G l u i n mutant and v a r i a n t p r o t e i n s s u p p o r t e d h i s t h e o r y . T h i s was a p p l i e d i n an e f f o r t t o p r e d i c t the secondary s t r u c t u r e o f lysozyme and tobacco mosaic v i r u s . Absence o f h y d r o p h o b i c bonding and weakening o f i n t e r p e p t i d e hydrogen bonding as a r e s u l t o f water c o m p e t i t i o n i n the v i c i n i t y o f those p o l a r r e s i d u e s might be the r e a s o n f o r the u n f a v o r a b l e e f f e c t o f those r e s i d u e s on h e l i x f o r m a t i o n . P r o t h e r o (1966) compared h i s r e s u l t s t o t h a t o f Guzzo (1965) on s i x p r o t e i n s and proposed a r u l e which seems to a c h i e v e a r e a s o n a b l e degree o f f i t w i t h the known p r o t e i n s t r u c t u r e s . The r u l e s t a t e s : any r e g i o n o f f i v e r e s i d u e s w i l l be a - h e l i c a l i f a t l e a s t t h r e e o f i t s r e s i d u e s are comprised o f A l a , V a l , Leu, or G l u . A l t e r n a t i v e l y , any r e g i o n of seven r e s i d u e s w i l l be a - h e l i c a l i f a t l e a s t t h r e e r e s i d u e s are comprised o f A l a , V a l , Leu, G l u and an a d d i t i o n a l r e s i d u e i n c l u d e s G i n , l i e , or Thr. U s i n g t h i s r u l e , goodness o f f i t between 65 and 681 was o b t a i n e d f o r a-, 3- and y-hemoglobin, lysozyme and m y o g l o b i n . P e r i t i ejt al_. (1967) c a r r i e d out a s y s t e m a t i c s t a t i s t i c a l a n a l y s i s o f the a v a i l a b l e d a t a f o r horse 16 hemoglobin, and sperm whale m y o g l o b i n . T h i s l e d them to the c o n s i d e r a t i o n o f h e l i c a l and a n t i - h e l i c a l p a i r s o f amino a c i d r e s i d u e s (1 2, 1 3, 1 4, .... , 1 7; 2 3, 2 4, .... , 2 8, 3 4, .... ). Histograms f o r the r e c o g n i t i o n o f h e l i c a l segments o f egg w h i t e lysozyme were c o n s t r u c t e d a c c o r d i n g to t h e i r method. F i n d i n g t h a t i t was u n d e s i r a b l e to r e p r e s e n t the h e l i c a l segments by the u s u a l l i n e a r way, S c h i f f e r and Edmunson (1967) proposed a t w o - d i m e n s i o n a l r e p r e s e n t a t i o n c a l l e d the " h e l i c a l wheel". The wheels are p r o j e c t i o n s o f the amino a c i d s i d e c h a i n s onto a p l a n e p e r p e n d i c u l a r to the a x i s of the h e l i x . S i d e c h a i n s i n t e r a c t i o n s and g e n e r a l c h a r a c t e r i s t i c s o f the h e l i c e s can be b e t t e r v i s u a l i z e d . U s i n g d a t a form f o u r p r o t e i n s , i t was observed t h a t areas w i t h h y d r o p h o b i c r e s i d u e s l o c a t e d i n the n+_ 3, n, and n^4 p o s i t i o n s have the g r e a t e s t p o t e n t i a l f o r h e l i c i t y . Such hy d r o p h o b i c a r c s are absent i n n o n h e l i c a l wheels'." Hence, the wheel r e p r e s e n t a t i o n may be o f h e l p to i d e n t i f y areas w i t h h e l i c a l p o t e n t i a l . Among the s i x p r o t e i n s chosen f o r t e s t i n g the wheel method, the p r e d i c t i o n o f h e l i c a l segments i n i n s u l i n i s the most a c c u r a t e and c l o s e s t to X-ray d a t a l a t e r p roposed by B l u n d e l l e_t a J . (1972) 17 Low ejt a_l. (1968) l o o k e d f o r sequence i d e n t i t i e s o f l e n g t h v a r y i n g between t h a t o f d i - and h e x a p e p t i d e s . The t h e o r y b e h i n d t h e i r method i s based on the assumption t h a t i f h e l i x - f o r m i n g sequences i n which l o c a l i n t e r a c t i o n s predominate can be r e c o g n i z e d then t h e i r p o s i t i o n a l o n g the p o l y p e p t i d e c h a i n may be i r r e l e v a n t . A computer program was w r i t t e n t o l o c a t e sequence i d e n t i t i e s from a v a i l a b l e d a t a . A l t h o u g h t h i s method g i v e s l e s s o v e r - p r e d i c t i o n o f h e l i c a l r e g i o n s compared to o t h e r methods, i t r e s u l t s i n more o m i s s i o n s . The a u t h o r s r e c o g n i z e d t h a t the p r o c e d u r e needs t o be improved by t a k i n g i n t o account the e f f e c t s o f l o n g -range i n t e r a c t i o n s and t h a t o f n o n - h e l i c a l sequences. K o t e l c h u c k and Scheraga (1969), _ f r o m e a r l i e r energy c o m p u t a t i o n s , f o r m u l a t e d a s e t o f r u l e s i n which v a r i o u s s i n g l e p e p t i d e u n i t s were a s s i g n e d as h e l i x - f o r m i n g ( A l a , V a l , Leu, H e , Met, Thr, G i n , G l u , Phe , Cys, H i s , and Arg) or h e l i x - b r e a k i n g ( S e r , Asn, Asp, T r p , T y r , and L y s ) . T h e i r d e s i g n a t i o n s were q u i t e similar- to those o f p r e v i o u s s t u d i e s ( P r o t h e r o , 1966; S c h i f f e r and Edmunson, 19 6 7 ) . T h i s a l l o w e d c o r r e c t i d e n t i f i c a t i o n o f 61% o f the helices and 78% o f the t o t a l r e s i d u e s i n f o u r p r o t e i n s ; m y o g l o b i n , lysozyme, t o s y l - a - c h y m o t r y p s i n and r i b o n u c l e a s e A. They d i d attempt to d e f i n e c o n d i t i o n s f o r h e l i x n u c l e a t i o n and t e r m i n a t i o n , r u l i n g t h a t f i v e o r more p e p t i d e 18 u n i t s c o n s t i t u t e the minimum l e n g t h f o r any h e l i c a l a r e a and t h a t a sequence o f two h e l i x - b r e a k e r s w i l l s t o p the h e l i x p r o p a g a t i o n . They agreed, however, t h a t t h e i r model was not v e r y a c c u r a t e f o r s m a l l e r p r o t e i n systems where lo n g - r a n g e i n t e r a c t i o n s may p l a y an i m p o r t a n t r o l e i n h e l i x n u c l e a t i o n and s t a b i l i z a t i o n . U s i n g a c o m b i n a t i o n o f the K o t e l c h u c k and Scheraga (1969) and the S c h i f f e r and Edmunson (1967) schemes, Leberman (1971) succeeded i n c o r r e c t l y a s s i g n i n g 82% o f a l l r e s i d u e s i n seven p r o t e i n s as h e l i c a l and n o n h e l i c a l r e g i o n s . The o m i s s i o n o f obser v e d r e g i o n s was e x p l a i n e d as an e f f e c t o f the t e r t i a r y or even the q u a t e r n a r y s t r u c t u r e , or the b i n d i n g o f a p r o s t h e t i c group (e . g . , human hemoglobin, m y o g l o b i n ) . Lewis et a l . (1970) based t h e i r method on the Zimm and Bragg (1959) a and s parameters f o r h e l i x i n i t i a t i o n and e l o n g a t i o n . The parameters were o b t a i n e d from m e l t i n g c u r v e s o f random copolymers o f amino a c i d s . H e l i x p r o b a b i l i -t y p r o f i l e s c o n s t r u c t e d f o r e l e v e n p r o t e i n s y i e l d 68% a c c u r a -cy. C o r r e l a t i o n between the p r o p e n s i t y o f a r e s i d u e t o be a h e l i c a l former i n the de n a t u r e d p r o t e i n and i t s o c c u r r e n c e i n a h e l i c a l a r e a i n the c o r r e s p o n d i n g n a t i v e p r o t e i n was suggested. The c o r r e l a t i o n s u p p o r t s the h y p o t h e s i s t h a t r e s i d u e s i n the a R c o n f o r m a t i o n may be i n v o l v e d i n the 19 n u c l e a t i o n o f p r o t e i n f o l d i n g . A i c o m p a r i s o n was made of the c o n f o r m a t i o n a l s t r u c t u r e o f d e n a t u r e d cytochrome c from .var-i o u s . s p e c i e s (Lewis and Scheraga, 1971). They showed t h a t , even though t h e r e were amino a c i d r e p l a c e m e n t s i n cytochrome c throughout e v o l u t i o n , t h e r e remains a c o n s e r v a t i o n o f the n a t u r e of the h e l i x - f o r m i n g power a t each p o s i t i o n i n the c h a i n . D e s p i t e the p r o g r e s s i n p r o t e i n p r e d i c t i o n t h e r e was s t i l l a l a c k o f i n f o r m a t i o n on 3-sheet s t r u c t u r e . I h i s \ was because the e a r l i e s t p r o t e i n s e l u c i d a t e d by X-ray d i f -f r a c t i o n were hemoglobin: and myo g l o b i n which are d e v o i d o f 3-sheet c o n f o r m a t i o n . Hence, most o f the r e s e a r c h e r s a t t h a t time o f t e n chose to i g n o r e the 3-sheet c o n f o r m a t i o n i n t h e i r c a l c u l a t i o n s . F u r t h e r m o r e , i t was d i f f i c u l t t o o b t a i n 3-sheet i n s o l u t i o n f o r s p e c t r o p h o t o m e t r i c a n a l y s i s . However, as more p r o t e i n s t r u c t u r e s - w e r e e l u c i d a t e d by X-ra y d i f f r a c t i o n , i t became i n c r e a s i n g l y apparent t h a t the presence o f 3-sheet was as i m p o r t a n t as t h a t o f a - h e l i x . o I n t e r p r e t a t i o n of an e l e c t r o n d e n s i t y map a t 2A r e s o l u t i o n i n d i c a t e s t h a t the predominant c o n f o r m a t i o n i n c o n c a n a v a l i n A i s . formed by two a n t i p a r a l l e l 3 - s h e e t s . Residues not i n -c l u d e d i n the 3 s t r u c t u r e s are a r r a n g e d i n r e g i o n s o f r a n -dom c o i l . One o f the p l e a t e d s h e e t s c o n t r i b u t e s ex-t e n s i v e l y t o the i n t e r a c t i o n s among the monomers to form 20 b o t h dimers and t e t r a m e r s (Edelman e_t a l . , 1972) . X-ray a n a l y s i s o£ t o s y l - a - c h y m o t r y p s i n r e v e a l e d o n l y a s m a l l f r a c t i o n o f a - h e l i x but s e v e r a l adjacent, a n t i - p a r a l l e l p l e a t e d s h e e t s s t a b i l i z e d by hydrogen bonds ( B i r k t o f t and Blow, 1972). P t i t s y n and F i n k e l s h t e i n (1970) c l a s s i f i e d the v a r i o u s amino a c i d r e s i d u e s as h e l i c a l or a n t i h e l i c a l , and t e n t a t i v e l y as $-breaker o r 3-former a c c o r d i n g t o t h e i r tendency of s t a b i l i z i n g the v a r i o u s B - s t r u c t u r e s . Nonpolar amino a c i d s (Leu, A l a , Met) except Cys and .Ty.r, have a g r e a t e r tendency to e n t e r : h e l i c a l zones than the p o l a r ones. The amino a c i d r e s i d u e s w i t h compact hydro-carbon s i d e g r o u p s are a s s i g n e d w i t h p o s i t i v e B - p o t e n t i a l whereas those w i t h charged s i d e groups and Pro are con-s i d e r e d as B - b r e a k e r s . A l t h o u g h t h e i r c l a s s i f i c a t i o n t a k e s i n t o account o n l y the i n t e r a c t i o n s o f the s i d e groups w i t h the main c h a i n backbone and not w i t h each other,' they o b t a i n e d good agreement between t h e i r p r e d i c t i v e method and X - r a y d a t a (Qa = 79% and = 79%) f o r n i n e p r o t e i n s . T h i s s u p p o r t s the s u g g e s t i o n t h a t i n s t e a d o f competing w i t h l o c a l i n t e r a c t i o n s and d i c t a t i n g the secondary s t r u c t u r e , d i s t a n t i n t e r a c t i o n s work i n harmony w i t h the l o c a l ones and h e l p t o s t a b i l i z e the c o n f o r m a t i o n w h i c h m a i n l y r e s u l t s from l o c a l i n t e r a c t i o n s . 21 Nagano (1973) dev e l o p e d a computer method to p r e d i c t h e l i c e s , l o o p s and 3 - s t r u c t u r e s from the p r i m a r y s t r u c t u r e . The b a s i s o f h i s method l i e s on the assumption t h a t s h o r t - r a n g e i n t e r a c t i o n s a re due to amino a c i d r e s i d u e p a i r s s e p a r a t e d by m r e s i d u e s (m = 0, 1, 2, 5, ... 6 ) . Four p r e d i c t i o n f u n c t i o n s ( h e l i x , l o o p , random c o i l , and 3-s t r u c t u r e ) were e s t i m a t e d by a l i n e a r c o m b i n a t i o n o f s t a -t i s t i c a l q u a n t i t i e s o f d i f f e r e n t m v a l u e s as a measure o f the s t a t i s t i c a l c o n s t r a i n t . The c o e f f i c i e n t s used i n the c o m b i n a t i o n were d e t e r m i n e d to make the number o f c o r r e c t assignments as l a r g e as p o s s i b l e . V e ry s u c c e s s f u l r e s u l t s were o b t a i n e d (85.3% f o r h e l i x p r e d i c t i o n , 64.4% f o r l o o p , and 90.1% f o r 3 - s t r u c t u r e s ) . On the b a s i s o f the i n f l u e n c e o f n e a r e s t n e i g h -b o u r i n g p a i r s o f amino a c i d s (n-1) and (n+1) on the con-f o r m a t i o n o f amino a c i d (n), Kabat and Wu (1973a, 1973b) d e s i g n e d , t h e n l a t e r r e v i s e d t h e i r 20x20 t a b l e o f f r e q u e n c y o f o c c u r r e n c e s o f v a r i o u s c o n f o r m a t i o n s t a b u l a t i n g t h r e e v a l u e s - a - h e l i x , 3-sheet and n e i t h e r . The f r e q u e n c i e s were then used to l o c a t e h e l i x - b r e a k i n g p o s i t i o n s i n v a r i o u s p r o t e i n s . Due to l i m i t e d d a t a on p r o t e i n s w i t h e x t e n s i v e 3-sheet fragments, r e c o g n i t i o n o f the 3-sheet b r e a k i n g r e g i o n s was made on p a p a i n o n l y . The r e g i o n s between two 3~sheet b r e a k i n g r e s i d u e s would be p e r m i s s i v e l y 3-sheet r e g i o n s . 22 A p p l i c a t i o n o f the method on c o n c a n a v a l i n A, which has many 3-sheet r e g i o n s , a l l o w s l o c a t i o n o f 10 out o f the 13 3-sheet a r e a s . A l t h o u g h no g u i d e l i n e s were g i v e n to p r e v e n t o v e r p r e -d i c t i o n o f a- and 3 - r e g i o n s , the c o n j u n c t i o n o f t h i s method w i t h the h e l i c a l wheel method or o t h e r schemes may l e a d to a h i g h e r degree o f a c c u r a c y (Chou and Fasman, 1978b). Lim (1974b) proposed another method t h a t t a k e s i n t o account b o t h q u a n t i t a t i v e e v a l u a t i o n " • o f energy and q u a l -i t a t i v e s t e r e o c h e m i c a l c o n s i d e r a t i o n s . Based on the most c h a r a c t e r i s t i c f e a t u r e s o f g l o b u l a r p r o t e i n s (compactness o f form; presence o f a t i g h t l y packed h y d r o p h o b i c c o r e ; a po-l a r s h e l l ) and the r o l e o f the d i f f e r e n t types o f l o n g - r a n g e i n t e r a c t i o n s , d i f f e r e n t r e q u i r e m e n t s were s e t up to f i n d the most e n e r g e t i c a l l y advantageous c o n f o r m a t i o n s f o r the p r o t e i n c h a i n . Lim (1974a) a l s o e l a b o r a t e d on the s t r u c t u r a l r o l e o f the d i f f e r e n t h y d r o p h i l i c s i d e groups i n the s t a b i l i z a t i o n o f the p r o t e i n s t e r t i a r y s t r u c t u r e . a - H e l i x and 3-sheet are c l a s s i f i e d i n t o v a r i o u s types a c c o r d i n g to t h e i r s p e c i f i c o r i e n t a t i o n r e l a t i v e to the g l o b u l e s u r f a c e . Regions which do not b e l o n g to h e l i x or 3-sheet type are c l a s s i f i e d as i r r e g u -l a r r e g i o n s . Through the use o f h e l i c a l and a n t i h e l i c a l p a i r s and t r i p l e t s a t p o s i t i o n s [ 1 - 2 ] , [ 1 ^ 3 ] , [ 1 - 4 ] , [ 1 - 5 ] , [1-2-5] and [1-4-5]-, Lim (1974b) developed a p r e d i c t i v e 23 a l g o r i t h m f o r h e l i c e s . The s e a r c h o f B - s t r u c t u r a l areas i s o n l y done on fragments o f t h e . c h a i n not a t t r i b u t e d to ot-h e l i c a l r e g i o n s , because i t i s e n e r g e t i c a l l y more advanta-geous to have one l o n g h e l i x than s e v e r a l s h o r t e r B - r e g i o n s . The a c c u r a c y o f the p r e d i c t i v e method a p p l i e d to 25 p r o t e i n s o f known s t r u c t u r e was 81% f o r a - h e l i x and 85% f o r 8-sheet. The c o n f o r m a t i o n o f 25 unknown p r o t e i n s was a l s o t e s t e d w i t h the method. Chou _et _ a l . (1972) through CD c o n f o r m a t i o n a l s t u d i e s o f p o l y ( N ( 3 - h y d r o x y p r o p y l ) - L - g l u t a m i n e ) and o f c o p o l -ymers o f h y d r o x y p r o p y l - L - g l u t a m i n e w i t h L - l e u c i n e reached the f o l l o w i n g c o n c l u s i o n s . The h e l i c a l c o n t e n t o f the homo-polymer and copolymers was found to i n c r e a s e w i t h : a) de-c r e a s i n g t e m p e r a t u r e , b) i n c r e a s i n g methanol c o n c e n t r a t i o n , and c) i n c r e a s i n g molar r a t i o s o f Leu i n the c o p o l y -mers. A s u r v e y o f the c o n f o r m a t i o n o f e l e v e n p r o t e i n s r e -v e a l s t h a t o f a l l the amino a c i d s o c c u r i n g i n the i n n e r h e l i c a l r e g i o n s Leu o c c u r s most f r e q u e n t l y . T h i s s u g gests t h a t Leu may be the s t r o n g e s t h e l i c a l - f o r m i n g amino a c i d r e s i d u e i n p o l y p e p t i d e s , as w e l l a s , i n p r o t e i n s (Chou and Fasman, 1973). For the f i r s t t i m e , the h e l i x and 8-sheet c o n f o r m a t i o n a l p o t e n t i a l o f a l l 20 amino a c i d s were es-t a b l i s h e d i n t h e i r h i e r a r c h i c a l . order.' F o l l o w i n g t h i s s t u d y more complete i n v e s t i g a t i o n (Chou and Fasman,1974a) 24 on the c o n f o r m a t i o n a l parameters P , P„ and P o f each Co p L amino a c i d r e s i d u e i n 15 p r o t e i n s s e r v e d as the b a s i s f o r a new p r e d i c t i v e method (Chou and Fasman, 1974b). The major advantages of t h e i r method are i t s s i m p l i c i t y and i t s a c c u r a c y . Without r e c o u r s e to c o m p l i c a t e d computer a n a l y s i s , one can e x p e d i e n t l y l o c a t e the h e l i x , 3-sheet and c o i l r e g i o n s o f p r o t e i n s w i t h 70-80% a c c u r a c y (Chou and Fasman, 1978a, 1978b) by s i m p l y a v e r a g i n g the P a , P^ and P^ v a l u e s o f the r e s i d u e s i n the segment under c o n s i d e r a t i o n . Another way o f l o c a t i n g the v a r i o u s c o n f o r m a t i o n s i s t o a s s i g n each r e s i d u e as a f o r m e r , an i n d i f f e r e n t , or a b r e a k e r based on i t s h e l i x and g-sheet p o t e n t i a l . The g - t u r n c o n f o r m a t i o n a l parameter P^ was a l s o computed, e n a b l i n g the p r e d i c t i o n o f c h a i n r e v e r s a l s and t e r t i a r y f o l d i n g i n p r o t e i n s . The s i m p l i c i t y and e f f e c t i v e n e s s o f the method are the main reasons f o r i t s wide use (Chou and Fasman, 1978b). Indeed, a c c o r d i n g t o Argos _et a J . (1976), the c o m p l e x i t y o f some proposed a l g o r i t h m s i s such t h a t t h e i r c o m p u t e r i z a t i o n has not been developed. T h i s problem may be the r e a s o n why these methods have l i m i t e d p o p u l a r i t y compared to the method o f Chou and Fasman or o t h e r p o p u l a r methods (Lim, 1974b; Kabat and Wu, 1973a). 25 MATERIALS AND METHODS The P r e d i c t i v e Method o f Chou and Fasman U s i n g the c r i t e r i a o f d i h e d r a l a n g l e s and hydro-gen bond f o r m a t i o n , Chou and Fasman (1978a, 1978b) f i r s t de-t e r m i n e d the d i f f e r e n t c o n f o r m a t i o n a l s t a t e s i n 29 p r o t e i n s . The f r e q u e n c y o f a l l 20 amino a c i d s i n each c o n f o r m a t i o n was then c a l c u l a t e d by d i v i d i n g t h e i r o c c u r r e n c e i n the conforma-t i o n under c o n s i d e r a t i o n by t h e i r t o t a l o c c u r r e n c e i n the 29 p r o t e i n s . The p e r c e n t a g e s o f r e s i d u e s i n the 29 p r o t e i n s found i n the h e l i c a l , s h e e t , c o i l , and 8-turn r e g i o n s are r e s p e c t i v e l y r e p r e s e n t e d by t h e i r average f r a c t i o n s <f a> = 0.38, <f Q> = 0.20, <f > = 0.42, and <f > = 0.20. Each r e s i -' 8 c ' t due i s a s s i g n e d t o the a, 8, or c o i l s t a t e so t h a t <f > + a <f„> + <f > = 1.00. The 8-turn r e s i d u e assignment i s made 3 c to i n d e p e n d e n t l y . Each amino a c i d i s then a s s i g n e d as f o r m e r , i n d i f f e r e n t , or b r e a k e r a c c o r d i n g t o i t s c o n f o r m a t i o n a l pa-rameters P^, Pg which are o b t a i n e d by d i v i d i n g the f r e q u e n -cy o f i t s o c c u r r e n c e i n a c o n f o r m a t i o n by the r e s p e c t i v e average f r e q u e n c y ( e . g . , P a = f a / < f a > , . P ^ = f g / < f >, P t = f. /<f >). The c o n f o r m a t i o n a l parameters P and P 0 f o r the t t a 3 20 amino a c i d s are l i s t e d i n T a b l e 1 i n h i e r a r c h i c a l o r d e r a l o n g w i t h t h e i r assignment as f o r m e r , i n d i f f e r e n t , o r b r e a k e r . 26 T a b l e 1. C o n f o r m a t i o n a l parameters f o r a..-helical and g-sheet r e s i d u e s based on 29 p r o t e i n s . H e l i c a l ^ g-Sheet a-Residues p a Assignment g-Residues Assignment G l u " 1. , 51 ... GL V a l 1 .70 H g Met 1. .45 H a l i e 1 . 60 H 3 A l a 1. ,42 H a Tyr 1 .17 H g Leu 1. . 21 H a Phe 1 . 38 h g Lys + 1. .16 V Trp 1 .37 h g Phe 1. ,13 h a Leu 1 . 30 h g Gin 1. ,11 h a Cys 1 .19 h g Trp 1. . 08 h a Thr 1 .19 h g l i e 1. .0.8 h a Gin 1 .10 h g V a l 1. , 06 h a Met 1 .05 h g Asp" 1. . 01 T a Arg 0 .93 h H i s 1. . 00 I a Asn 0 .89 Arg 0 , 98 i a H i s 0 .87 Thr" 0. .83 ia A l a 0 .83 Ser 0. .77 ia Ser 0 .75 b g Cys 0. .70 ia Gly 0 .75 b g Tyr 0 . 69 b a L y s+ 0 . 74 b B Asn 0 , 67 b a Pro 0 .55 B g Pro 0. . 57 B a Asp" 0 . 54 B g Gl y 0. . 57 B a G l u " 0 .37 B g aChou and Fasman (1978b) b H e l i c a l a s s i g n m e n t s : H^, s t r o n g a-fo'rmer; h a , a-former; I a , weak a-former; i a , a - i n d i f f e r e n t ; bd, a - b r e a k e r ; Bpi, s t r o n g a - b r e a k e r . c g - s h e e t assignements: Hg, s t r o n g g-former; hg, g-former; Ig , weak g-former; ig , g - i n d i f f e r e n t ; beg, g-breaker; Bg, s t r o n g g-breaker. The symbols H and h may be thought o f as s t r o n g and moderate hydrogen b o n d i n g , r e s p e c t i v e l y w i t h the s u b s c r i p t s a, 8 denot-i n g h e l i c a l or 8-sheet c o n f o r m a t i o n . Each amino a c i d r e s i d u e can a l s o be c h a r a c t e r i z e d by i t s boundary c o n f o r m a t i o n a l pa-rameters ( P a N , P a C , P n a N , P n a C , P 3 N , P 3 C , P n 3 N , P n 3 C ) as l i s t e d i n T a b l e s 2 and 3. When a l l the r e s i d u e s i n a p r o t e i n sequence ha-ve been c l a s s i f i e d , one can use the e m p i r i c a l r u l e s d i s c u s s e d below to p r e d i c t i t s secondary s t r u c t u r e (Chou and Fas-man, 1978a, 1978b). A. Search f o r H e l i c a l Regions The s e a r c h was c a r r i e d out a c c o r d i n g t o the meth-od o f Chou and Fasman (1978a, 1978b), which can be des-c r i b e d as f o l l o w s : 1. H e l i x n u c l e a t i o n . A c l u s t e r o f f o u r h e l i c a l r e s i d u e s ( h ^ or H &) out o f s i x r e s i d u e s a l o n g the p r o t e i n sequence w i l l i n i t i a t e a h e l i x . A weak h e l i c a l r e s i d u e ( I a ) counts as 1/2 h ( i . e . , t h r e e h and two I r e s i d u e s out o f a v ' a a s i c may a l s o cause h e l i x n u c l e a t i o n ) . 2. H e l i x p r o p a g a t i o n . Extend the h e l i c a l seg-ment i n bo t h d i r e c t i o n s as l o n g as a d j a c e n t t e t r a p e p t i d e s are not h e l i x b r e a k e r s (see b e l o w ) . When o v e r l a p p i n g seg-ments a l l s a t i s f y the h e l i x n u c l e a t i o n r u l e , they are l i n k e d t o g e t h e r i n t o a l o n g h e l i x . The n u c l e a t e d h e l i x o f s i x 28 T a b l e 2. C o n f o r m a t i o n a l Parameters o f H e l i c a l Boundary Residues i n 29 P r o t e i n s . P P P P aN ac. naN naC G l u ( - ) 2 .44 Asp(-) 2 .02 Pro 2 . 0 1 Trp 1 .47 A l a 1 . 2 9 G i n 1 . 22 Thr 1 .08 Asn 0 . 8 1 G l y 0 .76 Ser 0 .74 H i s ( + ) 0 . 7 3 Met 0 . 7 1 Tyr 0 .68 l i e 0 .67 Cys 0 .66 L y s ( + ) 0 .66 Phe 0 . 6 1 V a l 0 . 6 1 Leu 0 . 58 A r g ( + ) 0 .44 Lys(+) i . 8 3 His(+) 1. 77 Met 1. 57 V a l 1. 2 5 A r g ( + ) 1 . 20 G l u ( - ) 1. 24 G i n 1. 2 2 A l a 1. 20 Leu 1. 1 3 Cys 1. 1 1 Phe 1. 1 0 T J C 0. 98 Ser 0. 9 6 Thr 0. 7 5 Tyr 0. 7 3 Asp(-) 0. 6 1 Asn 0. 59 G l y 0. 4 2 Trp 0. 4 0 Pro 0. 00 Ser 1 . 5 5 Asn 1 .42 G l y 1 .41 H i s ( + ) 1 .22 Pro 1 . 1 0 Thr 1 .09 G l u ( - ) 1 .04 L y s ( + ) 1 . 0 1 Tyr 0 .99 Asp(-) 0 .98 Phe 0 . 9 3 Leu 0 .85 Met 0 . 8 3 H e 0 .78 G i n 0 .75 V a l 0 .75 A l a 0 .70 Cys 0 .65 Trp 0 .62 A r g ( + ) 0 . 34 H i s ( + ) 1 .86 Asn 1 .64 G l y 1 .64 Pro 1 . 58 Lys(+) 1 .49 Agr(+) 1 .24 Asp(-) 1 .06 Phe 1 .04 Tyr 0 .96 Cys 0 .94 Ser 0 . 9 3 H e 0 .87 Thr 0 .86 Leu 0 .84 G i n 0 .70 G l u ( - ) 0 . 59 A l a 0 .52 Met 0 .52 V a l 0 .32 Trp 0 . 1 6 H e l i x boundary r e s i d u e s i n c l u d e the t h r e e h e l i c a l r e s i d u e s on b o t h ends o f a h e l i c a l r e g i o n and the t h r e e n o n h e l i c a l r e s i d u e s a d j a c e n t to the h e l i c a l end r e s i d u e s , a t o t a l o f s i x r e s i d u e s on each end o f the h e l i x . P a ^ = n o r m a l i z e d f r e q u e n c y o f r e s i d u e s i n the N - t e r m i n a l h e l i x r e g i o n ; P a r = n o r m a l i z e d f r e q u e n c y o f r e s i d u e s i n the C - t e r m i n a l h e l i x r e g i o n ; P naN = n o r m a l i z e d f r e q u e n c y of r e s i d u e s i n the N - t e r m i n a l n o n h e l i c a l r e g i o n ; P n a c = n o r m a l i z e d f r e q u e n c y of r e s i d u e s i n the C - t e r m i n a l n o n h e l i c a l r e g i o n . 29 Table 3. C o n f o r m a t i o n a l Parameters o f 3-Sheet Boundary Residues i n 29 P r o t e i n s . P~ P P p 3N r 3 C n 3 N n 3 C l i e 1 .94 Tyr 1. 96 Asn 1 .86 Pro 1. 69 V a l 1 .69 V a l 1. 79 Pro 1 . 58 G l y 1. 68 G i n 1 .65 Phe 1. 50 G l y 1 .46 Trp 1. 59 Phe 1 .40 l i e 1. 35 Ser 1 .41 Ser 1. 49 Trp 1 .49 Leu 1. 27 Asp(-) 1 . 39 Asp(-) 1. 32 Met 1 .43 Asn 1. 21 Cys 1 .34 Thr 1. 16 Leu 1 .30 Trp 1. 19 Tyr 1 .23 Asn 1. 13 Thr 1 .17 Cys 1. 11 L y s ( + ) 1 .09 A r g ( + ) 1. 05 Tyr 1 .07 Met 0. 95 G i n 1 .09 Tyr 1. 01 Lys(+) 1 . 00 His(+) 0. 90 Thr 1 .09 H i s ( + ) 0. 96 A r g ( + ) 0 .90 A r g ( + ) 0. 90 G l u ( - ) 0 .92 Met 0. 85 Cys 0 .87 Asp(-) 0. 85 A r g ( + ) 0 .89 G l u ( - ) 0. 85 A l s 0 .86 Ser 0. 79 His(+) 0 .78 L y s ( + ) 0. 82 Pro 0 .66 Thr 0. 75 A l a 0 .67 Gi n 0. 77 Asn 0 .66 A l a 0. 75 H e 0 . 59 A l a 0. 74 G l y 0 .63 G l y 0. 74 Met 0 . 52 V a l 0. 59 Ser 0 .63 L y s ( + ) 0. 74 Trp 0 .48 Leu 0. 59 His(+) 0 . 54 Gi n 0. 65 Leu 0 .46 H e 0. 53 Asp(-) 0 .38 G l u ( - ) 0. 55 V a l 0 .42 Cys 0. 53 G l u ( - ) 0 . 35 Pro 0. 40 Phe 0 .30 Phe 0. 44 3-sheet boundary r e s i d u e s i n c l u d e the t h r e e r e s i d u e s on b o t h ends o f a 3 r e g i o n s and the t h r e e non-3 r e s i d u e s a d j a c e n t to the 3-sheet end r e s i d u e s , a t o t a l o f s i x r e s i d u e s on each end o f the 3-sheet r e g i o n . Pg^ = n o r m a l i z e d f r e q u e n c y o f r e s i d u e s i n t h e N - t e r m i n a l 3 r e g i o n ; P^Q = n o r m a l i z e d f r e q u e n c y o f r e s i d u e s i n the C - t e r m i n a l r e g i o n ; p n 3 N = n o r m a l i z e d f r e q u e n c y o f r e s i d u e s i n the N - t e r m i n a l non-3 r e g i o n ; P n g c = n o r m a l i z e d f r e q u e n c y o f r e s i d u e s i n the C - t e r m i n a l non-3 r e g i o n . 30 r e s i d u e s s h o u l d c o n t a i n a t l e a s t two t h i r d s h ' s , . w h i l e . t h e p r o p a g a t e d h e l i x s h o u l d be co m p r i s e d o f one h a l f o r more h e l i x f o r m e r s . I t i s i m p o r t a n t to u t i l i z e the r u l e t h a t a weak h e l i c a l former ( I a ) counts as l / 2 h i n the segment. Both the h e l i x n u c l e a t i o n segments and the e n t i r e h e l i x s h o u l d have fewer than one t h i r d h e l i x b r e a k e r s ( b a or B a ) • 3. H e l i x T e r m i n a t i o n . The pr o p a g a t e d h e l i x i s t e r m i n a t e d on b o t h s i d e s by the f o l l o w i n g t e t r a p e p t i d e b r e a k e r s w i t h <P a> < 1.00 : bq, b^i, b^h, b2i2> b 2 i h , b2h2» b i j , b i 2 h , b i l ^ , and i ^ . Some t e t r a p e p t i d e s , such as h i g and l ^ ^ ' may have <P a> < 1.00 but are not l i s t e d as b r e a k e r s s i n c e they a l l o w h e l i x p r o p a g a t i o n t o c o n t i n u e . Once the h e l i x i s d e f i n e d , some o f the r e s i d u e s (h or i ) i n the above t e t r a p e p t i d e b r e a k e r s may be i n c o r p o r a t e d a t the h e l i c a l ends. For example, the h i o f the b r e a k e r b b h i may be added t o the p r e d i c t e d h e l i x o n l y at the N - t e r m i n a l s i d e , but the bb may not be i n c l u d e d a t e i t h e r the N- or C - t e r m i n a l h e l i x . The n o t a t i o n s i , b, h i n the t e t r a p e p t i d e b r e a k e r s a l s o i n c l u d e I , B, and H, r e s p e c t i v e l y . A d j a c e n t 8 - r e g i o n s t h a t have h i g h e r 8- than a - p o t e n t i a l ( i . e . , <Pg> > < P a > ) c a n a l s o t e r m i n a t e h e l i x p r o p a g a t i o n . 4. P r o l i n e as H e l i x B r e a k e r . Pro cannot o c c u r i n the i n n e r h e l i x o r a t the C - t e r m i n a l h e l i c a l end but 31 I can occupy the f i r s t t u r n ( i . e . , t h i r d r e s i d u e s ) i n the N-t e r m i n a l h e l i x . 5. H e l i x b o u n d a r i e s . P r o , Asp^ ^ , G l u ^ ^ are i n c o r p o r a t e d i n t o the N - t e r m i n a l h e l i c a l end, w h i l e His'- + '', L y s ^ + ^ and A r g ^ + ^ are i n c o r p o r a t e d i n t o the C - t e r m i n a l h e l i c a l end. I assignments are g i v e n to Pro and Asp (near the N - t e r m i n a l h e l i x ) , as w e l l a s , A r g (near the C - t e r m i n a l h e l i x ) i f n e c e s s a r y to s a t i s f y c o n d i t i o n A . l . G l u i s s t i l l a s s i g n e d as H a t the N - t e r m i n a l h e l i x w h i l e H i s and Lys are s t i l l h and I , r e s p e c t i v e l y , a t the C - t e r m i n a l h e l i x . Rule 1. Any segment o f s i x r e s i d u e s or l o n g e r i n a n a t i v e p r o t e i n w i t h <P_> > 1.03 and <P > > <P„>, and ^ a — a 3-s a t i s f y i n g c o n d i t i o n s A . l through A.5, i s p r e d i c t e d as h e l i c a l . B. Search f o r 3-sheet Regions The s e a r c h f o r 3 - p l e a t e d sheet r e g i o n s was c a r r i e d out by a p p l y i n g the s e t o f r u l e s o u t l i n e d by Chou and Fasman (1978a, 1978b) as f o l l o w s : 1. 3-sheet N u c l e a t i o n . A sequence o f t h r e e 3-formers (hg or Hg) or a c l u s t e r o f t h r e e 3-formers out o f f o u r o r f i v e r e s i d u e s a l o n g the p r o t e i n sequence w i l l i n i t i a t e a 3-sheet 32 2. 8-Sheet P r o p a g a t i o n . Extend the 8-sheet segment i n bo t h d i r e c t i o n s as l o n g as a d j a c e n t t e t r a -p e p t i d e s are not 3-sheet b r e a k e r s (see b e l o w ) . 8-Sheet f o r m a t i o n i s u n f a v o r a b l e i f the e n t i r e segment c o n t a i n s one t h i r d o r more 8-sheet b r e a k e r s (b^ or B^) or l e s s t h a n one h a l f 8-sheet f o r m e r s . 3. 8-Sheet T e r m i n a t i o n . A p p l y c o n d i t i o n s A.3 o u t l i n e d f o r h e l i x t e r m i n a t i o n by u t i l i z i n g the same t e t r a -p e p t i d e b r e a k e r s w i t h <Pg> < 1 f o r s t o p p i n g 8-sheet p r o -p a g a t i o n . A d j a c e n t a - r e g i o n s t h a t have h i g h e r a- than 8 - p o t e n t i a l ( i . e . , <P a> > < ^ 3 > ) c a n a l s o t e r m i n a t e 8-p r o p a g a t i o n . 4. S t r o n g 8-Sheet B r e a k e r s . G l u and Pro are the s t r o n g e s t 8-sheet b r e a k e r s and s h o u l d not be i n c o r p o r a t e d i n t o 8-sheets u n l e s s they o c c u r i n t e t r a p e p t i d e s w i t h <P > < <P C> > 1. a 8 5. 8-Sheet B o u n d a r i e s . Charged r e s i d u e s and Pro are u n f a v o r a b l e t o 8-sheet f o r m a t i o n and s h o u l d not be i n c o r p o r a t e d i n t o 8-sheets u n l e s s they o c c u r i n t e t r a p e p t i d e s w i t h <P > < <P D> > 1. ot p Rule 2. Any segment o f t h r e e r e s i d u e s o r l o n g e r i n a n a t i v e p r o t e i n w i t h <Pg> > 1.05 and < p g > > < ^ a > ' and s a t i s f y i n g c o n d i t i o n s B . l t h r o u g h B.5 i s p r e d i c t e d as 8-sheet. 33 C. O v e r l a p p i n g a- and g-RegTons In most cases,, u t i l i z a t i o n o f the s e t o f r u l e s d e s c r i b e d above . was._ adequate to l o c a t e the secondary s t r u c t u r e s o f p r o t e i n s . However t h e r e were r e g i o n s i n p r o t e i n s c o n t a i n i n g b o t h a- and 3 r e s i d u e s where a m b i g u i t i e s a r o s e , so t h a t a d d i t i o n a l measures were r e q u i r e d t o r e s o l v e the dilemma. Chou and Fasman (1978a, 1978b) f o l l o w e d the pr o c e d u r e d e s c r i b e d below t o dete r m i n e whether the ov e r -l a p p i n g r e g i o n was p r e d o m i n a t e l y a or g. 1. C a l c u l a t e the <Pa> and <Pg> f o r the over-l a p p i n g r e g i o n ; i f <P a> > the r e g i o n i s h e l i c a l , i f <Pg> > i t i s g-sheet. The a- and g - p o t e n t i a l o f the o v e r l a p p i n g r e s i d u e s can a l s o be compared by g r o u p i n g the a- and g-assignments. Thus a r e g i o n o f s i x r e s i d u e s w i t h ( ^ h ^ i b ^ and (Hh^iB) ^  assignments s h o u l d be h e l i c a l , s i n c e t h e r e a re two s t r o n g a - f o r m e r s (H a) and one a-breaker ( b a ) compared t o one s t r o n g g-former (Hg) and one s t r o n g g-breaker (Hg). 2. Use T a b l e s 2 and 3 on the f r e q u e n c y o f h e l i x and a-sheet b o u n d a r i e s t o d e l i n e a t e whether the r e g i o n i s a o r g. 34 3. S i n c e h e l i c e s are l o n g e r than 3-sheets, a l o n g segment c o n t a i n i n g b o t h a- and B - p o t e n t i a l i s p r e d i c t e d as h e l i c a l i f <P > > < P C > > even though t h e r e may be a s m a l l e r fragment, t h a t i s , f i v e r e s i d u e s w i t h i n t h e segment whose < P g > > ^ o ^ - Hence, i n the example g i v e n above f o r c a r b o x y p e p t i d a s e , 173-186 i s p r e d i c t e d as one l o n g h e l i x i n s t e a d o f a s h o r t h e l i x 173-178 and a 3-r e g i o n 179-183. 4. Regions w i t h b o t h a- and 3 - p o t e n t i a l a d j a c e n t t o a p r e d i c t e d 3-turn (see below) a re p r e d i c t e d t o be 3 _ sheet as l o n g as t h e r e are a t l e a s t t h r e e 3-formers on each s i d e o f the 3 - t u r n ; t h a t i s , the minimum 3 l e n g t h i s reduced from f i v e t o t h r e e , w i t h the m i d d l e two r e s i d u e s o f the 3-turn c o u n t i n g as c o i l r e s i d u e s . For example, r e g i o n s 105-110 and 115-124 i n r i b o n u c l e a s e have b o t h a- and 3-p o t e n t i a l . However, the h i g h p r o b a b i l i t y o f a 3-turn a t 113-115 e a s i l y a l l o w s the assignment o f 105-110 [ ( H ^ h l b ) ^ > ( H h 2 I 2 i ) a and <P g> = 1.31 > <Pa> = 1.10] and 115-124 [ ( H 3 h 2 I i b 3 ) g > ( H h 5 i 2 b B ) a and <Pp > '= 1.13 > <P a> = 1.02] as 3-sheets r a t h e r than a - h e l i c e s . Rule 5. Any segment c o n t a i n i n g o v e r l a p p i n g a-and 3 - r e s i d u e s i s r e s o l v e d t h rough c o n f o r m a t i o n a l boundary a n a l y s i s (C.2) w i t h < P A > > < P R > f ° r t n e p r e d i c t e d 35 a - r e g i o n ( C l ) . 8-Formers may be i n c o r p o r a t e d i n t o a l o n g h e l i x i f t h e y are not h e l i c a l t e t r a p e p t i d e b r e a k e r s (C.3). H e l i x p r o p a g a t i o n may be t e r m i n a t e d by a r e s i d u e s i f th e s e same r e s i d u e s f a v o r the f o r m a t i o n o f a n t i p a r a l l e l 8-sheets. In summary, a c c o r d i n g t o Chou and Fasman (1978!b) , t h e r e are o n l y t h r e e b a s i c r u l e s f o r p r e d i c t i n g p r o t e i n secondary s t r u c t u r e . While the a and 8 s e a r c h c o n d i t i o n s e l a b o r a t e d above seem to be q u i t e e x t e n s i v e t h e y are g i v e n so t h a t i n c o r r e c t p r e d i c t i o n s w i l l be m i n i m i z e d . D. Search f o r 3-Turns At p r e s e n t , 408 8-turns have been e l u c i d a t e d from 29 p r o t e i n s and the f r e q u e n c y o f o c c u r r e n c e f o r the 20 amino a c i d s i n th o s e 408 t u r n s , a t p o s i t i o n s i t o i + 3, as w e l l as t h e i r P t v a l u e s (P^ = ft/<f+.>) are g i v e n i n Ta b l e 4. (Chou and Fasman, 1977 , 1979). The p r o b a b i l i t y o f 8-turn o c c u r r e n c e at r e s i d u e i i s computed from p t = ( f i ) ( f i + 1 ) 0 f i + 2 ) ( £ i + 3 ) w i t h t h e a i d o £ T a b l e 4-The average p r o b a b i l i t y o f 8-turn o c c u r r e n c e i s - 4 <p^> = 0.55 x 10 . Two c u t - o f f v a l u e s were s e l e c t e d : p = 1.0 x 10 ^ (a v a l u e a p p r o x i m a t e l y double t h a t o f the average) and p t = 0.75 x 10 ^ (a v a l u e t h a t i s 1 1/2 times t h a t o f the a v e r a g e ) . A c c o r d i n g to Chou and Fasman (1979), 3 6 Table 4. Frequency H i e r a r c h i e s o f Amino A c i d s i n the 8-Turns o f 29 P r o t e i n s . i i + 1 i + 2 i + 3 P t P t 2 Asn 0. 161 Pro 0. 301 Asn 0 . 101 Trp 0. 167 Asn 1. 56 Pro 2 . 04 Cys 0. 149 Ser 0. 139 Gly 0 . 190 Gly 0. 152 G l y 1. 56 Gly 1. 63 Asp 0. 147 Lys 0. 115 Asp 0 .179 Cys 0. 128 Pro 1. 52 Asp 1. 61 H i s 0. 140 Asp 0 . 110 Ser 0 .125 Tyr 0. 125 Asp 1 .46 Asp 1. 56 Ser 0. 120 Thr 0 . 108 Cys 0 . 117 Ser 0. 106 Ser 1. 43 Ser 1. 52 Pro 0. 102 A r g 0 . 106 Tyr 0 . 114 Gin 0. 098 Cys 1. 19 Lys 1. 13 Gly 0. 102 Gin 0. 098 Arg 0 . 099 Lys 0. 095 Tyr 1. 14 Tyr 1. 08 Thr 0. 086 Gly 0. 085 H i s 0 . 093 Asn 0. 091 Lys 1. 01 Arg 1. 05 Tyr 0. 082 Asn 0. 083 Glu 0 . 077 Arg 0. 085 G i n 0. 98 Thr 0. 98 Trp 0. 077 Met 0. 082 Lys 0 . 072 Asp 0. 081 Thr 0. 96 Cys 0 . 92 Gin 0. 074 A l a 0. 076 Thr 0 . 065 Thr 0. 079 Trp 0. 96 Gin 0. 84 A r g 0. 070 Tyr 0. 065 Phe . 065 ] Leu 0. 070 A r g 0. 95 Glu 0. 80 Met 0. 068 Glu 0 . 060 Trp 0 . 064 Pro 0. 068 H i s 0 . 95 H i s 0. 77 V a l 0. 062 Cys 0. 053 Gin 0 . 037 Phe 0. 065 G l u 0 . 74 A l a 0. 64 Leu 0. 061 V a l 0. 048 Leu 0 . 036 G l u 0. 064 A l a 0. 66 Phe 0. 62 A l a 0. 060 H i s 0. 047 A l a 0 . 035 A l a 0. 058 Met 0. 60 Met 0. 51 Phe 0. 059 Phe 0 . 041 Pro 0 . 034 H e 0. 056 Phe 0. 60 Trp 0. 48 G l u 0. 056 H e 0. 034 V a l 0 .028 Met 0. 055 Leu 0. 59 V a l 0. 43 Lys 0. 055 Leu 0. 025 Met 0 . 014 H i s 0. 054 V a l 0. 50 Leu 0. 36 l i e 0. 043 Trp 0. 013 H e 0 . 013 V a l 0. 053 H e 0. 47 H e 0. 29 Table 4. Frequency H i e r a r c h i e s of Amino A c i d s i n the 3-Turns o f 29 P r o t e i n s , (cont'd) i , i + 1 , i + 2 , and i+3 r e p r e s e n t the f r e q u e n c i e s of the f i r s t , second, t h i r d , and f o u r t h r e s i d u e s , r e s p e c t i v e l y , i n a r e v e r s e 3 - t u r n . Pt i s the c o n f o r m a t i o n a l p o t e n t i a l o f a r e s i d u e i n a B-turn based on a l l f o u r p o s i t i o n s o f a r e v e r s e t u r n . Pt2 i s the c o n f o r m a t i o n a l p o t e n t i a l o f a r e s i d u e i n a 3-turn based on the second and t h i r d p o s i t i o n s o f a r e v e r s e t u r n . This frequency t a b l e was based on 408 3-turns i n 29 p r o t e i n s . the lower c u t - o f f v a l u e p r e d i c t s more bend r e s i d u e s c o r r e c t l y w h i l e the h i g h e r c u t - o f f v a l u e p r e d i c t s more non-bend r e s i d u e s c o r r e c t l y . However i t appears t h a t the p r e d i c t i v e a c c u r a c y i s s i m i l a r f o r the two v a l u e s . The c u t - o f f v a l u e o f 0.75 x 10 ^ has been used by Chou and Fasman (1978b, 1979) i n t h e i r s e a r c h f o r 3-turns i n 29 p r o t e i n s . - 4 Rule 4. T e t r a p e p t i d e s w i t h p > 0.75 x 10 as w e l l as <P t> > 1.00 and <P a> < <P t> > <P^> are s e l e c t e d as p r o b a b l e bends. A d j a c e n t p r o b a b l e bends ( i . e . , 11-14, 12-15, 13-16) are compared p a i r w i s e , and the t e t r a p e p t i d e w i t h the h i g h e s t p t v a l u e i s p r e d i c t e d as a 3- t u r n . E. E v a l u a t i o n o f the P r e d i c t i v e A c c u r a c y To e v a l u a t e the success o f any p r e d i c t i v e scheme i t i s n e c e s s a r y t o compare the p r e d i c t e d c o n f o r m a t i o n a l s t a t e f o r each r e s i d u e o f a p r o t e i n w i t h the observ e d assignment'based on X-ray d i f f r a c t i o n . The pe r c e n t a g e o f r e s i d u e s n^ p r e d i c t e d i n the c o n f o r m a t i o n a l s t a t e k i s g i v e n by: 100 ( n k - n x ) Ik' = (1) 38 where k r e p r e s e n t s the a-, 3 - or c o i l r e g i o n s i n the n a t i v e p r o t e i n s t r u c t u r e as d e t e r m i n e d by x - r a y c r y s t a l l o g r a p h y and n i s the number o f i n c o r r e c t l y p r e d i c t e d r e s i d u e s i n the s t a t e k. The p e r c e n t a g e o f o v e r p r e d i c t i o n i s g i v e n by the c r i t e r i a : % nk = H£ (2) n n k where Ink r e p r e s e n t s the p e r c e n t a g e o f c o r r e c t l y p r e d i c t e d r e s i d u e s not i n the c o n f o r m a t i o n a l s t a t e k, = N - nk, and n i s the number of k r e s i d u e s o v e r p r e d i c t e d . Hence the nx r q u a l i t y o f p r e d i c t i o n f o r a g i v e n type o f c o n f o r m a t i o n a l k can be e x p r e s s e d as the mean o f Ik (eq. 1) and Ink (eq. 2 ) . Ik + Ink A v a l u e o f 100% f o r I k , Ink, and i n d i c a t e s t o t a l agreement between o b s e r v a t i o n and p r e d i c t i o n , w h i l e 0% i n d i c a t e s t o t a l disagreement (Chou and Fasman, 1978a, 1978b). R e c e n t l y , Matthews (1975) i n t r o d u c e d a c o r r e l a -t i o n c o e f f i c i e n t t h a t i n d i c a t e s how much b e t t e r . a g i v e n p r e d i c t i o n i s than .a random; one. 38a c = a r r r 172 [ C n a - a T n ) / N ] . - [ ( n a - a +a n)/N] (n a/N) < [ ( n a - a m + a o ) / N ] C n a / N ) U " n a / N ) [ 1 " K r < V a o ) / N ] } ' (3) The c o r r e l a t i o n c o e f f i c i e n t f o r B-sheet and B - t u r n may be o b t a i n e d by s u b s t i t u t i n g B and t , r e s p e c t i v e l y , f o r a i n e q u a t i o n 3. A c o r r e l a t i o n o f C=l i n d i c a t e s p e r f e c t agreement between p r e d i c t i o n and o b s e r v a t i o n , C=0 i n d i c a t e s t h a t a p r e d i c t i o n i s no b e t t e r than random, and C=-l i n d i c a t e s t o t a l disagreement or 0% a c c u r a c y . I f C a >^  0.6, the p r e d i c t e d s t r u c t u r e i s near t h a t o f the o b s e r v e d s t r u c t u r e w i t h no h e l i c a l r e g i o n s g e n e r a l l y m i s s e d but w i t h N- and C-t e r m i n a l p o i n t s o f f by a few r e s i d u e s . I f C a >_ 0.4, g e n e r a l l y one or two h e l i c a l r e g i o n s might be mis s e d o r o v e r p r e d i c t e d , however the p r e d i c t i o n would s t i l l be q u i t e u s e f u l . S i m i l a r s t a tements can be made r e g a r d i n g sheet and t u r n (Argos e_t a j l . , 1976) . Amino A c i d Sequence o f P r o t e i n s The amino a c i d sequence o f the v a r i o u s p r o t e i n s used f o r t e s t i n g our program comes from the A t l a s o f p r o t e i n sequence and s t r u c t u r e ( D a y h o f f , 1972, 1973, 1976, 1978). 39 I Programming The program was w r i t t e n i n F o r t r a n language and t e s t e d a t the UBC computing c e n t r e . The amino a c i d sequence of each p r o t e i n was c o n v e r t e d i n t o a sequence o f i n t e g e r s . The 20 amino a c i d r e s i d u e s were s o r t e d a l p h a b e t i c a l l y and each o f them a s s i g n e d a f i x e d number between 1 and 20. For i n s t a n c e : 1 A l a , 2 -> A r g , 19 -> T y r , and 20 -> V a l . Hence i n o r d e r to use the program, one must c o n v e r t the pro-t e i n sequence i n t o a c c orresponding s e r i e s o f i n t e g e r s . A l l the n e c e s s a r y d e t a i l s c o n c e r n i n g the use o f the program are g i v e n i n the appendix. 40 RESULTS AND DISCUSSION Programming of the method F o l l o w i n g the r u l e s o u t l i n e d by Chou and Fasman (1978a, 1978b) f o u r d i f f e r e n t programs were w r i t t e n to p r e -d i c t a - h e l i x , 3-sheet, and 3 - t u r n , and to s o l v e the o v e r l a p -p i n g areas between a - h e l i x and 3-sheet. Each program c o n s i s t e d o f the main program and sev-e r a l s u b r o u t i n e s . In every c a s e , the purpose o f the main program was to r e a d i n the sequence o f the p r o t e i n under con-s i d e r a t i o n , and then t o a s s i g n to each amino a c i d r e s i d u e the c o r r e s p o n d i n g v a l u e s o f the c o n f o r m a t i o n a l parameters (P^, Pg, P^) and the boundary c o n f o r m a t i o n a l parameters (P I T , P n , P M , P r , P D M , VDn, P O M , P o rO • The subrou-v aN' a C naN' naC 3N 3C n3N' n3C t i n e s were then c a l l e d on to s e a r c h f o r a - h e l i x , 3-sheet, and 3 - t u r n r e g i o n s , and to s o l v e o v e r l a p p i n g a r e a s . A. Scheme f o r the s e a r c h o f a - h e l i x and 3-sheet r e g i o n s In the case o f a - h e l i x and 3-sheet p r e d i c t i o n , once the whole sequence has been r e c o r d e d , the f i r s t subrou-t i n e i s c a l l e d to d e t e c t the areas i n the sequence w i t h he-l i x or 3-sheet p o t e n t i a l a c c o r d i n g to r u l e 1 or r u l e 2,re--s p e c t i v e l y . T h e n w i t h i n the l i m i t s o f those p o t e n t i a l a r e a s , the r u l e s f o r n u c l e a t i o n , p r o p a g a t i o n and t e r m i n a t i o n are 41 a p p l i e d t o l o c a t e the d i f f e r e n t s e c t i o n s more a c c u r a t e l y . Those r u l e s were e l a b o r a t e d i n the second and t h i r d s u b r o u t i n e s . The v a r i o u s i m p o r t a n t f a c t o r s such as s t r o n g h e l i x or g-sheet b r e a k e r s , and h e l i x or 3-sheet b o u n d a r i e s were a l s o t a k e n i n t o account. Main Program - Read p r o t e i n sequence - A s s i g n P , P„ to each r e s i d u e b a 3 Subrc u t i n e 1 Rule 1 / Rule 2 Search f o r p o t e n t i a l h e l i x or 3-sheet areas Subrc m t i n e 2 H e l i x / 3 - s h e e t n u c l e a t i o n w i t h i n those p o t e n t i a l areas 1 S u b r o u t i n e 3 H e l i x / 3 - s h e e t p r o p a g a t i o n and t e r m i n a t i o n P r i n t out h e l i x / 3 - s h e e t s e c t i o n s 42 B. Scheme f o r the 3--Tu'rh Search For the 8-turn s e a r c h , o n l y one s u b r o u t i n e was needed t o l o c a t e the d i f f e r e n t t u r n s a c c o r d i n g t o r u l e 3 and to compare the a d j a c e n t p r e d i c t e d t u r n s so as to c o n s i d e r o n l y the one w i t h the h i g h e s t p r o b a b i l i t y o f o c c u r r e n c e ( p t ) • Main Program - Read i n sequence - Assignment o f P^ and fr e q u e n c y o f o c c u r r e n c e S u b r o u t i n e - Rule 3 - Then comparison o f a d j a c e n t t u r n s 1 P r i n t out p o s i t i o n o f t u r n s . C. Scheme f o r S o l v i n g O v e r l a p p i n g a- and 8-Areas In t h i s c a s e , the purpose o f the main program was t o r e c o r d the whole sequence o f each p r o t e i n as w e l l as the c o n s e c u t i v e p a i r s o f o v e r l a p p i n g areas w h i c h wer.e f o r m a t t e d 43 i n the f o l l o w i n g manner: HI SI H2 S2 H3 S3 H4 S4 . . . HI - H2 : boundary v a l u e s o f the h e l i c a l fragment SI - S2 : boundary v a l u e s o f the 3-sheet fragment The f i r s t s u b r o u t i n e c a r r i e d out the comparison of the average P and P„ o f each fragment i t s e l f and t h a t o f & a 3 the o v e r l a p p i n g a r e a . In case the 3-sheet was c o n t a i n e d w i t h -i n -the. a - h e l i x , the o v e r l a p p i n g a r e a was the 3-sheet i t -s e l f . The r e s u l t s o b t a i n e d a t t h i s s t e p c o u l d a l r e a d y sug-ge s t whether - the e n t i r e fragment ( 3 - s h e e t / a - h e l i x ) and the o v e r l a p p i n g a r e a had a h i g h e r p r o p e n s i t y to e x i s t i n one o f the c o n f o r m a t i o n s than the o t h e r ( i . e . , i n h e l i c a l s t a t e i f <P > > <P„>," or i n 3-sheet c o n f o r m a t i o n i f <P > < <P C>) . a 3 a 3 In the second s u b r o u t i n e , i n s t e a d o f a s s i g n i n g to each amino a c i d r e s i d u e i n the fragments under c o n s i d e r a -t i o n the a l p h a b e t i c r e p r e s e n t a t i o n o f H , H R, I , I R , B , Bg, the a l p h a b e t i c r e p r e s e n t a t i o n s were c o n v e r t e d to numeri-c a l ones ( i . e . , H ,H Q + 2.00; h , h 0 + 1.00; I , I„ -»• 0.50; ^ ' a ' 3 ' a ' 3 ' a ' 3 i , i Q + 0.25; b , b D -> -0.50; B , B 0 -> -1,00). Hence, i n -a' 3 ' a' 3 ' a' 3 stead o f comparing s e t s o f c h a r a c t e r s (H^ h v 1^ i b z B^) as d i d Chou and Fasman (1978a, 1978b), n u m e r i c a l v a l u e s were used to r e p r e s e n t the c o n f o r m a t i o n a l p o t e n t i a l o f the r e g i o n s under c o n s i d e r a t i o n . T h i s " c h a r a c t e r a n a l y s i s " was performed 44 oh the a - h e l i x and 8-sheet f r a g m e n t s , as w e l l a s , on the over-l a p p i n g a r e a . The "boundary a n a l y s i s " was c a r r i e d out i n the t h i r d s u b r o u t i n e . T h i s c o n s i s t e d o f summing up the boundary c o n f o r m a t i o n a l parameters of the t h r e e r e s i d u e s b e l o n g i n g to the fragment and those o f the t h r e e r e s i d u e s a d j a c e n t to the fragment ends, u s i n g the v a l u e s from T a b l e s 2 and 3. e.g. P a N (HI) + P a N ( H l + 1 ) + P a N ( H l + 2 ) PaC ™ + PaC ( H 2 " ^ + PaC W2~V PnaN ^ H 1 - ^ + PnaN CH1-2) • P n a N (Hl-3) PnaC ^ H 2 + 1 ^ + PnaC ^ H 2 + 2 ^ + PnaC < H 2 + 3 ) S i m i l a r p r o c e d u r e s were a p p l i e d to the 8-sheet fragment. The "boundary a n a l y s i s " thus took i n t o c o n s i d e r a -t i o n the i n f l u e n c e o f the n e i g h b o u r i n g r e s i d u e s at the bound-a r i e s . Hence, i f a fragment has v e r y h i g h p o t e n t i a l f o r the h e l i c a l s t a t e , the n e i g h b o u r i n g r e s i d u e s at the bound-a r i e s may p a r t i c i p a t e i n s t a b i l i z a t i o n o f the h e l i x i f they are f a v o r a b l e to i t s p r e s e n c e . 45 Main Program - Read i n sequence - Read i n d i f f e r e n t o v e r l a p p i n g areas - Assignment o f P , S u b r o u t i n e 1 Comparison o f <Pa>, <Pg > - In each fragment i t s e l f - In the o v e r l a p p i n g a r e a S u b r o u t i n e 2 Grouping of a- and 8-assignments ( H a , Hg, ..., B a,-B 3) - In each fragment i t s e l f - In the o v e r l a p p i n g a r e a Subr o u t i n e 3 Boundary a n a l y s i s ( P ^ , P a C , Pn3N' Pn8C^ - For each fragment i t s e l f 46 E f f i c i e n c y o f the a - h e l i x p r e d i c t i o n When the r u l e s e s t a b l i s h e d by Chou and Fasman (1978a, 1978b) were s t r i c t l y f o l l o w e d , s e v e r a l areas were missed i n the p r e s e n t p r e d i c t i o n and the b o u n d a r i e s o f the p r e d i c t e d r e g i o n s were q u i t e d i f f e r e n t from those o f Chou and Fasman or from X-ray a n a l y s i s (Table 5, p. 189) However, when the r e s u l t s o b t a i n e d f o r the v a r i o u s p r o t e i n s were a n a l y z e d , the d i f f e r e n c e between the boundary v a l u e s o f the p r e s e n t s t u d y and those o f Chou and Fasman or from X-ray a n a l y s i s c o u l d be reduced by t a k i n g i n t o account f a c t o r s such as: a) the boundary c o n f o r m a t i o n a l parameters (P , P n , P • T, P n ) and b) the 3 - t u r n or 3-sh e e t poten-aN a C naN naC ; J r t i a l i n the v i c i n i t y o f the h e l i c a l b o u n d a r i e s . In o t h e r words, a f t e r g o i n g t h r o u g h the e n t i r e p r o c e d u r e o f h e l i c a l s e a r c h , i f a r e g i o n d e l i n e a t e d by two v a l u e s J l and J2 ( J l : N - t e r m i n a l pf the p r e d i c t e d r e g i o n and J 2 : C - t e r m i n a l o f the same r e g i o n ) was p r e d i c t e d as a - h e l i x then the v a l u e s P ^ o f J l and P a£ o f J2 would be compared to those o f t h e i r n e i g h -b o u r i n g r e s i d u e s so t h a t the new b o u n d a r i e s J l +_ n, J2 +_ n' (n and n': i n t e g e r s ) would have the most f a v o r a b l e P ^ and f o r h e l i x s t a b i l i z a t i o n . The parameters P n a N and Pna(-. of the n o n h e l i c a l r e s i d u e s a d j a c e n t to the h e l i c a l bound-47 a r i e s . were also' i mportant' i n t h i s "move o f the b o u n d a r i e s " . •When c o n s i d e r i n g the p o s s i b i l i t y o f B-t u r n p r e s e n c e a t the he-l i x b o u n d a r i e s or the o v e r l a p p i n g o f the end r e s i d u e s w i t h a fragment p o s s e s s i n g h i g h B-sheet p o t e n t i a l , i t may a l s o be n e c e s s a r y t o move J l and J2 to new p o s i t i o n s w h i c h a r e d i c -t a t e d by P a (- r e s p e c t i v e l y ( c f . s u b r o u t i n e s M0J1, M0J2, RMJ1, and RMJ2 f o r a - h e l i x p r e d i c t i o n ) . The f o l l o w i n g are some examples o f a - h e l i x bound-a r i e s adjustment to i l l u s t r a t e the concept o f "move o f bound-a r i e s " . (1) J l = J l - 2 a. q-Hemoglobin: 8-17 A l a Asp Lys- Thr . Asn ' Val" I ! I I ! ! 6 8 10 * 1 Asp (6). has the second h i g h e s t v a l u e . As t h e r e i s n e i t h e r B - t u r n nor B-sheet p o t e n t i a l i n t h i s r e g i o n , by moving back to Asp ( 6 ) , the h e l i c a l a r e a 8-17 g a i n s 1 h^, Lys ( 7 ) , and 1 I a , Asp ( 6 ) . There i s no need to move f u r -t h e r to the N - t e r m i n a l because the program has a l r e a d y p r e -d i c t e d the a r e a 1-8 as h e l i c a l . 48 b\ M y o g l o b i n : 24-36 Asp V a l A l a G l y H i s G l y G l u Asp __ ! ! t T t I t i _ 20 22 24 26 t I A l a (22) has a h i g h e r v a l u e than H i s ( 2 4 ) . The i n c o r p o r a t i o n o f a b r e a k e r , G l y (23) i s b a l a n c e d by t h a t o f A l a , a s t r o n g h e l i x former. T h i s boundary a d j u s t -ment h e l p s t o l i n k the h e l i c a l r e g i o n s 13-22 and 24-36. (2) J l = J l + 3 a. C a r b o x y p e p t i d a s e : 170-182 Lys Tyr A l a Asn Ser G l u V a l G l u i ! ! ! I f ! ! _ 169 171 173 175 I t The boundary adjustment i s j u s t i f i e d by the s t r o n g p o t e n t i a l 8-turn o f the t e t r a p e p t i d e 169-172 and by the v e r y h i g h P a N o f G l u (173). F u r t h e r m o r e , Asn (171) and Ser (172) have the h i g h e s t P n a I q v a l u e s , hence t h e i r p r e s e n c e i s f a v o r a b l e to G l u (173) i f t h i s r e s i d u e i s chosen as the N-boundary. 49 b. P a p a i n : 47-60 i Leu Asn G i n Tyr Ser G l u 4 5 4 7 49 I I By moving the N-boundary to p o s i t i o n 50 ( G l u ) , advantage i s t a k e n o f the good P ,T o f G l u and at the same time the h e l i x b r e a k e r Tyr (48) and the h e l i x : ' i n d i f f e r e n t Ser (49) are removed. Ser (48) has h i g h p r o p e n s i t y to be found a t the n a n h e l i c a l N-boundary. (3) J2 = J2 + 2 a. Lysozyme: 105-112 V a l A l a Trp Arg Asn Arg Cys Lys G l y I t I I I I I | |__ 110 112 114 116 i 1 The r e g i o n 105-112 has enough h e l i x formers to b a l a n c e the i n c o r p o r a t i o n o f an e x t r a h e l i x b r e a k e r , Asn (113). And A r g (114) has good P ^ v a l u e which j u s t i f i e s i t s c o n s i d e r a t i o n as the new C-boundary. The r e s i d u e s Cys (115), Lys (116) and Gly (117) are f a v o r a b l e to the new p o s i t i o n o f J 2 . 50 b . C a r b o x y p e p t i d a s e : 297-303 Met G l u H i s Thr V a l Asn Asn l ! ! t t t t _ 301 303 305 307 I 1 D e s p i t e the lower ? a C o f V a l (305) compared to t h a t o f H i s (303) , the move of J2 t o J2 + 2 a l l o w s the a d d i t i o n o f an e x t r a i (Thr) and H ( V a l ) to the r e g i o n . In f a c t P a c o f V a l i s h i g h e r than the average v a l u e and the two r e s i d u e s Asn (306, 307) are l i s t e d second f o r t h e i r PnaC' (4) J2 = J2 - 5: a .Papain: 47-60 Asp Cys Asp A r g Arg Ser Tyr G l y 56 58 60 62 t : i The t e t r a p e p t i d e 57-60 has 8-turn p o t e n t i a l and a l t h o u g h P a C o f Asp (57) i s l o w e r than t h a t o f Cys ( 5 6 ) , the h e l i c a l c o n f o r m a t i o n a l parameter o f Asp ( I a ) i s h i g h e r than t h a t o f Cys ( i ). The r e s i d u e s Arg (58, 59) e x h i b i t S ° o d PnaC-51 b. g-Chymotrypsin: 172-186 A l a Gly A l a Ser Gly V a l Ser T 1 I I I I J__ 184 186 188 t I The t e t r a p e p t i d e 185-188 e x h i b i t s B -turn p o t e n t i a l and by moving J2 t o J 2 - 3 , t h e r e a r e two advantages. F i r s t , the b r e a k e r , Gly (184), i s a v o i d e d and second, a new bound-ar y w i t h r e l a t i v e l y good P AQ> A l a (183), i s o b t a i n e d . The boundary adjustment p r o c e d u r e s were e l a b o r a t e d i n the s u b r o u t i n e s M0J1, RMJ1 and M0J2, RMJ2 f o r the r e s i d u e s J l and J 2 , r e s p e c t i v e l y . A l t h o u g h such c o n s i d e r a t i o n s are not always s i m p l e and may g i v e unexpected r e s u l t s because the boundary c o n d i t i o n s v a r y from fragment to fragment as w e l l as from p r o t e i n , to p r o t e i n , they s t i l l h e l p t o save p a r t o f the a n a l y s i s o f o v e r l a p p i n g areas between h e l i x and B-sheet and t o a v o i d c o n f l i c t s between B-turns and h e l i c e s . A c e r t a i n number of segments were m i s s e d i n the p r e d i c t i o n by the p r e s e n t program due to one o f the f o l l o w i n g r e a s o n s : I t was r u l e d t h a t the n u c l e a t i o n segment s h o u l d c o n t a i n fewer than one t h i r d h e l i x b r e a k e r s (B or b ) ., ^ a or T h i s c o n d i t i o n s t r i c t l y e l i m i n a t e d some segments which have two b r e a k e r s out o f s i x r e s i d u e s a l t h o u g h they met 52 the r e q u i r e m e n t o f h a v i n g a t l e a s t two t h i r d s h's (e.g. a-hemoglobin 23-28 and p a p a i n 120-126). The n u c l e a t i o n segment d i d not have at l e a s t two t h i r d s h's (e.g. c a r b o x y p e p t i d a s e 116-121 and lysozyme 80-85) , a l t h o u g h by i n c o r p o r a t i n g an e x t r a r e s i d u e , the f i n a l segment ( c a r b o x y p e p t i d a s e 116-122) would r e s p e c t the r u l e , or by s h i f t i n g the whole fragment by one p o s i t i o n to the l e f t (lysozyme 79-84) the new b o u n d a r i e s ( J l - 1 , J2-1) would have b e t t e r and r e s p e c t i v e l y . The p o s i t i o n o f the r e s i d u e Pro a t the N-t e r m i n a l end i s a l s o c r i t i c a l . For example, i n c o n c a n a v a l i n A 83-88, a l t h o u g h t h i s fragment had the r i g t h number of h's, the presence o f Pro as the f o u r t h r e s i d u e ( p o s i t i o n 86) impeded the fragment from b e i n g t a k e n i n t o accoung. In t h i s case i t was not p o s s i b l e to s h i f t the fragment to the r i g h t t o p o s i t i o n 84-89 because from p o s i t i o n 89 the a r e a had h i g h e r 3-sheet than a - h e l i x p o t e n t i a l . T h e r e f o r e we attempted a p r e l i m i n a r y c o n s i d e r a t i o n o f the fragment 83-88 as a p o s s i b l e h e l i x then t r i e d to s h i f t i t to a v o i d h a v i n g Pro as the f o u r t h r e s i d u e (e.g. c o n c a n a v a l i n A 80-85). For R u s s e l l ' s V i p e r Venom 47-55, as t h e r e were more I , i and b than H and h i n t h i s p a r t o f the polypep-a ' a a a a r r J r r t i d e c h a i n , the n u c l e a t i o n s e a r c h s k i p p e d the e n t i r e a r e a be-cause none of the c o m b i n a t i o n s o f s i x c o n s e c u t i v e a m i n o . a c i d 53 r e s i d u e s had a t l e a s t two t h i r d s h's. N e v e r t h e l e s s the "one h a l f .h's " r e q u i r e m e n t was met by the e n t i r e fragment 47-55 (5 h's out o f 9 amino a c i d r e s i d u e s ) . Hence t h i s r e q u i r e m e n t c o u l d not be a p p l i e d s t r i c t l y i n a l l c a s e s , and i t may be mo-d i f i e d to such an e x t e n t t h a t the f i n a l p r e d i c t e d segment w i l l n o t be c o n s i d e r e d as h a v i n g d e v i a t e d from the normal c r i t e r i a . The g a t h e r i n g o f two or t h r e e Pro r e s i d u e s i n the same ar e a was another p o s s i b l e r e a s o n f o r m i s s i n g a fragment (e.g. b o v i n e c o l o s t r u m i n h i b i t o r 5-10)'. The fragment 1-10 o f t h i s , p r o t e i n " c o n t a i n e d t h r e e Pro a t p o s i t i o n s 4, 5, and 11, hence the program c o u l d o n l y d e t e c t the segment 9-14 as the most s u i t a b l e t o a v o i d h a v i n g Pro i n the i n n e r h e l i x . Howev-e r - , i f the r e s i d u e Pro 5 was c o n s i d e r e d a c c e p t a b l e as an N - t e r m i n a l end r e s i d u e (good P ^ , a l t h o u g h not a t the t h i r d p o s i t i o n ) , then the fragment 5-10 would be a p o t e n t i a l a-he-* l i x s i n c e i t met the r e q u i r e m e n t f o r two t h i r d s h's. In summary, i n o r d e r to o b t a i n r e s u l t s w hich are c l o s e r t o t h o s e o f Chou and Fasman or t o X-ray d a t a , the nu-c l e a t i o n r u l e was s l i g h t l y m o d i f i e d ( i . e . , under s p e c i f i c c i r c u m s t a n c e s the n u c l e a t i o n segment may have one t h i r d b r e a k e r s , which then must be compensated by the a d d i t i o n o f h's d u r i n g the a - h e l i x p r o p a g a t i o n , and the presence o f Pro a t the 2 f i r s t p o s i t i o n s o f the N - t e r m i n a l end i n s t e a d o f 54 a t the t h i r d one does not always c o n s t i t u t e an o b s t a c l e to a - h e l i x f o r m a t i o n ) . In a d d i t i o n , b e f o r e a s s e r t i n g a segment of the p o l y p e p t i d e c h a i n as a - h e l i x , the s e a r c h f o r i t s most s u i t a b l e b o u n d a r i e s was f i r s t c a r r i e d out. T h i s e x t r a a n a l y -s i s was d e v e l o p e d i n two e x t r a s u b r o u t i n e s , the f i r s t one d e a l i n g w i t h the N - t e r m i n a l r e s i d u e ( c f . s u b r o u t i n e s M0J1, RMJ1) and the second one w i t h the C - t e r m i n a l r e s i d u e ( c f . s u b r o u t i n e s M0J2, RMJ2). The f o l l o w i n g program, f o r the a - h e l i x s e a r c h , was e v e n t u a l l y adopted. 55 1 2 C C 3 c 4 c 5 6 7 c c c MAIN PROGRAM OF HELIX PREDICTION 8 9 10 1 1 c c c c 12 c PURPOSE 13 c TO READ IN THE SEQUENCE OF THE PROTEIN AND TO ASSIGN TO EACH AMI 14 c NO ACID RESIDUE ITS CONFORMATIONAL PARAMETERS(PA,PB,PT) AND ITS 15 c BOUNDARY CONFORMATIONAL PARAMETERS(PAN,PAC,PNAN,PNAC,PBN,PBC. 16 c PNBN.PBNC) 17 c 18 c 19 c 20 c 21 REAL S ,T1 ,T2 .A1 ,A2 , T 3 , T 4 , T 5 , T T , P 22 INTEGER G,F,H,U,D,V1,V2,W, V 3 , V 4 , V 5 , V 6 . V 7 . V 8 , 0 23 LOGICAL HELLO,BYE ,BALL,MOVE 24 DIMENSION S (1000 ,20 ) ,M (1000 ) ,H (1000 ) ,D (1000 ,16 ) ,P (1000 ,10 ) 25 COMMON S , T 1 , T 2 , T 3 , T 4 , T 5 , T T , A 1,A2,P,F,H,U,D,W,M.M1,M2,M3,M4,M5,M6 26 1 L , I,K , L 1 , L 2 , N Z , N Y , J A , J B , J C , J D , J 1 , J 2 , K M , N 1 , N 2 , N N , J , G , K 3 , V 1 , V 2 , V 3 , ' 27 2,V5,V6,V7,0.HELLO,BYE,BALL,MOVE 28 c 29 c 30 c 31 c DESCRIPTION OF PARAMETERS 32 c S - ARRAY RECORDING THE DIFFERENT CONFORMATIONAL PARAMETERS FOR 33 c EACH AMINO ACID RESIDUE (K) 34 c S(K,1) - PA 35 c -S(K, 2) - PB 36 c S(K ,5 ) - PT 37 c S(K,6) - PNAN 38 c S(K,7) - PNAC 39 c S(K,8) - PAN 40 c S (K.9) - PAC 41 c T1 - SUM OF PA OF N AMINO ACID RESIDUES 42 c T2 - SUM OF PB OF N AMINO ACID RESIDUES , 43 c T5 - SUM OF PT OF N AMINO ACID RESIDUES 44 c T3 - SUM OF THE ASSIGNMENTS AS FORMER,BREAKER,INDIFFERENT IN 45 c THE NUCLEATION FRAGMENT 46 c T4 - SUM OF THE ASSIGNMENTS AS FORMER,BREAKER,INDIFFERENT IN 47 c THE ENTIRE PREDICTED HELICAL AREA 48 c TT - ALLOWED NUMBER OF BREAKERS IN THE ENTIRE PREDICTED AREA 49 c ( EQUAL TO ONE THIRD OF THE LENGTH) 50 c. P - FREQUENCY OF THE RESIDUES IN A REVERSE B-TURN 51 C P(K,1) - FREQUENCY OF THE FIRST RESIDUE 52 C P(K,2) - FREQUENCY OF THE SECOND RESIDUE 53 C P(K,3) - FREQUENCY OF THE THIRD RESIDUE 54 C P(K,4) - FREQUENCY OF THE FOURTH RESIDUE 55 C M - ARRAY RECORDING THE NUMERICAL ASSIGNMENT OF EACH AMINO 56 C ACID RESIDUE 57 C NN - TOTAL NUMBER OF RESIDUES OF THE PROTEIN 58 C N - NUMBER OF LINES USED TO ENTER THE WHOLE SEQUENCE (16 RESI 59 C DUES PER LINE) 60 C D - ARRAY RECORDING THE POSITION OF EACH AMINO ACID RESIDUE 61 C ON THE NTH LINE 62 C D(K,L) - AMINO ACID RESIDUE AT POSITION K ON LINE L 63 C 64 C REMARK 65 C SOME OF THE PARAMETERS WILL BE DESCRIBED IN THE SUBSEQUENT SUBROU 66 C TINES SINCE THEIR DEFINITION MAY CHANGE FROM ONE SUBROUTINE TO ANO 67 C THER 68 C 69 PRINT 100 70 100 FORMAT('1' 35X '*********************************') 7 1 PRINT 102 72 102 FORMAT(' ' ,35X, '*' ,31X, '*' ) 73 PRINT 103 74 103 FORMAT(' ' ,35X, '*' .4X. 'ALPHA-HELIX PREDICTION',5X,'*' ) 75 PRINT 102 76 PRINT 104 77 104 FORMAT(' ' 35X '*********************************'//) 78 READ (5,106) NN ,N 79 106 FORMAT(6X,14,6X,14) 80 WRITE (6,107) NN 8 1 107 FORMAT('0','TOTAL NUMBER OF AA:',I7) 82 WRITE (6,108) N 83 108 FORMAT(' ', 'NUMBER OF DATA LINES: ' ,15,/) 84 PRINT 109 85 109 FORMAT('0','PROTEIN SEQUENCE') 86 PRINT 110 87 1 10 FORMAT( ' ' , ' '/) 88 RE AD (5, 111) ((D(d,K),K=1,16),d=1,N) 89 1 1 1 FORMAT (1615) 90 WRITE (6,112) ((D(d.K),K=1, 16) ,d=1 ,N) 9 1 1 12 F0RMAT(' ',1615) 92 C 93 c TO CHECK THE NUMERICAL ASSIGNMENT OF EACH AMINO ACID RESIDUE IN 94 c THE SEQUENCE SO TO ASSIGN ITS CORRESPONDING CONFORMATIONAL PARAMETERS 95 c 96 1 = 1 97 DO 21 d=1,N 98 DO 22 K=1,16 99 M( I )=D(d,K) 100 IF (M(I).EQ.O) GO TO 999 101 1 = 1 + 1 102 22 CONTINUE 103 21 CONTINUE 104 999 DO 32 K =  1 , NN 105 IF (M K ) EO. 1) GO TO 1 106 IF (M K ) EQ. 2) GO TO 2 107 IF (M K ) EO. 3) GO TO 3 108 IF (M K ) EO. 4) GO TO 4 109 I F (M K ) EO. 5) GO TO 5 1 10 IF (M K ) EO. 6) GO TO 6 1 1 1 IF (M K ) EO. 7) GO TO 7 1 1 2 IF (M K ) EO. 8) GO TO 8 1 13 IF (M K ) EO. 9) GO TO 9 1 14 IF (M K ) EO. 10) GO TO 10 1 15 IF (M K ) EO. 11) GO TO 1 1 1 16 IF (M K ) EO. 12) GO TO 12 1 17 I F (M K) EO. 13) GO TO 13 1 18 IF (M K ) EO. 14) GO TO 14 1 19 IF (M K ) EO. 15) GO TO 15 120 IF (M K ) EO. 16) GO TO 16 121 IF (M K ) EO. 17) GO TO 17 122 IF (M K ) EO. 18) GO TO 18 123 IF (M K ) EO. 19) GO TO 19 124 IF (M K ) EO. 20) GO TO 20 125 IF (M K) EO. 25) GO TO 25 126 C 127 C 128 1 S(K , 1 = 1 42 129 S(K , 2 =0 83 130 S(K , 5 =0 66 131 S(K , 6 =o 70 • 132 S(K , 7 =0 52 133 S(K,8 = 1 29 134 S(K ,9 = 1 20 135 P(K , 1 =0 060 136 P(K , 2 =0 076 137 P(K , 3 =0 035 138 P(K , 4 =o 058 139 GO TO 32 140 2 S(K , 1 =0 98 14 1 S(K, 2 =0 93 142 S(K,5 =o 95 143 S(K ,6 =0 34 144 S(K , 7 = 1 24 145 S(K,8 =0 44 146 S(K ,9 = 1 25 147 P(K, 1 =0 070 148 P(K,2 =0 106 149 P(K , 3 =0 099 150 P(K ,4 = 0 085 151 GO TO 32 152 3 S(K, 1 )=0 67 153 S(K,2)=0 89 154 S(K,5)=1 56 155 S(K,6)=1 42 15G S(K,7)=1 64 157 S(K,8)=0 81 158 S(K,9)=0 59 159 P(K, 1 )=0 16 1 160 P(K,2)=0 083 161 P(K,3)=0 191 162 P(K,4)=0 09 1 163 GO TO 32 164 4 S(K , 1 ) = 1 01 165 S(K,2)=0 54 166 S(K,5)=1 46 167 S(K,6)=0 98 168 S(K,7)=1 06 169 S(K,8)=2 02 170 S(K,9)=0 61 171 P(K, 1 )=0 147 172 P(K,2)=0 1 10 173 P(K,3)=0 1 79 174 P(K,4)=0 081 175 GO TO 32 176 5 S(K, 1 )=0 70 177 S(K.2)=1 19 178 S(K,5)=1 19 179 S(K,6)=0 65 180 S(K,7)=0 94 181 S(K,8)=0 66 182 S(K,9)=1 1 1 183 P(K, 1 ) =0 149 184 P(K,2)=0 053 185 P(K,3)=0 1 17 186 P(K,4)=0 128 187 GO TO 32 188 6 S(K, 1 ) = 1  1 189 S(K,2)=1 10 190 S(K,5)=0 98 191 S(K,6)=0 75 192 S(K.7)=0 70 193 S(K,8)=1 22 194 S(K,9)=1 22 195 P(K. 1 )=0 074 196 P(K,2)=0 098 197 P(K,3)=0 037 198 P(K,4)=0 098 199 GO TO 32 200 7 S(K, 1 ) = 1 51 as o 201 S(K,2 )=0 37 202 S(K, 5 )=0 74 203 S(K,6 )= 1 04 204 S(K,7 )=0 59 205 S(K,8 = 2 44 206 S(K,9 = 1 24 207 P(K, 1 =0 056 208 P(K , 2 =0 060 209 P(K.3 =0 077 210 P(K,4 =0 064 2 1 1 GO TO 32 212 8 S(K, 1 =0 57 2 13 S(K, 2 =0 75 2 14 S(K,5 = 1 56 2 15 S(K,6 = 1 4 1 2 16 S(K.7 = 1 64 217 S(K,8 =0 76 2 18 S(K.9 =0 42 2 19 P(K , 1 =0 102 220 P(K,2 =0 085 221 P(K,3 =0 190 222 P(K , 4 =0 152 223 GO TO 32 224 9 S(K, 1 = 1 00 225 S(K , 2 =0 87 226 S(K,5 =0 95 227 S(K,6 = 1 22 228 S(K , 7 = 1 86 229 S(K,8 =0 73 230 S ( K , 9 = 1 77 231 P(K, 1 =0 140 232 P(K , 2 =0 047 233 P(K, 3 =0 093 234 P(K , 4 =0 054 235 GO TO 32 236 10 S(K, 1 = 1 08 237 S(K,2 = 1 60 238 S(K, 5 =0 47 239 S(K,6 =0 78 240 S(K,7 =0 87 24 1 S(K,8 =0 67 242 S(K,9 =0 98 243 P(K , 1 =0 043 244 P(K,2 =0 034 245 P(K.3) =0 013 246 P(K , 4 =0 056 247 GO TO 32 248 1 1 S(K, 1 = 1 21 249 S(K,2 = 1 30 250 S(K,5 =0 59 251 S(K,6 =0 85 252 S(K,7 =0 084 253 S(K,8 =0 58 254 5(K,9 = 1 13 255 P(K, 1 =0 061 256 P(K,2 =0 025 257 P(K, 3 =0 036 258 P(K, 4 =0 070 259 GO TO 32 260 12 S(K , 1 = 1 16 26 1 S(K , 2 =0 74 262 S(K,5 = 1 01 263 S(K , 6 = 1 01 264 S(K . 7 = 1 49 265 S(K,8 =0 66 266 S(K , 9 = 1 83 267 P(K, 1 =0 055 268 P(K,2 =0 1 15 269 P(K,3 =0 07 2 270 P(K, 4 =o 095 27 1 GO TO 32 272 13 S(K. 1 = 1 45 273 S(K, 2 = 1 05 274 S(K , 5 =0 60 275 S(K,6 =0 83 276 S(K , 7 =0 52 277 S(K,8 =0 7 1 278 S(K,9 = 1 57 279 P(K , 1 =0 068 280 P(K,2 =0 082 28 1 P(K,3 =0 014 282 P(K,4 =0 055 283 GO TO 32 284 14 S(K , 1 = 1 13 285 S(K,2 = 1 38 286 S(K , 5 =0 60 287 5(K,6 =0 93 288 S(K,7 = 1 04 289 S(K,8 =0 61 290 S(K,9 = 1 10 291 P(K , 1 =0 059 292 P(K , 2 =0 04 1 293 P(K,3 =0 065 294 P(K , 4 =0 065 295 GO TO 32 296 15 S(K, 1 =0 57 297 S(K,2 =0 55 298 S(K,5 = 1 52 299 S(K,6 = 1 10 300 S(K,7 = 1 58 301 S(K.8 = 2 01 302 S(K,9 =0 00 303 P(K, 1 =0 102 304 P(K, 2 =0 301 305 P(K , 3 =0 034 306 P(K,4 =0 068 307 GO TO 32 308 16 S(K, 1 =0 77 309 S(K, 2 =0 75 310 S(K, 5 = 1 43 31 1 S(K,6 = 1 55 312 S(K,7 =0 93 313 S(K,8 =0 74 314 S(K,9 =0 96 315 P(K , 1 =0 120 316 P(K, 2 =0 139 317 P(K,3 =0 125 318 P(K,4 =0 106 3 19 GO TO 32 320 17 S(K , 1 =0 83 32 1 S(K.2 = 1 19 322 S(K,5 =0 96 323 S(K , 6 = 1 09 324 S(K,7 =0 86 325 5(K,8 = 1 08 326 S(K,9 = 0 75 327 P(K, 1 =0 086 328 P(K , 2 =0 108 329 P(K , 3 =0 065 330 P(K,4 =0 079 331 GO TO 32 332 18 S(K, 1 = 1 08 333 S(K , 2 = 1 37 334 S(K,5 =0 96 335 S(K , 6 =0 62 336 S(K,7 =0 16 337 S(K,8 = 1 47 338 S(K,9 =0 40 339 P(K, 1 =0 077 340 P(K , 2 =0 013 34 1 P(K, 3 =0 064 342 P(K,4) =0 167 343 GO TO 32 344 19 S(K, 1 =0 69 345 S(K,2 = 1 47 346 S(K,5) = 1 14 347 S(K,6) =0 99 348 S(K,7) = 0 96 349 S(K,8) =0 68 350 S (K ,9) =0 73 351 P(K,1)=0.082 352 P(K,2)=0.065 353 P(K,3)=0.114 354 P(K,4)=0.125 355 GO TO 32 356 20 S(K,1)=1.06 357 S(K,2)=1.70 358 S(K,5)=0.50 359 S(K,6)=0.75 360 S(K.7)=0.32 361 S(K,8)=0.61 362 S(K,9)=1.25 363 P(K,1)=0.062 364 P(K,2)=0.048 365 P(K,3)=0.028 366 P(K,4)=0.053 367 GO TO 32 368 25 S(K,1)=0.00 369 S(K,2)=0.00 370 5(K,5)=0.00 371 S(K,6)=0.00 372 S(K,7)=0.00 373 S(K,8)=0.00 374 S(K,9)=0.00 W 375 P(K,1)=0.00 376 P(K.2)=0.00 377 P(K,3)=0.00 378 P(K,4)=0.00 379 32 CONTINUE 380 C 38 1 C 382 PRINT 40 383 40 FORMAT( 12X.'PRELIMINARY SEARCH FOR REGIONS WITH HELIX POTENTIA 384 1L - RULE 1') 385 PRINT 41 386 41 FORMAT(' ',12X.' 387 1 ' ) 388 C 389 C TO CALL SUBROUTINE ONE TO CARRY OUT THE PRELIMINARY SEARCH OF HELI 390 C CAL REGIONS 391 C 392 CALL ONE 393 STOP 394 END End of F i l e 1 2 C C 3 4 5 6 7 8 9 C C C C C C SUBROUTINE ONE PRELIMINARY SEARCH FOR HELICAL REGIONS 10 C 1 1 C 1 2 C 13 C 1 4 C 15 C 16 C PURPOSE 17 C PRELIMINARY SEARCH FOR HELICAL REGIONS BY APPLYING RULE 1 : 18 C <PA> > 1 . 0 3 AND <PA> > <PB> 19 C 2 0 C 21 C 22 c 23 REAL S , T 1 , T 2 , A 1 , A 2 , T 3 , T 4 , T 5 , T T , P 24 INTEGER G , F , H , U , D , V 1 , V 2 , W , V3 , V4 , V5 , V.6 , V7 , V8 , 0 25 LOGICAL HELLO,BYE ,BALL,MOVE 26 DIMENSION S ( 1 0 0 0 , 2 0 ) , M ( 1 0 0 0 ) , H ( 1 0 0 0 ) , D ( 1 0 0 0 , 1 6 ) , P ( 1 0 0 0 , 1 0 ) 27 COMMON S , T 1 , T 2 . T 3 . T 4 , T 5 . T T , A 1 , A 2 . P , F , H , U , D , W , M , M 1 , M 2 , M 3 , M 4 , M 5 , M 6 28 1 L , I , K , L 1 , L 2 , N Z . N Y , d A , J B , J C . U D , <J 1 , J 2 . K M . N 1 , N 2 , N N , d , G , K 3 , V 1 , V 2 , V 3 , ' 29 2 , V 5 , V 6 , V 7 , 0 . H E L L O , B Y E , B A L L , M O V E 3 0 c 31 c 32 c DESCRIPTION OF PARAMETERS 33 c 34 c H - BOUNDARY RESIDUES OF A PREDICTED REGION 35 c H ( K ) - N-TERMINAL RESIDUE 36 c H ( K + 1 ) - C-TERMINAL RESIDUE 37 c J - F IRST RESIDUE OF A SECTION TO BE CONSIDERED FOR THE PRELI 38 c MINARY SEARCH BUT WILL CHANGE DURING N-PROPAGATION ( J - 1 ) 39 c JA - F IRST RESIDUE OF A SECTION TO BE CONSIDERED FOR THE PRELI 4 0 ' c MINARY SEARCH BUT WILL CHANGE DURING C-PROPAGATION ( J A + 1 ) 4 1 c N1 - F IRST RESIDUE OF A SECTION TO BE CONSIDERED FOR THE PRELI 42 c MINARY SEARCH 4 3 c N2 - LAST RESIDUE OF A SECTION TO BE CONSIDERED FOR THE PREL1 44 c MINARY SEARCH 4 5 c A1 - AVERAGE <PA> OF A SECTION 46 c A2 - AVERAGE <PB> OF A SECTION 47 c I - SWITCHING VALUE FOR DECIS ION MAKING 48 c 1=1 N-PROPAGATION 4 9 c 1=2 C-PROPAGATION 5 0 c K - COUNTER USED WITH THE ARRAY H TO STORE THE BOUNDARY RESI <7\ U l 51 C DUES OF PREDICTED REGIONS 52 C 53 C THE SEARCH WILL STOP WHEN THE LAST SEGMENT AT THE C-TERMINAL HAS 54 C ONLY 5 AMINO ACID RESIDUES. IT IS NOT LONG ENOUGH FOR THE HELICAL 55 C STATE 56 C 57 10 K = 2 58 H(K)=0 59 H(K-1)=0 60 NZ=NN-5 61 J= 1 62 JA= 1 63 15 1=0 64 20 N2=dA+5 65 HELLO=.FALSE. 66 IF (d.EQ.H(K)) HELLO=.TRUE. 67 IF (HELLO) N1=H(K)+1 68 IF (.NOT.HELLO) N1=d 69 c 70 c IF ARG OR CYS IS AT THE C-TERMINAL THEY CAN BE ADDED TO THE POTEN 7 1 c TIAL FRAGMENT BECAUSE OF THEIR GOOD PAC VALUE 72 c 73 c 74 c TO CALCULATE THE AVERAGE <PA>,<PB> AND TO COUNT THE NUMBER OF BREA 75 c KERS IN THE SECTION N1-N2 76 c 77 T1 = 0 78 T2 = 0 79 L =0 80 LB = 0 8 1 L = N1+1+(N2-N1)/2 82 DO 25 LN=L,N2 83 IF (M(LN).EQ.2.OR.M(LN).EO.5) S(LN,1)=1.00 84 25 CONTINUE 85 DO 30 L=N1,N2 86 T1 = T1 + S(L, 1 ) 87 T2 = T2 + S(L.2) 88 IF (S(L,1).LE.0.69) LB=LB+1 89 30 CONTINUE 90 A1 = T1/(N2-N1+1) 91 A2 = T2/(N2-N1+1) 92 c 93 c 94 c IF <PA> < 1.03 TO START THE SEARCH AGAIN FROM NEXT POSITION d+1 95 c 96 IF (A1 .LT. 1 .03000000) GO TO 45 97 c 98 c SPECIAL SITUATION WHERE THE SECTION MAY HAVE HELICAL POTENTIAL EVEN 99 c THOUGH <PA> < <PB> 100 c 101 IF (A1.GT.1.1100.AND.(A2-A1).IT.0.0640.AND.M(N1).EO.4.AND.M(N2+1 102 1 .EO.2.AND.M(N1 + 3) .EO. 1 .AND.M(N1 - 1) .EO. 11.AND.M(N1-2).E0.8.AND. 103 2S(N2, 1).GT. 1 .01 .AND.LB.EO.O) GO TO 60 104 C 105 C IF <PA> < <PB> EVEN IF <PA> > 1.03 TO START SEARCH AGAIN FROM NEXT 106 C POSITION d+1 UNLESS THE LAST AMINO ACID RESIDUE HAS BEEN REACHED 107 C 108 IF (A1.LT.A2 .AND. N2.EQ.NN .AND.(N2+1-N1).E0.6) GO TO 80 109 IF (A1.LT.A2 .AND. N2.E0.NN .AND.(N2+1-N1).GT.6) GO TO 70 1 10 IF (A1.LT.A2 .AND. N2.NE.NN) GO TO 45 1 1 1 C 1 12 C TO PROPAGATE AT THE C-TERMINAL SIDE WHEN THE SEARCH HAS NOT REACHED 1 13 C THE LAST AMINO ACID RESIDUE YET (NN) 1 14 C 1 15 IF (I.EQ.2 .AND. N2.EQ.NN) GO TO 55 1 16 IF (I.E0.2 .AND. N2.NE.NN) GO TO 50 1 17 C 1 18 C TO START N-PROPAGATION WHEN <PA> > 1.03 AND <PA> > <PB> UNLESS THE 1 19 C HELICAL SEGMENT STARTS FROM POSITION 1 120 C 121 J = J-1 122 I = 1 123 BYE=.FALSE. 124 IF (J.EO.H(K)) BYE=.TRUE . 125 IF (BYE) I = 2 126 IF (BYE) GO TO 50 127 IF (.NOT. BYE) GO TO 20 128 C 129 C TO SWITCH FROM N-PROPAGATION TO C-PROPAGATION WHEN THE REMAINING 130 C SECTION OF THE SEQUENCE HAS MORE THAN 5 RESIDUES 131 C 132 45 J=d+1 133 IF (I.EQ.2) GO TO 70 134 IF (I.EQ.1) I = 2 135 50 JA=UA+1 136 IF (JA.LE.NZ) GO TO 20 137 IF (UA.GT.NZ) GO TO 80 138 C 139 C TO PRINT OUT THE LAST HELIX POTENTIAL AREA H(K),H(K+1) AND THE MA 140 C XIMUM VALUE OF THE COUNTER K WHICH WILL BE USED INT THE NEXT SUBROU 14 1 C TINE 142 c 143 55 K=K+1 144 H(K)=N1 145 K=K+1 146 H(K)=N2 147 PRINT 58,H(K-1),H(K) 148 58 FORMAT('0',30X,16,10X,16) 149 KM = K 150 GO TO 80 151 C 152 C 153 C TO PRINT OUT THE HELIX POTENTIAL AREAS H(K),H(K+1),THEN THE PRELI 154 C MINARY SEARCH STARTS AGAIN FROM POSITION (H(K+1) +1) 155 C 156 60 K = K+1 157 H(K)=N1 158 K = K+1 159 H(K)=N2 160 GO TO 75 161 70 K = K+1 162 H(K)=N1 163 K = K + 1 164 H(K)=N2-1 165 75 PRINT 78,H(K-1) ,H(K) 166 78 FORMAT('0',30X, 16,10X,16) 167 J=H(K) 168 JA=H(K) 169 KM = K 170 IF (UA.LE.NZ) GO TO 15 17 1 80 PRINT 85 ,KM 172 85 FORMAT('0',40X, 'KM:',14) 173 K = 2 174 W = 1 175 PRINT 90 176 90 FORMAT('-',12X, 'SEARCH FOR ACTUAL HELICES FROM THE POTENTIAL REGIO 177 1 NS ' ) 178 PRINT 95 1 79 95 FORMAT(' ',12X, 1 . . '//) 180 181 C 182 C TO CALL SUBROUTINE TWO TO CARRY OUT THE NUCLEATION SEARCH ON THOSE 183 • C POTENTIAL AREAS 184 C 185 CALL TWO 186 RETURN 187 END End of F i l e 1 c 2 C 3 SUBROUTINE TWO 4 C 5 C 6 C 7 C 8 C 9 C SEARCH FOR HELIX NUCLEATION 10 C 11 C 12 C 13 C 14 C 15 C 16 C 17 C PURPOSE 18 C SEARCH FOR NUCLEATING HELICAL REGIONS WHICH SHOULD CONTAIN AT 19 C LEAST 4 FORMERS OUT OF 6 RESIDUES 20 C 21 C 22 C 23 REAL S,T1,T2,A1,A2 ,T3,T4,T5,TT,P 24 INTEGER G,F,H,U,D,V1,V2,W, V3,V4,V5,V6.V7,V8,0 25 LOGICAL,HELLO,BYE .BALL,MOVE cy, 26 DIMENSION S(1000,20),M(1000),H(1000),D(1000,16).P(1000,10) 00 2 7 COMMON S,T1,T2,T3,T4,T5,TT,A 1,A2,P,F,H,U,D,W,M,M1,M2,M3,M4,M5,M6. ' 28 1L,I,K,L1,L2,NZ,NY,JA,JB,JC,JD, J 1,J2,KM,N1,N2,NN,J,G,K3,V1,V2,V3,V4 29 2, V5,V6,V7,0,HELLO,BYE,BALL.MOVE 30 C 31 C 32 C DESCRIPTION OF PARAMETERS 33 C J FIRST RESIDUE OF THE 6 RESIDUE PEPTIDE SUBJECTED TO THE 34 C NUCLEATION SEARCH 35 C JA - SIXTH RESIDUE OF THE 6 RESIDUE PEPTIDE SUBJECTED TO THE 36 C NUCLEATION SEARCH 37 C W - SWITCHING VALUE FOR DECISION MAKING 38 C W=1 THE CURRENT POTENTIAL AREA IS STILL LONG ENOUGH (> 39 C 6 RESIDUES) TO BE SUBJECTED TO THE NUCLEATION SEARCH 40 C W=2 THE CURRENT POTENTIAL AREA IS TOO SHORT FOR ANOTHER 41 C HELIX SO TO START WITH THE NEXT POTENTIAL AREA 42 C 43 C REMARKS 44 C UNLESS NOTIFIED THE OTHER PARAMETERS STILL HAVE THE SAME DEFINITION 45 C 46 C 47 C IF W = 2 THE NUCLEATION SEARCH WILL START ON A NEW POTENTIAL AREA 48 C SINCE THE PREVIOUS ONE HAS BEEN THOUROUGHLY ANALYZED. EACH TIME K 49 C INCREASES BY 1 THE NEXT POTENTIAL AREA IS SUBJECTED TO THE NUCLEA 50 C TION PROCEDURE cn 51 C 52 10 IF (W.E0.2) GO TO 20 53 15 K=K+ 1 54 IF (K.GT.KM) GO TO 170 55 N1=H(K) 56 K = K+1 57 N2=H(K) 58 IF (W.E0.1) d = N1 59 NY=N2-5 60 20 dA=d+5 61 C 62 C TO COUNT THE DIFFERENT TYPES OF ASSIGNMENTS (T3) AND THE NUMBER OF 63 C BREAKERS (L) IN THE SEGMENT d~dA 64 C S(I,3) = 0.0 IF RESIDUE I IS A BREAKER OR AN INDIFFERENT 65 C S(I,3) = 0.5 IF RESIDUE I IS A WEAK FORMER 66 C S(I,3) = 1.0 IF RESIDUE I IS A FORMER 67 C 68 T3 = 0 69 L =0 70 DO 25 I=J,dA 7 1 S(I.3)=0 72 IF (S(I . 1).GE. 1 .00) S(I,3)=0.5 73 IF (S(I , 1),GE. 1 .06) S(I,3) = 1.0 74 T3 = T3+S(I,3) 75 IF (S(I, 1 ) .LE.0.69) L = L+1 76 25 CONTINUE 77 PRINT 30,d,dA,T3,L 78 30 FORMAT(' ',1OX,'J :',14,5X,'JA:',14,5X,'T3:',F7.4,5X,'L:',13,5X 79 1'HELIX NUCLEATION') 80 C 8 1 C IF CASE ARG IS AT THE C-TERMINAL IT MAY SWITCH FROM INDIFFERENT TO 82 C FORMER SO THAT THE NUCLEATION RULE CAN BE SATISFIED 83 C 84 IF (T3.EO.3.5.AND.M(dA).EO.2) S(dA,1)=1.00 85 IF (T3.EQ.3.5.AND.M(dA).EQ.2) T3=4.0 86 C 87 C 88 C LIST OF SPECIAL SITUATIONS WHERE THE NUCLEATION RULE AND THE TYPES 89 C OF RESIDUES IN THE SEGMENT SHOULD BE COMBINED TOGETHER SINCE THE 90 C NUCLEATION RULE BY ITSELF IS TOO DISCRIMINATIVE 91 c 92 IF ((UA+2).GT.NN.OR.(d-2).LE.0) GO TO 35 93 IF (T3 . GE . 4 .0. AND . L . LE . 2 . AND .M(d).EQ.7. AND . M( <JA ) . E-Q . 1 . AND .M(dA-94 1.EQ.7.AND.M(J+3).EO- 1 .AND.M(d~2).EQ. 1 .AND.S(JA+1, 1).GT. 1 . 16.AND 95 3S(dA+2,1).GT. 1.16) GO TO 90 96 c 97 35 IF ((JA+1).GT.NN.OR.(J-3).LE.0) GO TO 40 98 IF (T3.GE.4.5.AND.L.EQ.1.AND.M(U+3).EO.15.AND.M(J).EQ.4.AND. M (d 99 1.EO.11.AND.M(d+4).EQ.7.AND.M(OA).EQ.18.AND.S(d-3,8).GE.2.01.AND 100 2 S(d-2, 1).GT. 1 . 16.AND.S(dA+1 , 1 ).GT. 1 .01) GO TO 110 101 c 102 40 IF ((dA+2) .GT.NN.OR. (d-4) .LE.O) GO TO 45 103 IF (T3.GE.3.5.AND.L.EQ.0.AND.M(J).EO.14.AND.M(d+1).EO.1.AND.M(JA+1 104 1).E0.7.AND,M(dA-1).EO.9.AND.S(J-1,1).LT.0.67.AND. S(dA + 2,1).LE.0.69 105 2 .AND.5(J-2,8).LT.1.08.AND.S(d-3,8).GT.1.47.AND.S(d-4,8).LT.1.08) 106 3 GO TO 120 107 C 108 45 IF ((d-2).LE.O) GO TO 50 109 IF (T3.GE.4.0.AND.L.LE.2.AND.M(d+1).EO.6.AND.M(d+3).EO.1.AND.M(dA 1 10 1 - 1 ) .EO. 1 1 .AND.M(JA) .EO. 1 1 .AND.S(d,1).LE.0.69.AND.S(d-1, 1 ).LE.0.69 111 2.AND.S(J-2,8).GT.1.47) GO TO 110 112 C 113 50. IF ((JA+2).GT.NN) GO TO 55 114 IF (T3.GE.4.0.AND.L.EO. 1 . AND.M(J).EO. 15.AND.M(J+1).EQ.4.AND.M(dA) 115 1.E0.7.AND.M(d+3).EO.5.AND.M(dA+1).EO.15.AND.M(dA+2).EO.15) GO TO 116 2 130 117 C 118 55 IF ((dA+1).GT.NN.OR.(d-2).LE.0) GO TO 60 119 IF (T3.GE.3.5.AND.L.EQ.0.AND.M(J-1).EQ. 15.AND.5(d+2, 1 ) .GT . 1 .21 .AND 120 1 .S(d+3, 1).GT.1.16.AND.S(d+4, 1).GT. 1. 16.AND. S (dA , 9 ) . GT . 0 . 75 .AND.S( 121 2 dA+1.9).GT.0.75.AND.S(d-2,8).LT.1.08) GO TO 140 122 C 123 60 IF ((dA+2).GT.NN.OR.(d-1).LE.0) GO TO 65 1 24 IF (T3.GE.3.0.AND.L.EQ.3.AND.M(d).EQ. 15.AND.M(d+2).EQ. 1 .AND.M(J+3 ) 1 25 1 .EQ.20.AND.M(J + 4) .EQ. 13.AND.M(dA).EQ.8.AND.S(JA+1 ,2).LT.O.93.AND. -J 126 2S( JA+2 , 2) .LT.0.74.AND.S(J-1,2).LT.O.93) GO TO 130 ° 127 C 128 65 IF ((JA + 7 ) .GT.NN) GO TO 70 129 IF (T3.EQ.2.5.AND.L.EQ.2.AND.M(d+2).EQ.14.AND.5(d+3,8).GT.2.02.AND 130 1 .S(d+4. 1).GT.0.7 7.AND.S(dA, 1 ) .GT.0.83.AND.S(JA+1,8).GT.2.01.AND. 13 1 2 S(JA + 5,9).GT. 1 . 10.AND.S(JA + 5, 1 ) .GT. 1 . 16.AND.M(JA + 2).NE. 15.AND.S( 132 3 JA+3,9).GT.1.10.AND.S(JA+4,9).GT.1.24.AND.S(JA+6,9).LT.1.10.AND.S 133 4 (JA + 7, 1 ) .LT. 1 .06) GO TO 150 134 C 135 70 IF ((JA+1).GT.NN.OR.(J-3).LE.0) GO TO 75 136 IF (T3.GE.4.0.AND.L.LE. 1 .AND.M(JA) .EQ. 15.AND.S(JA+1, 1 ) .LT.S(JA- 1 , 1 137 1 ) . AND.S(JA-1, 1 ) .GT. 1 . 16.AND.S(JA- 1,9).GT. 1. 10.AND.S(d,8).GT.2.01 138 2 .AND.S(d-1,8).GT.1.29.AND.S(d-2,6).GT.1.09.AND.S(J-3,8).LT.S(d-1 139 3.8).AND.S(d+1,1).GT.1.16.AND.S(d+2,9).GT.1.10.AND.S(d+3.9).GT.1. 140 4 20) GO TO 140 14 1 C 142 75 IF ((dA+3).GT.NN.OR.(d-3).LE.0) GO TO 80 143 IF (T3.GE.3.50.AND.L.LE.1.AND.M(d).EQ.15.AND.S(dA,9).GE.1.10.AND.S 144 1 (dA, 1 ) .GT. 1 .08.AND.S(dA+1, 1) . LE.0.69.AND.S(dA+2, 1 ) .LE.0.69.AND.S( 145 2 dA + 3,9) .LT.0.98.AND.S(d+1, 1 ) . GT. 1 . 16.AND.S(d+2, 1) .GT. 1 . 16.AND.S(d 146 3 +3,9).GE.1.57.AND.S(d+4,9).GT.0.75.AND.S(d-1,1).GT.1.16.AND.S(d-2 147 4 . 1 ) .GT. 1 . 13.AND.S(d-3, 1 ) .GT. 1.01) GO TO 130 148 C 149 C THE NUCLEATION RULE BY ITSELF IS THE CRITERIA FOR SELECTION IF NO 150 C NE OF THE ABOVE CONDITIONS IS SATISFIED 151 C 152 80 IF (T3.GE.4.0.AND.L.LT.2 ) GO TO 90 153 C 154 C 155 C 156 C THE NUCLEATION SEARCH FAILED FOR THE SEGMENT J-JA. TO START AGAIN 157 C FROM NEXT POSITION d+1 158 d = d+1 159 IF (d.LE.NY) GO TO 20 160 GO TO 15 16 1 C 162 C 163 C A VALID NUCLEATION SEGMENT ACCORDING TO RULE HELIX-4 SHOULD NOT HA 164 C VE PRO RESIDUE IN THE INNER HELIX 165 C 166 90 DO 95 I=d,dA 167 IF (M(I).EQ.15 .AND. I.E0.(d+2)) d1=d 168 IF (M(I).E0.15 .AND. I.E0.(d+2)) GO TO 100 169 IF (M(I).E0.15 .AND. I.NE.(d+2)) GO TO 105 170 95 CONTINUE 17 1 C 172 C TO CALL SUBROUTINE THREE FOR THE PROPAGATION OF THE VALID NUCLEATI 173 C NG SEGMENT 174 C 175 100 CALL THRE 176 GO TO 10 177 C 178 C THE PRESENCE OF PRO IN THE INNER HELIX IS UNFAVORABLE TO THE NUCLE 179 C TION SO TO START THE SEARCH AGAIN FROM NEXT POSITION d+1 180 C 18 1 105 d = d+1 182 IF (d.LE.NY) GO TO 20 183 GO TO 15 184 C 185 c 186 c TO PRINT OUT THE POSSIBLE HELICAL REGIONS WHICH ARE THEN SUBdECTED 187 c TO THE BOUNDARY ADdUSTMENT(SUBROUTINE M0d1). THOSE ARE ALSO SPECIAL 188 c CASES BECAUSE THE PROPAGATION PROCEDURE IS OMITTED 189 c 190 1 10 PRINT 115,d,dA 191 115 FORMAT('0',10X,'PSEUDO HELIX FR0M',5X.'d :',I5,3X,'T0 JA:',I5.10X 192 1'SPECIAL CASE' / ) 193 d1=d 194 d2 = dA 195 GO TO 160 196 c 197 120 d1=d - 3 198 d2=dA+1 199 PRINT 125,d1,d2 200 125 FORMAT('0',10X,'PSEUDO-HELIX FROM',5X,'d1:',I5,3X,'TO d2:',15,10X 201 1 'SPECIAL CASE'/) 202 GO TO 165 203 C 204 130 J1=d 205 J2 = JA 206 PRINT 125, U1 , J2 207 GO TO 165 208 C 209 140 J1=J-1 2 10 J2=JA-1 21 1 * PRINT 125, J1 , J2 2 12 GO TO 165 213 C 214 150 J1= d+2 2 15 J2=JA+5 216 PRINT 125,01,02 217 GO TO 165 2 18 c 2 19 c 220 c TO CALL SUBROUTINE M0J1 FOR THE BOUNDARY ADJUSTMENT OF THE PREDIC 22 1 c TED AREA. WHEN RETURNING FROM THAT PROCEDURE IF THE POTENTIAL AREA 222 c IS NOT LONG ENOUGH FOR ANOTHER HELIX THEN TO START ANALYZING THE 223 c NEXT POTENTIAL . AREA 224 c 225 160 CALL M0J1 226 165 IF (J2.LT. NY) J=J2+1 227 IF (J2.LT. NY) W=2 228 IF (J2.GE. NY) W=1 229 GO TO 10 230 c 231 170 PRINT 175 232 175 FORMAT('-' , 'END OF PROGRAM' ) 233 RETURN 234 END End of F i l e co 1 C 2 C 3 SUBROUTINE THRE 4 C 5 C 6 C 7 C 8 C 9 C PROPAGATION OF THE A L P H A - H E L I X 10 C 1 1 C 12 C 13 C 14 C 15 C 16 C PURPOSE 17 C TO ADD TO THE NUCLEATING FRAGMENT TETREPEPTIDES WHICH HAVE 18 C <PA> > 1 . 0 0 AND WHICH SATISFY THE PROPAGATION SET OF RULES 19 C 2 0 C 21 C 22 C 23 REAL S , T 1 , T 2 , A 1 , A 2 , T 3 , T 4 , T 5 , T T , P 24 INTEGER G , F , H , U , D , V 1 , V 2 . W , V 3 , V 4 . V 5 , V 6 , V 7 , V 8 , 0 25 LOGICAL HELLO.BYE ,BALL,MOVE 26 DIMENSION S ( 1 0 0 0 , 2 0 ) , M ( 1 0 0 0 ) , H ( 1 0 0 0 ) , D ( 1 0 0 0 , 1 6 ) , P ( 1 0 0 0 , 1 0 ) 27 COMMON S , T 1 , T 2 , T 3 , T 4 , T 5 , T T , A 1 , A 2 , P , F , H , U , D , W , M , M 1 , M 2 , M 3 , M 4 , M 5 , M 6 , 28 1 L , I , K , L 1 , L 2 . N Z , N Y , J A , J B , J C , J D , J 1 , J 2 , K M , N 1 , N 2 . N N , J , G , K 3 , V 1 , V 2 , V 3 , V 4 29 2 , V 5 . V 6 , V 7 , 0 , H E L L O , B Y E , B A L L , M O V E 3 0 C 31 c 32 c DESCRIPTION OF PARAMETERS 33 c JB - WHETHER I T I S N- OR C-PROPAGATION JB WILL ALWAYS BE THE 34 c FIRST LEFT RESIDUE OF THE ADJACENT TETRAPEPTIDE 35 c JC - WHETHER I T I S N- OR C-PROPAGATION JC WILL ALWAYS BE THE 36 c FOURTH RESIDUE OF THE ADJACENT TETRAPEPTIDE 37 c N1 - N-TERMINAL RESIDUE OF THE CURRENT POTENTIAL AREA 38 c U - SWITCHING VALUE FOR DECIS ION MAKING 39 c U=1 N-PROPAGATION 4 0 c U=2 C-PROPAGATION 4 1 c 42 c 4 3 c I F PRO OCCUPY THE F IRST TURN OF THE NUCLEATING SEGMENT TO START C-44 c PROPAGATION IMMEDIATELY BECAUSE N-PROPAGATION I S NOT POSSIBLE ACCOR 4 5 c DING TO RULE H E L I X - 4 46 c 47 10 M1=0 48 M2=0 49 M3=0 5 0 M4= 1 51 M6 = 0 52 IF (M(I).E0.15 .AND. I.E0.(J+2)) GO TO 25 53 U= 1 54 C 55 C AS LONG AS JB BELONGS TO THE CURRENT POTENTIAL AREA THE N-PROPAGA 56 C TION CAN BE CARRIED OUT 57 20 M1=M1+1 58 JB=J-(4*M1) 59 IF (JB.GT.0.AND.JB.GE.N1) GO TO 30 60 IF (JB.LT.N1.AND.M1.EO.1) J1=J 61 IF (JB.LT,N1 .AND.M1 .NE. 1) J1=J-4*(M1- 1) 62 25 U=2 63 M2=0 64 30 T3=0 65 IF (U.EO.1) GO TO 35 66 C 67 C TO START C-PROPAGATION WHEN N-PROPAGATION HAS BEEN STOPPED AND AS 68 C LONG AS THE ADJACENT TETRAPEPTIDE IS WfTHIN THE LIMITS OF THE POT 69 C ENTIAL AREA 70 C 71 IF (M2.NE.0) JB=JA+1+(4*M2) 72 IF (M2.E0.O) JB=JA+1 73 M2=M2+1 74 IF (JB.GT.N2) GO TO 70 75 C 76 C TO CALCULATE THE <PA> OF THE ADJACENT TETRAPEPTIDE (JB-JC) 77 C 78 35 JC=JB+3 79 IF (JCGT.N2 . AND . JB . LE . N2) GO TO 70 80 DO 40 I=JB,JC 81 T3 = T3 + S(I, 1 ) 82 40C0NTINUE 83 C 84 PRINT 45,JB,JC,T3 85 45 FORMAT(' . ' , 10X, 'JB: ' . 14,5X, 'JC: ' ,I4,5X. 'T3: ' ,F7.4, 15X, 'HELIX PROPA 86 1GATI0N') 87 C 88 C 89 C IF <PA> > 1.00 TO CHECK THE NUMBER OF BREAKERS AND FORMERS IN THE 90 C SECTION FORMED BY THE TETRAPEPTIDE AND THE TWO ADJACENT RESIDUES 91 C OF THE NUCLEATING FRAGMENT OR OF THE PROPAGATING ONE 92 C 93 IF (T3.GE.4.0) GO TO 190 94 C 95 C TETRAPEPTIDES WITH <PA> <1.00 SHOULD NOT CONTAIN ANY BREAKER NOR 96 C ONLY 4 IA IN ORDER TO ALLOW HELIX PROPAGATION TO CONTINUE 97 C 98 DO 50 I=JB,JC 99 IF (SO,1).LE.0.69) GO TO 60 100 50 CONTINUE 101 L=0 102 DO 55 I=dB,dC 103 IF (S(I, 1 ).LE . 1 .01 .AND.S(I. 1).GE.0.70) L = L+1 104 55 CONTINUE 105 IF (L.EQ.4) GO TO 60 106 IF (L.NE.4) GO TO 190 107 C 108 C TO SWITCH TO C-PROPAGATION WHEN N-PROPAGATION HAS BEEN STOPPED 109 C 1 10 60 BALL=.FALSE . 1 1 1 IF (U.EO.1) BALL=.TRUE. 1 12 IF (BALL) d1=dB+4 1 13 IF (BALL) U=2 1 14 IF (BALL) GO TO 30 1 15 C 1 16 C 1 17 C BOTH N- AND C-PROPAGATIONS BY TETRAPEPTIDE ADDITION HAVE BEEN STOP 1 18 C PED . TO START ADDING ONE RESIDUE AT A TIME TO N-TERMINAL FIRST 1 19 C THEN TO C-TERMINAL OF THE PROPAGATING SECTION. 120 C WHEN ADDING IA TO EACH END TO CHECK IMMEDIATELY WHETHER THE RULE 121 C OF AT LEAST HALF OF FORMERS IS STILL SATISFIED OR NOT 122 C 123 70 IF (M(d1+2).EO. 15) GO TO 80 124 75 L 1 = J 1 - 1 125 IF (L1.LT.(N1) .0R.L1.E0.0) GO TO 80 126 IF (M(L1).E0.4 .OR.M(L1).EO.17) S(L1,1)=1.00 127 IF (S(L1,1).GT.1.00) d1=L1 128 IF (S(L1 , 1 ) .LE . 1.00.AND.S(L1, 1),GE.0.70) d1=L1 129 IF (S(L1 , 1).GT. 1 .00) GO TO 75 130 80 d2=dB-1 131 85 L2=d2+1 132 IF (L2.GT.NN) GO TO 90 133 IF (L2.GT.(N2) ) GO TO 90 134 IF (M(L2).EO.2.OR.M(L2).E0.5) S(L2,1)=1.00 135 IF (S(L2,1).GT.1.00) d2 = L2 136 IF (S(L2,1).LE.1.00 .AND. S(L2,1).GE.0.70) d2=L2 137 IF (S(L2,1) .GT.1.00) GO TO 85 138 C 139 C 140 C CHECK FOR THE ff OF HELIX FORMERS IN THE ENTIRE HELIX... 14 1 C 142 C TO COMPARE THE ACTUAL NUMBER OF FORMERS (T4) TO ITS THEORITICAL 143 C ONE (TT: EQUAL TO AT LEAST HALF OF THE SECTION) 144 c 145 90 T4=0 146 DO 95 1=01 ,J2 147 S( I ,4)=0 148 IF (S(I, 1 ) GE. 1.00) S(I,4)=0.5 149 IF (S(I,1).GE.1.06) S(I,4)=1.0 150 T4=T4+S(I,4) CTv 151 95 CONTINUE 152 TT=(02-01+1)/2.0 153 PRINT 100,0 1 ,02,T4,TT 154 100 FORMAT(' ' , 10X, '01 : ' ,I4,5X, ' 02 : ' ,I4,5X, 'T4: ' ,F7.4,5X, 'TT: ' ,F7 . 4  155 1 4X , ' ACTUAL AND THEORIT. H FORMERS FROM J1 TO L)2 ' ) 156 C 157 C TO CONTINUE ADDING ONE RESIDUE AT A TIME TO BOTH ENDS IF T4 > TT 158 c 159 IF (T4.GE.TT .AND. S(J1-1.1) .LE.0.69) GO TO 110 160 IF (T4.GE.TT .AND. S(d1 - 1, 1) .GT.0.69.AND.L1 .GT.(N1)) GO TO 70 161 1 10 IF (L2.GT.NN) GO TO 170 162 IF (T4.GE.TT .AND. S(d2+1,1) .GT.0.69.AND.L2.LT.(N2)) GO TO 85 163 IF((T4.GE.TT.AND.S(d2+1,1).LE.0.69) .OR.(T4.GE.TT.AND.S(d2+1, 1 ) .GT 164 1.0.69.AND.L2.GE. N2)) GO TO 170 165 c 166 c 167 c IF T4 < TT THEN TO WITHDRAW SOME BOUNDARY RESIDUES (ESPECIALLY 168 c BA, ,IA) SO THAT T4 > TT 169 c 170 120 IF (S(d2,1) .LT.1.00) GO TO 125 171 IF (S(d1 , 1 ) . LT . 1 .00 .AND.M(d1 + 2).NE. 15) GO TO 130 172 IF (S(d2,1) .LT.1.06) GO TO 135 173 IF (S(d1,1).LT.1.06 .AND.M(d1+2),NE.15) GOTO 140 174 125 02=02-1 175 IF (S(d2+1.1).LT.1.00) GO TO 150 176 130 01=01+1 177 IF (S(01-1, 1 ) .LT . 1.00) GO TO 150 178 135 02=02-1 179 IF (S(d2+1,1).LT.1.06) GO TO 150 180 140 01=01+1 181 IF (S(d1-1, 1 ) . LT . 1 .06) GO TO 150 182 c 183 c 184 c TO CHECK T4 AND TT EVERY TIME A BOUNDARY RESIDUE IS WITHDRAWN 185 c 186 150 T4=0 187 DO 155 1=01,02 188 S( I , 4)=0 189 IF (S(I,1).GE.1.00) S(I,4)=0.5 190 IF (S(I,1).GE.1.06) S(I,4)=1.0 191 T4=T4+S(1,4) 192 155 CONTINUE 193 TT=(d2-d1+1)/2.0 194 PRINT 160,d1,d2,T4,TT 195 160 FORMAT(' ',1OX,'01:',I4,5X,'02:',I4,5X,'T4:',F7.4,5X,'TT:',F7 . 4 , 196 1 4X. 'ACTUAL AND THEORIT. H FORMERS FROM 01 TO'02') 197 IF (T4.GE.TT) GO TO 170 198 IF (T4.LT.TT) GO TO 120 199 170 PRINT 175,01,02 200 175 FORMAT('0' , 10X, 'PSEUDO-HELIX FROM 01 : ' ,15,3X, 'TO 02:',15,/) 201 C 202 C 203 C TO CALL SUBROUTINE M0J1 TO CARRY OUT THE BOUNDARY ADJUSTMENT 204 C 205 CALL M0J1 206 IF (J2.LT.NY) J=J2+1 207 IF (J2.LT.NY) W=2 208 IF (J2.LT.NY) N1=J2 209 IF (J2.LT.NY) RETURN 210 180 W= 1 21 1 RETURN 212 C 213 C CHECK FOR THE NUMBER OF FORMERS IN THE 6 RESIDUE UNIT ... 2 14 C 215 C PRO I CAN ONLY EXIST AT THE FIRST TURN OF N-TERMINAL SIDE. ANY OTH 216 C ER POSITION ESPECIALLY AT THE C-TERMINAL WILL IMPEDE THE PROPAGA 217 C TION 218 C 2 19 190 DO 200 I=JB,JC 220 IF (M(I).EO.15.AND.I.EO.(JB+2).AND.U.EO.1) GO TO 210 22 1 IF (M(I).E0.15.AND.I.NE.(JB+2).AND.U.EO.1) GO TO 220 222 IF (M(I).EQ.15.AND.U.EO.2) GO TO 70 223 200 CONTINUE 224 IF (U.EO.1) GO TO 210 225 IF (JB.EO.(JA+1)) JB=JA-1 226 IF (JB.NE.(JA-1 ) ) JB = JB-2 227 C 228 C IF PRO IS NOT FOUND IN THE TETRAPEPTIDE THEN TO CHECK THE NUMBER 229 C OF FORMERS OF THE 6 RESIDUE UNIT (= TETRAPEPTIDE + 2 ADJACENT RESI 230 C DUES) 231 C 232 210 JC=JB+5 233 T4=0 234 DO 215 I=JB.JC 235 S(I,4)=0 236 IF (S(I, 1 ) .GE. 1 .00) S(I.4)=0.5 237 IF (S(I,1).GE.1.06) S(I.4)=1.0 238 T4 = T4 + S(I.4) 239 215 CONTINUE 240 PRINT 218,JB,JC,T4 24 1 218 FORMAT(' ' , 10X, 'JB: ' ,I4,5X, 'JC: ' ,I4,5X, 'T4: ' ,F7.4, 14X, ' HELIX FORM 242 1IN 6 OVERL. RESIDUES' ) 243 IF (T4.GE.4.0) GO TO 240 244 C 245 C IF THE 6 RESIDUE UNIT DOES NOT HAVE AT LEAST TWO THIRDS FORMERS 246 C THEN EITHER TO SWITCH FROM N-PROPAGATION TO C-PROPAGATION OR TO 247 c START ADDING ONE RESIDUE AT A TIME TO BOTH ENDS 248 c 249 IF (U.EO.2) GO TO 230 250 220 U = 2 00 251 J1=JB+4 252 GO TO 30 253 230 JB=JC-3 254 GO TO 70 255 C 256 C ... TO CHECK THE NUMBER OF BREAKERS IN THE ENTIRE POLYPEPTIDE . . . 257 C 258 C DESCRIPTION OF PARAMETERS 259 C JB - N-TERMINAL RESIDUE OF THE HELICAL POLYPEPTIDE 260 C JD - C-TERMINAL RESIDUE OF THE HELICAL POLYPEPTIDE 261 C M3 - COUNTER 262 C M4 - COUNTER 263 C 264 C 265 C IF THE ACTUAL NUMBER OF BREAKERS (L) IS LESS THAN THE THEORITICAL 266 C ONE (M5: ONE THIRD OF THE SECTION) THEN THE REGION CAN KEEP ON PRO 267 C PAGATING. OTHERWISE EITHER TO SWITCH FROM N-PROPAGATION TO C-PROPA 268 C GATION OR TO START ADDING ONE RESIDUE AT A TIME 269 C 270 240 M5=0 27 1 IF (U.EO.1) GO TO 250 272 JB=JB-(4*M4 ) 273 250 JD=JB+9+(4*M3) 274 M3=M3+1 275 M4=M4+1 276 M5= (JD-JB+1)/3 277 L = 0 278 DO 255 I=JB,JD 279 IF (S(I.1).LE.0.69) L=L+1 280 255 CONTINUE 281 PRINT 258,JB,JD,M5 ,L 282 258 FORMAT(' ' , 10X, 'JB: ' , 14 , 5X, ' JD: ' , 14,5X, 'M5: ' , 17,5X, ' L: ' ,I 3,5X, 283 1 'THEORIT. AND ACTUAL # BREAKERS FROM JB TO JD') 284 IF (L.LT.M5.AND.U.EO. 1 .AND.M(JB+2).EO. 15) GO TO 260 285 IF (L.LT.M5.AND.U.EO.1) GO TO 20 286 IF (L.LT.M5.AND.U.EO.2 ) GO TO 30 287 M6 = M2 288 IF (U.EO.2.AND.M6.EO.O) JB=JB+6 289 IF (U.E0.2.AND.M6.NE.O) JB=JB+6+(4*M6) 290 IF (U.EO.2) GO TO 70 291 U = 2 292 J1=JB+4 293 GO TO 30 294 260 J1=JB 295 U = 2 296 GO TO 30 297 END End of F i l e 1 c 2 C 3 SUBROUTINE MO<J1 4 C 5 C G C 7 C 8 C 9 C BOUNDARY MOVE OF THE N-TERMINAL 10 C 11 C 12 C 13 C 14 C PURPOSE 15 C TO FIND OUT THE MOST FAVORABLE N-BOUNDARY RESIDUE FOR THE PREDIC 16 C TED HELIX BASED ON THE BOUNDARY CONFORMATIONAL PARAMETERS OF THE 17 C ADJACENT RESIDUES 18 C 19 C . 20 C 21 REAL S.T1,T2,A1 ,A2 , T3,T4.T5.TT,P 22 INTEGER G,F,H,U,D,V1,V2,W, V3,V4,V5,VS,V7,V8,0 23 LOGICAL HELLO,BYE ,BALL,MOVE 24 DIMENSION S(1000,20),M(1000),H(1000),D(1000,16),P(1O0O.10) 25 COMMON S,T1 ,T2,T3.T4,T5,TT.A1.A2,P.F.H.U.D,W.M.M1.M2.M3,M4,M5,M6, 26 1L, I ,K,L1 ,L2.NZ,NY,JA,JB,JC, <JD , J 1 , J2 , KM , N 1 , N2 , NN ,J,G,K3,V1 .V2.V3.V4 27 2,V5.V6,V7.0.HELLO.BYE,BALL,MOVE 28 C 29 C 30 C DESCRIPTION OF PARAMETERS 31 C V1 - ACTUAL NUMBER OF BREAKERS IN THE PREDICTED HELIX (=L) 32 C V2 - COUNTER INDICATING THE POSITION OF THE ADJUSTMENT BECAUSE 33 C THE PROCEDURE CONTAINS SEVERAL DIFFERENT POSSIBILITIES OF AD 34 C JUSTMENT (COUNTER USED FOR N-TERMINAL ADJUSTMENT) 35 C J1 N-TERMINAL RESIDUE OF THE PREDICTED HELIX 36 C J2 - C-TERMINAL RESIDUE OF THE PREDICTED HELIX 37 C K3 - C-TERMINAL RESIDUE OF THE PREVIOUS PREDICTED HELIX 38 C 39 C 40 C SITUATION WITH J1 CLOSE TO ZERO 41 C 42 C TO TAKE INTO ACCOUNT THE POSITION OF J1 WHEN IT IS CLOSE TO THE N-43 C TERMINAL OF THE PROTEIN SINCE THERE IS LESS FREEDOM FOR MOVING IT 44 C TOWARDS THIS SIDE 45 C 46 C 47 C 48 V1=L 49 V2=0 50 V3=0 51 C 52 PRINT 5 53 5 FORMAT('O',30X,'BOUNDARY ANALYSIS OF THE N-TERMINAL') 54 C 55 Q * * * -j * * * 56 IF ( (d1-1).LE.0) GO TO 10 57 BALL=.FALSE. 58 IF (d1.EQ.2.AND.S(J1,8).GT. 1.47.AND. S (d1 - 1,1).LE.0.69.AND.S(J 1 + 1 , 59 2 1) .GT. 1 .01 .AND,S(d1+2,8).GE.S(d1,8) .AND. M ( d 1 - 1) .NE. 15)BALL=.TRUE. 60 IF (BALL) d1=d1 61 IF (BALL) V2=1 62 IF (BALL) GO TO 300 63 C 65 10 BALL=.FALSE. 66 IF (d1.EQ.1.AND.S(J1,8) .GT. 1 .08.AND.S(J1 + 1 ,8).LT.S(d1,8).AND.S(d1 + 67 1 2,8) .LE.S(d1.8).AND.S(d1+3,8).LT. 1.08) BALL=.TRUE. 68 IF (BALL) d1=d1 69 IF (BALL) V2=2 70 IF (BALL) GO TO 300 71 C 72 C *** 3 *** 73 BALL=.FALSE. 74 , IF (d1.EQ. 1.AND.S(d1,8).GT. 1.08.AND.S(d1, 1 ) . GT. 1 .01.AND.S(d1 + 1, 1). 00 75 1 LT.1.06.AND.S(d1+2,8).LT.S(d1.8).AND.S(d1+3,8).LT.1.08) BALL== O 76 2 .TRUE. 77 IF (BALL) d1=d1 78 IF (BALL) V2=3 79 IF (BALL) GO TO 300 80 C 81 C ++*4*#* 82 BALL=.FALSE. 83 IF (d1.EQ. 1 .AND.S(d1, 1 ) . GT. 1 . 16.AND.S( d 1 + 1 ,8 ) .GT.2.02.AND.S(d1+ 2, 84 1 8).GT.2.02.AND.S(d1+3,1).GT.1.11.AND.S(d1+4.1).GT.1.16) BALL= 85 2 .TRUE. 86 IF (BALL) d1=d1 87 IF (BALL) V2=4 88 IF (BALL) GO TO 300 89 C gO C *** 5 *** 91 BALL=.FALSE. 92 T1=0 93 T2=0 94 T5=0 95 T1=S(d1+1 , 1 )+S(d1+2,1) + S(d1+3, 1 ) + S(d1+4, 1) 96 T2=S(d1+1,2)+S(d1+2,2)+S(d1+3,2)+S(d1+4,2) 97 T5=S(d1+1,5)+S(d1+2,5)+S(d1+3,5)+S(J1+4,5) 98 PRINT 2,T1,T2,T5 99 2 FORMAT(' ' ,30X. 'T1,T2,T5' ,3(F7.3 ) , ' STEP 5,M0d1 CLOSE TO 0') 100 IF (T5.GT.T1 .AND.T5.GT.T2.AND.S(d1 ,8 ) .LT. 1 .08.AND.S(d1+4,8).LT. 1 . 101 1 08 . AND . S ( J 1 +5 , 8 ) . GT . 1 . 47 . AND . S(d 1+6 , 8 ).. GT . 1 .08 .AND . S( d 1 , 8 ) . LT . 1 . 0 102 2 8.AND.S(d1 + 2,8).LT.0.66.AND.S(d1 + 2,6).LT.1.01 .AND.S(d1+ 3,8 ) . LT . 1 . 103 3 08) BALL=.TRUE. 104 IF (BALL) d1=d1+5 105 IF (BALL) V2=5 106 IF (BALL) GO TO 300 107 C 108 C *** g *** 109 BALL=.FALSE. 110 IF (d 1 .EO. 1 .AND.S(d1,8).LT. 1.08.AND.S(d1 + 1,8).GE. 1.08.AND.S(d1 + 2, 111 18).LT.S(d1+1,8).AND.S(d1+3,8).LT.S(d1+1,8).AND.S(d1+4,8).LT.S(d1+ 112 2 1,8)) BALL= . TRUE. 113 IF (BALL) d1=d1+1 114 IF (BALL) V2=6 115 IF (BALL) GO TO 300 116 C 117 C * + * 7 * * * 118 BALL=.FALSE. 119 IF (d1.EO.1.AND.S(d1,8).LT.1.08.AND.S(d1+1,8).LT.1.08.AND.S(d1+2,8 120 1 ),GE. 1 .08.AND.S(d1 + 3,8) .LT. 1 .08.AND.S(d1+4,8).LT. 1.08) BALL = 12 1 2 .TRUE. 122 IF (BALL) d1=d1+2 123 IF (BALL) V2=7 124 IF (BALL) GO TO 300 00 1 25 C 1 - 1 126 C *** 8 *** 127 BALL=.FALSE. 128 IF ( J1.EO.1.AND.S(d1,8).LT.1.08.AND.S(d1+1,8).LT.1.08.AND.S(d1+2, 129 1 8).LT. 1,08.AND.S(d1 + 3.8).GE. 1.08) BALL= . TRUE. 130 IF (BALL) d1=d1+3 131 IF (BALL) V2=8 132 IF (BALL) GO TO 300 133 C 134 C * * * g * * * 135 BALL=.FALSE. 136 IF (K.E0.3) K3=N2 137 IF(S(d1,8).LT.1 .08.AND.(d1-2) .LT . (K3-1) .AND.S(d1 + 1.8) .LT. 1 .08.AND 138 1 .S(d1+2,1).LE.0.69.AND,M(d1+2).NE.15.AND.S(d1+3,8).GE.1.08) BALL 139 2 =.TRUE. 140 IF (BALL) d1=d1+3 141 IF (BALL) V2=9 142 IF (BALL) GO TO 300 143 C ' . 144 C *** 10 *** 145 IF ((J1-3).LE.O) GO TO 6 146 BALL=.FALSE. 147 IF (S(d1,2).GE. 1 .47.AND.S(d1- 1,2).GE. 1.47.AND.S(d1-2,2) .GT.0.93.AN 148 1D.S(d1+2,2).GE. 1.47.AND.S(d1+ 3,8).GT. 1.47.AND.S(d1-3, 1 ) . LT . 1 .06.AN 149 2D.(S(J1+1,2).GT.O.75 .OR.M(d1+2).EO.1)) BALL=.TRUE. 150 IF (BALL) d1=d1+3 151 IF (BALL) V2=10 152 IF (BALL) GO TO 300 153 C 154 C * + + 1 1 * * * 155 6 BALL=.FALSE. 15G IF ( (U1--2 ) . LE .O) GO TO 15 . 157 IF (d1 .EO.3.AND.S(J 1 ,8).LT. 1 .08.AND.S(d1 + 1,8).LT . 1 .08.AND.S(d1+2, 158 1 8).LT . 1 .08.AND.S(d1+ 3,8 ) .LE. 1.08.AND.S(d1+ 4,8).GT. 1.08.AND.S(d 1-159 2 1,8).LT. 1 .08.AND.S(d1-2,8).LT. 1 .08) BALL= . TRUE. 160 IF (BALL) d1=d1+4 16 1 IF (BALL) V2=11 162 IF (BALL) GO TO 300 163 C 164 C 165 C .. TO REPEAT THE B-TURN CHECK 166 C 167 C TO CHECK THE PRESENCE OF TURNS IN THE VICINITY OF THE HELIX BOUNDA 168 C RIES WHICH MAY FORCE THE PREDICTED BOUNDARIES TO BE MOVED TO A NEW 169 c POSITION. WE CHECK IT FROM POSITION J1-3 (1=0) TO d1 + 3 (1=6) 170 c 171 15 1=0 172 LE=d1-3 173 IF (LE.LE.O) GO TO 200 174 20 LF = LE + 3 175 IF ((LE+3).GT,NN) GO TO 210 176 c 177 c TO COMPARE PA (T1).PB (T2),AND PT (T5) AND TO CALCULATE THE PROBABI 178 c LITY OF B-TURN OCCURRENCE (TT) OF THE TETRAPEPTIDE LE-LF 179 c 180 T1=0 181 T2 = 0 182 T5=0 183 TT=0 184 HELLO=.FALSE. 185 DO 25 L=LE,LF 186 T1=T1+S(L, 1 ) 187 T2=T2+S(L,2) 188 T5=T5+S(L.5) 189 25 CONTINUE 190 c 19 1 TT=P(LE,1)*P(LE+1,2)*P(LE+2.3)*P(LE+3.4) 192 PRINT 30, LE , T 1 , T-2 . T5 , TT , I 193 30 FORMAT(' '.10X,'LE,T1,T2,T5,TT,I',I5,3(F7.4,2X),F13.9.I4,3X, 194 1 'B-TURN SEARCH AT N-TERMINAL') 195 c 196 IF (T5.GT.T1.AND.T5.GT.T2.AND.TT.GT.0.000075000) HELLO=.TRUE. 197 c 198 c * * * 1 * * * 199 IF (HELLO.AND.LE.EO.(d1-3).AND.S(d1 + 1,8).GE. 1.08.AND.S( d1 ,8) . LT. 1 200 1 .08.AND.S(U1+2,8).GT.1.08.AND.S(d1+3,8).GT.1.08) GO TO 101 201 C 202 C ***2+ + * 203 IF (HELLO.AND.LE.E0.(J1-2).AND.S(J1-2,5).GT.1.52.AND.S ( J1 - 1 . 5).GT. 204 1 1.52.AND.S(d1,5).GT.1.43.AND.S(J1,1).LT.1.06.AND.S(J1+1,1).GT.1.0 205 2 6.AND.S(d1 +1,8).GT.1.08.AND.S(J1+2.1).LT.S(J1+1,1)) GO TO 101 206 C 207 C *** 3 *** 208 IF (HELLO.AND.LE.EO.(J1- 1).AND.S(01+2,8).GT. 1 .47.AND.S(J 1+4,8 ) . LT. 209 1 1 .08.AND.S(J1+5,8).LT. 1.08.AND.S(J 1+6,8).LT.S(d1+2.8).AND.S(d1 + 1 . 210 2 8).LT.S(J1+2,8)) GO TO 102 211 C 212 C *+*4+** . 213 IF (HELLO.AND.5(J1+2,8).LT.1.08.AND.S(J1+3.8).LT.1.08.AND.LE.EO.(J 2 14 11-2).AND.S(J1+5, 1 ) .GT.1.13.AND.S(J1+6,8).LT. 1.08.AND.S(d1+7,8).LT 215 2 . 1 .08.AND. (S(d1+4,8 ) . LT. 1 .08.OR.S(J1+4, 1).LT. 1 .06)) GO TO 105 216 C 217 C *** 5 *** 2 18 IF (HELLO.AND.LE.EO.J1 .AND.S(J1+4, 1 ) .GT. 1 . 1 1 .AND.5(01 + 5, 1).GT. 1.21 219 1 .AND.S(J1+6, 1 ) .GT . 1 .21.AND.S(J1 + 3, 1 ) . LT . S(J 1+4, 1 ) .AND.S(J1 + 3 .6) . 220 2 GT .1.01. AND .S(d1+2,6) . GT .1.22) GO TO 104 221 C 222 C * * * g * * * 2 23 IF (HELL0.AND.S(J1 + 3,8).GT. 1 . 47 . AND.S(d1+4,8).LT. 1.08.AND.LE.EO.( 224 1 J 1 - 1).AND.S(J1+5,8).LE.S(J1+3,8).AND.S(J1- 1 . 1 ) . LT. 1 . 16.AND . S(<J1 -2 00 2 2 5 2 , 1 ) .LE.0.69.AND.S(J1 + 2, 1).LT.0.98.AND.S(J1+2.6).GT. 1 .41 ) GOTO 226 3 102 227 C 228 C * * + 7 * * * 229 IF (HELLO.AND.S(J1+5,8).GE.1.08.AND.S(J1+6,8).LT.1.08.AND.S(J1+7,8 230 1 ).LT.1.08.AND.LE.EQ.(d1+2)) GO TO 105 231 C 232 C **+g**+ 233 IF (HELLO.AND.LE. EQ.(J1-2).AND.S(J1+2.8).LT.1.08.AND,S(d1+3,8).GE. 234 1 1.08.AND.S(J1+3,1).GT.1.01.AND.S(d1+4,8).LE.S(d1+3,8).AND.S(d1,1) 235 2 .LT.0.83.AND.(S(J1+1,2).GT.1.47.OR.S(d1+1.1).LT.O.67).AND.(S(d1+2 236 3 ,2 ) .GT. 1 .47.OR.S(d1 + 2, 1).LT.0.83)) GO TO 103 237 C 238 C *** 9 * * * 239 IF (HELLO.AND.S(d1+4,8).GT.1.47.AND.S(d1+3,8).LE.S(d1+4,8).AND.LE. 240 1 EO.d1.AND.S(d1+5,8).LT.1.08.AND.S(d1+6,8).LT.S(d1+4,8)) GO TO 104 241 C 242 C *** 10 *** 243 IF (HELLO.AND.LE.E0.d1.AND.S(d1+3,8).LT.1.08.AND.S(d1+4,8).LT.1.08 244 1 .AND.S(d1+5.8).LT.1.08.AND.S(d1+6.8).LT.1.08.AND.S(d1+4,1).GT.0. 245 2 69.AND.S(d1,8).LT. 1 .47.AND.S(d1 + 1, 1 ) . LT . 1 . 16.AND.S(d1+2, 1).LT . 1 . 246 3 21) GO TO 104 247 C 248 C *** 11 *** 249 IF ((J1-1).LE.0) GO TO 40 250 IF(HELLO.AND.S(d1+3,8 ) .LT. 1 .08.AND.S(d1+4,8).GE. 1.08.AND.LE.EO.(d1 251 1 -1 ) .AND.(S(01+2,1).LE.0.69.OR.S(01+1,1).LE.0.69).AND.S(J1-1,1).LE 252 2.0.69) GO TO 104 253 C 254 C ***-|2*** 255 40 IF (HELLO.AND.LE.EQ.(01+1).AND.S(01+4 ,8) .LE. 1 .08.AND.S(J1+ 5.8 ) . LT 256 1 . 1,08.AND.S(01+6,8).GT . 1.47) GO TO 106 257 C 258 C *** 13 *** 259 IF (HELLO.AND,LE.EQ.(01+2).AND.S(J1+6.8).GT.1.08.AND.S(01+5,8).LT. 260 1 S(01+6,8) ) GO TO 106 261 C 262 C ***14*** 263 IF (HELLO.AND.LE.EO.(J1+1).AND.S(01+6,8).GE.S(J1+5,8).AND. S(01+6, 1 264 1 ).GT.S(J1+5.1).AND.S(01+7,8).LT.S(J1+6,8).AND.S(01 + 4.8).LT.1.08) 265 2 GO TO 106 266 C 267 C *** 15 *** 268 IF ((01-3).LE.0) GO TO 50 269 IF (S(01,8).LT.1.08.AND.S(01,2).GE.1.47.AND.S(01-1,2).GT.1.38.AND. 270 1S(01-3,1).LE.0.69.AND.S(01+1,8).GT.1.47.AND.S(01+2,2).GT.1.19.AND. 271 2S(01+3.8).LT.1.08.AND.HELLO.AND.LE.EQ.(01+3)) GO TO 1 0 7 272 C 273 C 274 50 IF (HELLO.AND.LE.EO.(01-3).AND.S(01+1,8).LT.1.08.AND.S(01+2,8).LT. 275 1 1.08.AND.S(01+3,8).LT. 1 .08.AND.S(01+4,8).GT. 1.08.AND.S(01+4, 1 ) . GT 276 2 . 1 .08.AND.S(01 + 5, 1 ) . LT . S(01 + 4, 1)) GO TO 104 277 C 278 C ***-|7+** 279 IF (HELLO.AND.S(01+3,8).LT.1.08.AND.S(01+4,8).LT.1.08.AND.S(01+5,8 280 " 1 ).GT.1.08.AND.S(01+5,1).GT.1.08.AND.S(01+6,8).LT.1.08.AND.S(01+5. 281 2 1).GT.S( 01+4,1).AND.LE.EO.(01-1)) GO TO 105 282 C 283 C *** 18 *** 284 IF ((01+7).GT.NN) GO TO 80 285 . IF (HELLO.AND.S(01+4,8).LT.1.08.AND.5(01+5,8).LT.1.08.AND.S(01+6, 286 1 8) . LT. 1.08.AND.S(01+6, 1).LE.0.69.AND.S(01+7,8).GE. 1.08.AND.LE.EO. 287 2 (01+1)) GO TO 107 288 C 289 C *** 19 *** 290 80 IF (HELLO.AND.LE.EO.01.AND.5(01+3,8).LT.1.08.AND.S(01+4.8).LT.1.08 291 1 .AND,S(01+5.1).GT.1.16.AND.S(01+6.8).LT.1.08.AND.(01+7).GE.02) 292 2 GO TO 105 293 C 294 C +** 20 *** 295 IF ((01+8).GT.NN.OR.(01-1).LE.0) GO TO 90 296 IF (HELLO.AND.LE.EO.01.AND.S(01+2,5).GT.0.74.AND.S(01+3,5).GT.1.52 297 1 .AND.S(01 + 1,5).GT.0.98.AND.S(01+4,2).GT. 1 .47.AND.S(01+5,2 ) .GT . 1 .6 298 2 O.AND.5(01+6,8).LT.0.58.AND.S(01+7, 1) . GT. 1 . 13.AND.S(01+7,8).GT.S( 299 301+8,8).AND.S(01+8, 1).GT. 1.01 .AND.S(01 - 1,8).LT. 1 .08.AND.5(01-1,1). 300 4 LE.0.69) GO TO 107 00 301 C 302 C * # * 21 * * * 303 90 IF ((J1+13).GT.NN) GO TO 100 304 IF (HELLO.AND.S(J1+2,8).LT.1.08.AND.LE.EQ.(J1-2).AND.S(J1+3,2) 305 1 0.93.AND.S(J1+4,2).GT.1.38.AND.S(J1+5,2).GT.1.19.AND.M(J1+6). 306 2 .AND.S(J1+7,8).LT . 1.08.AND.S(J1+8,2).GT. 1 .38.AND.S(J1+9,8).LT 307 3 8.AND.M(J1+9).EO.M(J1+10).AND.M(J1+11).EQ.M(J1+9).AND.S(J1+12 308 4 GT.0.81.AND.S(J1+13,8).GT.2.02) GO TO 112 309 C 310 100 IF (I.EO.O) GO TO 200 31 1 IF (I.EQ.1) GO TO 200 312 IF (I.EQ.2) GO TO 200 313 IF (I.EQ.3) GO TO 200 314 IF (I.EQ.4) GO TO 200 315 IF (I.EQ.5) GO TO 200 3 16 IF (I.EQ.6) GO TO 210 317 C 318 C 319 C MOVE OF N-BOUNDARY AS A CONSEQUENCE OF STRONG B-TURN POTENTIAL IN 320 C THE VICINITY OF THE PREDICTED HELIX 321 C 322 101 J1=J1+1 323 GO TO 110 324 102 J1=J1+2 325 GO TO 110 326 103 J1=J1+3 327 GO TO 110 328 104 J1=J1+4 329 GO TO 110 330 105 J1=J1+5 331 GO TO 110 332 106 J1=J1+6 333 GO TO 110 334 107 J1=J1+7 335 GO TO 110 336 1 12 J1=J1+12 337 GO TO 110 338 C 339 1 10 V2 = 80 340 GO TO 300 34 1 C 342 200 1 = 1 + 1 343 LE=LE+1 344 GO TO 20 345 C 346 C 347 C .. B-TURN PROBLEMS OR OTHER PROBLEMS 348 C 349 C ADJUSTMENT OF N-BOUNDARY MAY ALSO BE CAUSED BY EITHER RANDOM COIL 350 C OR B-SHEET POTENTIAL OR BY THE LOW BOUNDARY CONFORMATIONAL PARAME 351 C TER OF THE CURRENT BOUNDARY RESIDUE 352 C 353 C 354 C *** 12 *** 355 210 BALL=.FALSE. 356 IF ((J 1 + 7).GT.NN) GO TO 230 357 LC=0 358 JN=J1+6 359 DO 215 L = J1.JN 360 IF (S(L,2).LE.0.75) LC=LC+1 361 215 CONTINUE 362 JN=J1+4 363 JM=J1+1 364 T1=0 365 T2=0 366 T5=0 367 DO 218 L=JM,JN 368 T1=T1+S(L,1) 369 T2=T2+S(L.2) 370 T5=T5+S(L,5) 371 218 CONTINUE 372 PRINT 220.T1,T2,T5,LC 373 220 FORMAT(' ' ,SOX, 'T1,T2,T5' ,3(F7 . 3),2X, 'LC: ' ,13, ' STEP 12 ,M0J1, 374 1 B-TURN PROBLEM') 00 375 IF (LC.GT.2.AND.T5.GT.T1.AND.(T2-T5).LT.0.500.AND.S( J1+5,8).LT. 1 .0 °^ 376 1 8.AND.S(J1+6.8).GT. 1 .47.AND.S(J1+7.8).LT.2.01.AND.S(J1, 1 ) . LT. 1 . 21 377 2 .AND.S(J1+5,1).LT.1.21.AND.S(J1-1.6).LT.1.01) BALL=.TRUE. 378 IF (BALL) J1=J1+6 379 IF (BALL) V2=12 380 IF (BALL) GO TO 300 381 C 382 C *** 13 *** 383 BALL=.FALSE. 384 IF (J1.LE.K3.AND.(P(J1+1,1)*P(J1+2,2)*P(J1+3,3)*P(J1+4,4)).GT.0.00 385 1 0100.AND.P(J1 + 1, 1).GT.0. 120.AND.P(J1+2,2).GT.O. 139.AND.S(J1 ,5 ) . 386 2 GT.0.96.AND.S(J1+4,2).GT.1.19.AND.S(J1+4,8).LT.1.08.AND.S(J1+5,2) 387 3 .GT . 1 .47.AND . S(J1+5,8).LT.S(J1+6,8).AND.S(J1+7,8).LT.S ( J1+ 6,8).AN 388 4 D.S(J1+6.1).GT.0.69) BALL=.TRUE. 389 IF (BALL) J1=J1+6 390 IF (BALL) V2=13 391 IF (BALL) GO TO 300 392 C 393 C *** 14 *** 394 230 BALL=.FALSE. 395 IF ((J1-2).LE.0) GO TO 250 396 T1=0 397 T2=0 398 T5=0 399 T1=S(J1-2, 1 ) + S(J1-1 , 1 ) + S(J1 . 1 ) + S(J1 + 1, 1 ) 400 T2=S(J1-2,2)+S(J1-1,2)+S(J1.2)+S(J1+1,2) 401 T5 = S(d1-2,5)+S(d1-1,5) + S(d1,5) + S(d1 + 1 . 5) 402 PRINT 235.T1.T2.T5 403 235 FORMAT(' ' , 30X, 'T1,T2,T5' ,3(F 7.3), ' STEP 14,M0d1 B-T PROBL.') 404 IF (T5.GT.T1.AND.T5.GT.T2.AND.S(J1+1,8).GT.1.47.AND.S(J1+2,8).LT. 405 11 .08.AND.S(d1 + 3,8).LT,S(d1 + 1 , 8)) BALL= . TRUE. 406 IF (BALL) J1=J1+1 407 IF (BALL) V2=14 408 IF (BALL) GO TO 300 409 C 410 C *** 15 *** 411 BALL=.FALSE. 412 IF (S(J1,2).GT.1.37.AND.S(J1+1,2).GT.1.47.AND.S(d1+2,2).GT.1.47.AN 413 1D.S(d1+3,1).LE.0.69.AND.S(J1+3,8).LT.1.08.AND.S(J1+4,8).GT.1.08.A 4 14 2 ND.S(J1+4, 1).GT. 1 . 16.AND.S(J1- 1,2) .GT. 1 . 10.AND.S(J1-2,8) .LT. 1 .08. 415 3AND.S(d1+5, 1 ) . LT . S(d1 + 4, 1)) BALL=.TRUE. 416 IF (BALL) d1=d1+4 417 IF (BALL) V2=15 418 . IF (BALL) GO TO 300 419 C 4 20 C ** + + + 421 BALL=.FALSE. 422 IF ((U1+7).GT.NN) GO TO 240 423 IF ( (P (J1-2, 1)*P(d1- 1 ,2)*P(d1,3)*P(U1 + 1,4)).GT.0.000075.AND.S(d1 + 4 24 1 8,8).GE.1.08.AND,(P(d1+4.1)*P(d1+5,2)*P(d1+6,3)*P(d1+7,4)).GT. 00 425 2 0.000075) BALL=.TRUE. —1 426 IF (BALL) d1=d1+8 427 IF (BALL) V2=16 428 IF (BALL) GO TO 300 429 C 430 C +++17+++ 431 240 BALL=.FALSE. 432 IF ((U1-3).LE.0) GO TO 250 433 IF(S(J1 , 1).LE.0.69.AND.M(J1).NE. 15.AND.S(J1-1, 1 ) .LE.O.69.AND.M(d1 -434 1 1).NE. 15.AND.(S(d1-2, 1 ) .LE.0.69.OR.S(J1-2.8).LT. 1.08).AND.S(d1-3, 435 22).GT.0.93.AND.S(d1+1,8).GE. 1 . 08 .AND.S(d1+2,8).LT. 1 .08.AND.S(d1 + 3, 436 3 D.GT.1.01) BALL= . TRUE. 437 IF (BALL) d1=d1+1 438 IF (BALL) V2=17 439 IF (BALL) GO TO 300 440 C 441 C *** 18 *** 442 BALL=.FALSE. 443 IF (S(d1,8) .LT. 1 .08.AND.(P(d1-3,1)*P(d1-2,2)+P(d1-1,3)*P(d1,4)). 444 1GT.0.000075.AND.S(d1+1, 1 ) .GT. 1 . 1 1 .AND.S(d1+2, 1).GE. 1. 13.AND.S(d1 + 3 445 2 ,1).GT.0.69.AND.S(d1+4,1).GT.1.21.AND.(S(d1+5,1).GT.1.21.OR.S(d1+ 446 3 5,2).LE.0.75)) BALL=.TRUE. 447 IF (BALL) d1=d1+1 448 IF (BALL) V2=18 449 IF (BALL) GO TO 300 450 C 45 1 C * * H< 1 g * * * 452 BALL=.FALSE . 453 IF (S(J1,8) . LT. 1 .08.AND.S(d1+1, 1).LE.0.69.AND.M(d1 + 1).NE. 15.AND.S( 454 1 d1+2,8).GE . 1 .08.AND.S(d1+3,8).LT. 1.08.AND.S(d1+ 4,8).LE.S(d1 + 2,8) 455 2 .AND.(P(d1-3,1)*P(d1-2,2)*P(d1-1,3)*P(d1,4)).GE.0.000075) BALL 456 3 =.TRUE. 457 IF (BALL) d1=d1+2 458 IF (BALL) V2=19 459 IF (BALL) GO TO 300 460 C 46 1 C * * * 20 * * * 462 BALL=.FALSE. 463 IF ((d1-4).LE.0) GO TO 250 464 IF (S(d1,8).LT.1.08.AND,S(d1,1).LE.0.69.AND.S(d1+1,1).GT.1.08.AND. 465 1 S(d1 + 2,8) .LT . 1.08.AND.S(d1 + 2, 1).GT.0.69.AND.S(d1+ 3,8).LT.2.01 .AND 466 2 .(P(d1-4,1)*P(d1-3,2)*P(d1-2,3)*P(d1-1,4)).GT.O.000075) BALL= 467 3 .TRUE. 468 IF (BALL) d1=d1+1 469 IF (BALL) V2=20 470 IF (BALL) GO TO 300 47 1 C 472 C * * * 21 * * * 473 BALL=.FALSE . 474 IF (S(d1,8).LT. 1 .08.AND.S(d1 + 1,8).LT . 1.08.AND.(S(d1+2,8).GT. 1 . 47 . 475 1 OR.S(d1 + 2,8 ) .GT.S(d1+3,8)).AND.S(d1 + 3,8).LT.1.47.AND,S(d1 + 4,8).LT 476 2 .1.47.AND,(P(d1-4,1)*P(d1-3,2)+P(d1-2,3)*P(d1-1,4)).GE.0.000075.A 477 3 ND.S(d1+1,8).LT.0.73.AND.S(d1.2).GT.1.19.AND.S(d1+1,2).GT.1.47) 478 4 BALL=.TRUE. 479 IF (BALL) d1=d1+2 480 IF (BALL) V2=21 481 IF (BALL) GO TO 300 482 C 483 C * * * 22 * * * 484 BALL=.FALSE. 485 T1=0 486 T2=0 487 T5=0 488 T1=S(d1-4,1)+S(d1-3,1)+S(d1-2,1)+S(d1-1,1) 489 T2=S(d1-4,2)+S(d1-3,2)+S(d1-2,2)+S(d1-1,2) 490 T5=S(d1-4,5)+S(d1-3,5)+S(d1-2,5)+S(d1-1,5) 491 PRINT 245,T1,T2,T5 492 245 FORMAT(•' ' ,30X, 'T1 ,T2,T5' ,3(F7.3), ' STEP 22,M0d1 B-T PROBL.') 493 IF (T5.GT.T1 . AND.T5.GT,T2.AND.S(d1,8).LT. 1.08.AND.S(d1, 1 ) .LT . 1 .01 . 494 1 AND.S(d1 + 1,8) . LT . 1.08.AND.S(d1 + 2,8).GT.1.08.AND.S(d1+3,8).LE.S(d1 495 2 +2,8)) BALL=.TRUE. 496 IF (BALL) d1=d1+2 497 IF (BALL) V2=22 498 IF (BALL) GO TO 300 499 C 500 c * * * 23 * * * 501 BALL=.FALSE. 502 IF (S(d1, 1 ) . LT . 1 .06.AND.S(d1 - 1.2).GT. 1 .38.AND.S(d1-2,2).GT. 1.60.AN 503 1 D.S(d1-4,2).GT.1.38.AND.S(d1+1,2).GT.1.19.AND. S ( J1 + 1 , 8 ) . LT . 0 . 66 . A 504 2 ND.S(d1+2,8).GT.0.81.AND.S(d1+2,1).GT.0.77.AND.S(d1+3,8).LT.S(d1+ 505 3 2,8) .AND.S(d1 + 3, 1 ) .GT. 1 . 13) BALL=.TRUE. 506 IF (BALL) d1=d1+2 507 IF (BALL) V2 = 23 508 IF (BALL) GO TO 300 509 C 5 1 0 C ' * * * 24 * * * 511 BALL=.FALSE. 512 IF ((J1-5).LE.0) GO TO 250 513 IF (S(d1,8).LT.1.08.AND.S(d1+2,8).GT.1.08.AND.S(d1+1,8).LT.S(d1+2, 514 1 8 ) . AND.S(d1- 1 ,8) . LT. 1.08.AND.(S(d1+3,8).LE.S(d1+2,8).0R.S(d1 + 3,8) 515 2 .LT.2.01) .AND.S(d1+2,1).GT.1.01.AND.(P(d1-5,1)*P(d1-4,2)*P(d1-3. 516 3 3)*P(d1-2,4)).GE.0.000075) BALL=.TRUE. 517 IF (BALL) J1=d1+2 518 IF (BALL) V2=24 519 IF (BALL) GO TO 300 520 C 521 C **+25*** 522 BALL=.FALSE. 523 IF ((d1-6).LE.O) GO TO 250 524 IF (S(J1 ,8) . LT . 1.08.AND.S(d1+4,8).GT. 1 .47.AND.S(d1-1, 1).LE.0.69 00 525 1 .AND.M(d1-1).NE.15.AND.S(d1-2,8).LE.S(d1+4,8).AND.S(d1+1,8).LT. VD 526 2 1.08.AND.S(d1+2,8).LT.1.08.AND.S(d1+2,1).LE.0.69.AND.S(d1+3,8).LT 527 ' 3 .1.08.AND.(P(d1-6,1)*P(d1-5,2)*P(d1-4,3)*P(d1-3,4)).GT.0.000100) 528 4 BALL=.TRUE. 529 IF (BALL) d1=d1+4 530 IF (BALL) V2 = 25 531 IF (BALL) GO TO 300 532 C 533 C *** 26 *** 534 250 IF ((d1-1).LE.0) GO TO 260 535 BALL=.FALSE. 536 T1=0 537 T2=0 538 T5=0 539 T1=S(J1-1,1)+S(d1,1)+S(d1+1,1)+S(d1+2,1) 540 T2=S(d1-1,2)+S(d1,2)+S(d1+1,2)+S(d1+2.2) 54 1 T5=S(d1-1,5)+S(d1,5)+S(d1+1.5)+S(d1+2.5) 542 PRINT 255,T1,T2,T5 543 255 FORMAT(' ' ,30X, ' T 1 , T2 , T5' , 3(F7.3 ) , ' STEP 26,M0d1 B-T PROBL. ' ) 544 IF (T5.GT.T 1 .AND.T5.GT.T2.AND.S(d1+3,8).GE. 1 .08.AND.S(d1+4,8) .LT. 545 1 1 .47.AND.S(d 1+5,8).LT. 1 .47.AND.((d1+6).GE.d2.OR.S(d1+6,8).LT.S(d1 546 2 + 3,8)).AND.S(d1,5).GT. 1 . 19.AND.S(d1+1,5).GT.0.74.AND.S(d1 + 1. 1 ) .LT . 547 3 1.21.AND.S(d1+3,1).GT.S(d1,1).AND.S(d1+2,2).GT.1.19.AND.S(d1+3,2) 548 4 .GT. 1.05.AND.S(d1+4,2).GT. 1 .05.AND.S(d1+5,2).GT.0.75.AND.S(d1 + 1 , 549 5 2).GT.0.89) BALL=.TRUE. 550 IF (BALL) d1=d1+3 o 551 IF (BALL) V2 = 26 552 IF (BALL) GO TO 300 553 C 554 C * * * 27 * * * 555 260 BALL=.FALSE. 556 IF ( S ( J1+4 ,8 ) .GT .1 .47 .AND.S ( J1+5 ,8 ) . LE . S (d1+4 ,8 ) .AND.S (d1+6 ,8 ) . LE . 557 1 S (J1+4,8 ) .AND. (P (d1+1,1 ) *P (d1+2,2 ) *P (d1+3,3 ) *P (d1+4,4 ) ) .GT.0 .0001 558 2 00.AND.S(d1+3,1 ).LT.S(d1+4 ,1 ) .AND.S (d1+2,8 ) .LT.2 .01.AND.S (d1+1.8 ) 559 3 . LT .2 .01 ) BALL=.TRUE. 560 IF (BALL) d1=d1+4 561 IF (BALL) V2=27 562 IF (BALL) GO TO 300 563 C 564 C 565 C I F NONE OF THE ABOVE CONDITIONS IS SATISFIED TO CALL THE NEXT SUB 566 c ROUTINE RMd1 TO KEEP ON CHECKING FOR POSSIBILITIES OF N-TERMINAL 567 c ADJUSTMENT 568 c 569 CALL RMd1 570 RETURN 57 1 c 572 c N- TERMINAL OF THE PREDICTED HELIX HAS BEEN ADdUSTED TO CALL SUBROU 573 c TINE M0d2 FOR C-TERMINAL ANALYSIS 574 c 575 300 CALL M0d2 576 RETURN 577 END End of F i l e 1 C 2 C 3 A SUBROUTINE RMd 1 5 c 6 c 7 c 8 c 9 c RMd1 = REMAINING OF MOVE OF 01 10 c 1 1 c 12 c 13 c 14 c 15 c 16 c PURPOSE 17 c TO KEEP ON CHECKING FOR THE BEST POSITION FOR N-BOUNDARY,THIS 18 c SUBROUTINE IS A CONTINUATION OF M0d1 19 c 20 c 21 c 22 c 23 REAL S,T1 .T2,A 1 ,A2 , T 3 , T 4 , T 5 , T T , P 24 INTEGER G,F,H,U,D,V1,V2,W, V 3 , V 4 , V 5 , V 6 , V 7 , V 8 , 0 25 LOGICAL HELLO,BYE .BALL,MOVE 26 DIMENSION S (1000 ,20 ) ,M (1000 ) ,H (1000 ) ,D (1000 ,16 ) ,P (1000 ,10 ) 27 COMMON S .T1,T2,T3,T4,T5,TT,A1,A2,P ,F ,H,U,D.W,M,M1,M2,M3,M4,M5,M6, 28 1 L , I , K , L 1 , L 2 . N Z , N Y , d A , d B , d C , J D , J 1 , J 2 . K M . N 1 , N 2 , N N , J , C K 3 , V 1 , V 2 , V 3 , V 4 29 2,V5,V6,V7,0.HELLO,BYE,BALL,MOVE 30 c 3 1 c 32 c REMARKS 33 c THE PARAMETERS DESCRIBED IN THE SUBROUTINE M0d1 STILL KEEP THE SA 34 c ME DEFINITION IN THIS SUBROUTINE 35 c 36 c THE DIFFERENT COMMENTS J1=J1+1,J1=J1+5 d1=d1-1 INDICATE THE EV 37 c ENTUAL POSITION OF J1 IF ITS ENVIRONMENT MEETS ONE OF THE CONDI 38 c TIONS DESCRIBED BELOW. IF NOT J1 WILL STILL REMAIN AT THE SAME PO 39 c SITION BECAUSE IT APPEARS TO BE THE MOST FAVORABLE ONE 40 c 41 c 42 c . . . U1 = J1+7 43 c 44 c 45 c * * * 28 * * * 46 BALL=.FALSE. 47 IF ( (d1+8).GT.NN) GO TO 20 48 IF ( d 1 .LE .K3.AND. (P (d1+1,1 ) *P (d1+2,2 ) *P (d1+3,3 ) *P (d1+4,4 ) ) .GT.0 .00 49 1 007500.AND.S(d1 + 3 ,5 ) .GT . 1.43.AND.S(d1+4,5).GT. 1 . 19.AND.S(d1+ 5,8 ) 50 2 .LT .0 .66 .AND.S (d1+6,8 ) .LT .1 .08 .AND.S (d1+7,8 ) .GT.0 .71.AND.S (d1+7,1 51 3 ).GT.0.G9.AND.S(J1+8,8).LT.S(J1+7,8).AND.S(J1+8,1).GT.1.01.AND. 52 4 S(J1+6.1).LE.0.69) BALL=.TRUE. 53 IF (BALL) d1=d1+7 54 IF (BALL) V2=28 55 IF (BALL) GO TO 300 56 C 57 C ... J1 = J1+5 58 C 59 C 60 C *** 29 *** 61 20 BALL=.FALSE. 62 IF ((J 1-2).LE.O) GO TO 300 63 T1=0 64 T2=0 65 T5=0 66 T1=S(J1-2,1)+S(d1-1,1)+S(d1,1)+S(d1+1,1) 67 T2=S(d1-2.2)+S(d1-1,2)+S(d1,2)+S(d1+1,2) 68 T5=S(d1-2,5)+S(d1-1,5)+S(d1,5)+S(d1+1,5) 69 PRINT 25,T1,T2,T5 70 25 FORMAT ( ' • ' , 30X , 'T1.T2.T5' ,3(F7.3), ' STEP 29, J1+5 , RM<J 1 ' ) 7 1 7 2 IF (T5.GT.T1.AND.T5.GT.T2.AND.S(J1+1.8).LT.1.08.AND.S(J1+2,8).LT. 7 3 11.08.AND.S(d1+3,8).LT.1.08.AND.S(d1+ 4,8 ) .LT. 1 .08.AND.S(d1+5,8).GE. 74 2 1.08.AND.S(d1+4, 1 ) . LT . 1 .06.AND.S(d1+ 3, 1).LE.0.69.AND.S(d1 + 1, 1).LT 75 3 . 1.06) BALL= .TRUE . >^ 76 IF (BALL) d1=d1+5 77 IF (BALL) V2=29 78 IF (BALL) GO TO 300 79 C 80 C 81 C ... d1 = d1+4 82 C 83 C 84 C *** 30 *** 85 BALL=.FALSE. 86 IF ((d1-3).LE.0) GO TO 300 87 IF (S(d1,8).LE.1.08.AND.S(d1+1.8).LT.1.08.AND.S(d1+2,8).LT.1.08.AN 88 1 D.S(d1+4,8).GT. 1 .08.AND.S(d1 - 1,8).LT. 1 .08.AND.S(d1-2,8).LT. 1.08 89 2 .AND. (S(d1-3,8).LT. 1 .08.OR.S(d1 -3, 1) .LE.0.69) .AND,S(d1+3,8).LE. 90 3 1.08.AND.(S(d1+4,8).GT:1.29.OR.(S(d1+4,8)-S(d1,8)).GT.0.65)) BALL 9 1 4 =.TRUE. 92 IF (BALL) d1=d1+4 93 IF (BALL) V2 = 30 94 IF (BALL) GO TO 300 95 C 96 C *** 31 *** 97 BALL=. FALSE. 98 IF (S(d1,8) .LE . 1.08.AND.S(d1+4,8).GT. 1.47.AND.S(d1+1,8).LT. 1.08.AN 99 1D.S(d1+2,8).LT.2.01.AND.S(d1+3,8).LT.2.O1.AND.S(d1-1,8).LT.1.08 100 2 .AND.(S(d1-2,8).LT.1.08.OR.S(d1-2,8).LT.S(J1+4.8)).AND. S(J1-3,8) 101 3 .LT.S(J1 + 4,8)) BALL = . TRUE ., 102 IF (BALL) 01=01+4 103 IF (BALL) V2=31 104 IF (BALL) GO TO 300 105 C 106 C 107 C . .. 01 = 01-5 108 C 109 C 1 10 C *** 32 *** 1 1 1 IF ((01-6).LE.0) GO TO 30 112 BALL=.FALSE. 1 13 IF (S(01 ,8) .LT. 1 .08.AND.M(01 + 1).EO. 4. AND.M(01 -2).EO.7.AND.S(J1-1,8 1 14 1 ) . LT. 1.08.AND.S(01- 1, 1 ) . GT. 1 .01 .AND. M(01-3) .E0.4.AND.S(01-4, 1).GT 1 15 2.1.01.AND.S(01-4.8).LT.S(01-5,8).AND. S(01 -5,8).GE. 1.08.AND.S(01-6, 1 16 3 6) .GE. 1 . 22) BALL=.TRUE. 1 17 IF (BALL) 01=01-5 1 18 IF (BALL) V2=32 1 19 IF (BALL) GO TO 300 120 C 121 C *** 33 *++ 122 BALL=.FALSE . 123 IF (S(01.8).LT . 1 .08.AND.S(01 , 1 ) .GT. 1. 01.AND.M(J1-5).EO.1.AND.S(01+ 124 1 1,8).GE.1.08.AND.S(01+2.8).GE.1.08.AND.S(01+3,8).GE.1.08.AND.M(01 125 2 - 1).EO. 18.AND.S(01-2,8).GE.0.81.AND. S(01-3,1).GT.1.O1.AND.S(01-4, 126 3 1).GT. 1 .01 .AND.S(01-3,8 ) .LT. 1.08.AND .S(01-4.8).LT.1.08.AND.S(01-6 127 4 ,6).GT.1.04) BALL=.TRUE. 128 IF (BALL) 01=01-5 129 IF (BALL) V2=33 130 IF (BALL) GO TO 300 131 C 132 C . .. 01 = 01-4 133 C 134 C 135 C * + * 34 * * * 136 30 IF ((01-5).LE.0) GO TO 40 137 BALL=.FALSE. 138 IF (S(J1,8) . LT . 1 .08.AND.S(01. 1).GT. 1. 0 .AND.S(01-4,8).GT.1.47.AND. 139 1 S(01-3,8).GE.2.01.AND.S(01- 1 ,8) . LT. 1 .08.AND.S(J1-2.8).LT.2.01.AND 140 2 .S(J1-2.1).GT.1.01.AND,S(01-5,8).LT. 1.08.AND.S(01+1,8).LT.1.08. 14 1 3 AND.S(J1+2,8).LT.1.08.AND.S(01+2,1). GT.1.01.AND.S(01+3,8).LT.1.08 142 4 .AND.S(01 + 3 . 1).GT . 1 .01 .AND.S(01 + 1. 1) GT. 1.01) BALL=.TRUE . 143 IF (BALL) 01=01-4 144 IF (BALL) V2=34 145 IF (BALL) GO TO 300 146 C 147 C *** 35 *** 148 • BALL=.FALSE . 149 IF (S(01,8) .LT. 1 .08.AND.S(01-4,8).GT. 1.29.AND.S(01-5,6).GT.1.10. 150 1 AND.S(01-3,8).LT.1.08.AND.S(01-2,8). LT.1.08.AND.5(01-1.8).LT.1.08 151 2 .AND.S(d1-2,1).GT.1.01.AND.S(J1-3.1).GT.1.01.AND.S(d1+1.8).LT. 152 3 1.08.AND.S(d1+1,1).GT.1.01.AND.S(d1+2,8).GE.2.02.AND.S(d1+3,8).GT 153 4 .1.08.AND.S(d1+4,8).GT.1.08) BALL= . TRUE . 154 IF (BALL) d1=d1-4 155 IF (BALL) V2 = 35 156 IF (BALL) GO TO 300 157 C 158 C +** 36 +** 159 BALL=.FALSE. 160 IF ( S(d1,8).LT. 1 .08 .AND.S(d 1 , 1).GT. 1 .01.AND.S(d1 + 1,8).LT . 1 .08.AND. 161 1 S(d1 + 2,8).LE.S(d1-4,8).AND.S(d 1-4,8 ) .GT. 1.47.AND.S(J1-5,8).GT. 1 . 4 162 2 7.AND.S(d1-1, 1).GT. 1 .01.AND.S(d1-2, 1 ) .GT.0.69.AND.S(d1 -3, 1).GT. 1 . 163 3 01.AND.S(d1-1,8).LT.2.01.AND.S(d1-2,8).LT.2.01.AND.S(d1-3,8).LT. 164 4 2.01) BALL=.TRUE. 165 IF (BALL) V2=36 166 IF (BALL) d1=d1-4 167 IF (BALL) GO TO 300 168 169 C . .. d1 = d1+3 170 C 17 1 C 172 C * * * 37 * * * 173 40 BALL=.FALSE. 174 IF ((d1-3).LE.O) GO TO 300 175 IF (S(d1,1).LE.0.69.AND.S(d1,8).LT. 1 .08.AND.S(d1 - 1,8) .LT. 1 .08.AND. 176 1 S(d1-2,8).LT.1.08.AND.S(d1-3,8).LT.1.08.AND.S(d1+1,8).LT.1.08.AND 177 2 . S(d1+2,8).LT. 1.08.AND.S(d1+3,8).GE. 1.08.AND.S(d1+3, 1 ) .GT . 1.01) 178 3 BALL=.TRUE. 179 IF (BALL) d1=d1+3 180 IF (BALL) V2=37 181 IF (BALL) GO TO 300 182 C 183 C *** 3g *** 184 BALL=.FALSE . 185 IF (S(d1,8).LT. 1 .08.AND.S(d1 + 1,8).LT. 1.08.AND.S(d1 - 1,8).LT. 1 .08.AN 186 1D.S(d1-2,8).LT.1.08.AND.S(d1 -3,8).LT,1.08.AND.S(d1+3,8).GT.S(d1+2, 187 2 8).AND.S(d1+2.1).LT.S(d1+3,D) BALL=.TRUE. 188 IF (BALL) d1=d1+3 189 IF (BALL) V2=38 190 IF (BALL) GO TO 300 191 c 192 c +** 3g *** 193 IF ((d1-4).LE.0) GO TO 50 194 BALL=. FALSE. 195 IF (S(d1,8).LT.1.47.AND.S(d1+1,8).LT.1.08.AND.S(d1+1,1).LE.0.69.AN 196 1 D.S(d1 + 2,6).GT.1. 10.AND.S(d1+3,8).GT. 1.47.AND.S(d1 - 1,8) .LT. 1 .08.A 197 2 ND.S(d1-3,8).LT.1.08.AND.S(d1-2,8).LT.1.08.AND.S(d1-4,8).LT.1.08) 198 3 BALL=.TRUE. 199 IF (BALL) d1=d1+3 200 IF (BALL) V2=39 201 IF (BALL) GO TO 300 202 C 203 C *** 40 * * * 204 BALL=.FALSE. 205 IF (S( J1 ,8) . LT . 1 .08.AND.S(d1 , 1 ) . LE .0 . 69 . AND . S (<J 1 - 1 , 1 ) . LE .0.69 .AND 206 1 .M(J1 - 1) .NE. 15 .AND.S (J1 -2 ,8 ) .LT. 1 . 0 8 . A N D . S ( J 1 - 3 , 8 ) . L T . S ( d 1 + 3 , 8 ) . A 207 2 N D . S ( J 1 - 4 , 8 ) . L T . 1 . 0 8 . A N D . S ( J 1 + 1 , 8 ) . L T . 1 . 0 8 . A N D . S ( d 1 + 2 , 8 ) . L T . 1 . 0 8 208 3 .AND.S(J1+3,8) .GT. 1 .08) BALL=.TRUE . 209 IF (BALL) d1=d1+3 210 IF (BALL) V2=40 21 1 IF (BALL) GO TO 300 212 C 213 c * + + 4 1 * * * 214 BALL=.FALSE . 215 IF (S(J1 ,8) .GE. 1 .08.AND.S(J1+ 3 ,8 ) .GT.S (d1 ,8 ) .AND.S (d1 + 1 , 1 ) . L E . 0 . 6 9 216 1 .AND.M(d1 + 1).NE. 15.AND.S(d1 + 2 , 8 ) . L T . 1 .08.AND.S(d1 - 1 ,8 ) .LT . 1 .08.AN 217 2 D . S ( d 1 - 2 , 8 ) . L T . 1 . 0 8 . A N D . S ( d 1 - 3 , 8 ) . L T . 1 . 0 8 . A N D . ( d 1 - 4 ) . L T . ( K 3 - 2 ) ) 2 18 3 BALL=.TRUE. 2 19 IF (BALL) V2=41 220 IF (BALL) d1=d1+3 22 1 IF (BALL) GO TO 300 222 c 223 c * * + 42 * * * 224 BALL=.FALSE. 225 IF ( S ( d 1 + 3 , 8 ) . G T . 1 . 4 7 . A N D . S ( d 1 , 8 ) . L T . 1 . 4 7 . A N D . S ( d 1 + 1 , 8 ) . L T . 1 . 0 8 . A N 226 1 D.S(d1 + 2 ,8 ) .LT.S (d1+3,8) .AND.S (d1+ 2, 1 ) . LT . 1 . 16 .AND.S(d 1 - 1 ,8 ) . LT . 227 2 1 . 0 8 . A N D . S ( d 1 - 2 , 8 ) . L T . 1 . 0 8 . A N D . S ( d 1 - 3 , 8 ) . L T . 1 . 0 8 . A N D . S ( d 1 - 4 , 8 ) . L T 228 3 ' .1.08) BALL=.TRUE. 229 IF (BALL) d1=d1+3 230 IF (BALL) V2=42 23 1 IF (BALL) GO TO 300 232 c 233 c . . . J1 = d1-3 234 c 235 c 236 c * + * 43 * + * 237 BALL=.FALSE . 238 IF ( S ( d1 ,8 ) .GT . 1 .47 .AND.S (d1 -3 .8 ) .GE .S (d1 ,8 ) .AND.S (d1 - 1 ,8 ) .LT . 1.08 239 1 .AND.S(d1-2, 1) .GT. 1.01.AND.S(d1 - 2 , 8 ) . L T . S ( d 1 - 3 , 8 ) . A N D . S ( d 1 - 4 , 8 ) . 240 2 LT . 1 .08.AND.S(d1+2,8) .LT. 1.08.AND.S(d1+1,8).LT. 1.08.AND.S(d1 + 3,8) 24 1 3 .GT.1 .47) BALL=.TRUE . 242 IF (BALL) d1=d1-3 243 IF (BALL) V2=43 244 IF (BALL) GO TO 300 245 c 246 c * * * 44 * * * 247 BALL=.FALSE. 248 IF ( S ( d 1 , 8 ) . L T . 1 . 0 8 . A N D , S ( d 1 + 1 . 8 ) . L T . 1 . 0 8 . A N D . S ( d 1 + 2 , 8 ) . G T . 1 . 2 9 . 249 1 A N D . S ( d 1 - 1 , 8 ) . G E . 0 . 8 1 . A N D , S ( d 1 - 2 , 8 ) . G E . 1 . 0 8 . A N D . ( S ( d 1 - 2 , 1 ) . G T . 1 . 0 250 2 1 .0R . S (d1 -2 .8 ) .GT .2 .01 ) . A N D . S ( d 1 - 3 , 8 ) . G T . 1 . 0 8 . A N D . S ( d 1 - 4 . 8 ) . L E . 251 3 S(J1-3,8)) BALL=.TRUE. 252 IF (BALL) d1=d1-3 253 IF (BALL) V2=44 254 IF (BALL) GO TO 300 255 C 256 C *** 45 *** 257 BALL=.FALSE. 258 IF (S(<J1 ,8) . LT . 1 .08 . AND.S(d1 -3,8) . GE . 1 . 47 . AND . S ( J 1 - 1 , 8 ) . LT . 1 . 08 . AN 259 1 D . S(d1-2,8).LT. 1.08.AND.S(d1-4,8).LT. 1 .08.AND.S(d1+1,8).LT. 1.08 260 2 .AND.S(d1 + 2.8).LE. 1.08.AND.S(d1+3,8).LT. 1 .08.AND.S(d1, 1).GT. 1 .01 261 3 .AND.S(d1+1, 1).GT. 1 .01 .AND.S(d1+3, 1 ) .GT. 1 .01) BALL=.TRUE. 262 IF (BALL) J1=d1-3 263 IF (BALL) V2 = 45 264 IF (BALL) GO TO 300 265 C 266 C *** 46 *** 267 BALL=.FALSE. 268 IF (M(d1).EO.1.AND.S(d1-3,8).GE.1.08.AND.M(d1-4).EO.8.AND.S(d1-1,8 269 1 ) . LT. 1 .08.AND.S(d1 - 1, 1 ) .GT. 1.01.AND.S(d1 -2,8).LT. 1.08.AND.S(d1-2, 270 2 1).GT.0.69.AND.S(d1+1,8).LT.1.08.AND,S(d1+2,8).LE.S(d1-3,8).AND. 271 3 S(d1+3,8).LT.1.08) BALL=.TRUE. 272 IF (BALL) d1=J1-3 273 IF (BALL) V2=46 i£> 274 IF (BALL) GO TO 300 CTi 275 C * 2 7 6 C * * * 4 7 * * * * 277 BALL=.FALSE. 278 IF (S(d1 ,8) .LT. 1 .08.AND.M(d1 - 1).EO. 15.AND.S(d1 -2,8).LT.S(d1-3,8). 279 1 AND,M(d1-3).EO.1.AND.S(d1-4,8).LT.1.08.AND.S(d1+1,8).LT.1.08.AND. 280 2 M(d1+2).EQ.1.AND.M(d1+4).EQ.1) BALL=.TRUE . • . 281 IF (BALL) J1=d1-3 282 IF (BALL) V2=47 283 IF (BALL) GO TO 300 284 C 285 C *** 48 *** 286 BALL=.FALSE. 287 IF (M(d1).EO.1.AND.S(d1-3,8).GE.1.08.AND.S(d1-4,6).GE.1.22.AND. 288 1 S(d1-1,8).LT.1.08.AND.S(d1-1,1).GT.0.69.AND.S(d1-2,8).LT.1.08.AND 289 2 .S(d1-2,1).GT.1.01.AND.S(d1+1,8).LT.1.08.AND.S(d1+2,8).LT.S(d1-3 290 3 ,8) .AND.S(d1+3,8) .LT. 1.08) BALL=.TRUE. 291 IF (BALL) J1=d1-3 292 IF (BALL) V2=48 293 IF (BALL) GO TO 300 294 C 295 C *** 49 *** 296 BALL=.FALSE. 297 IF (S(d1,8).GE.1.08.AND,S(d1+1,8).GE.1.08.AND.S(d1+2,8).LT.1.08.A 298 1 ND.S(d1 + 3,8).LT. 1.08.AND.M(d1-3).E0.15.AND.S(d1 - 1,8).LT. 1 .08.AND. 299 2 S(J1-1, 1).GT. 1.01.AND.S(d1-2,8).LT. 1.08.AND.S(d1 -2, 1).GT.0.69.AND 300 3 .S(d1-4,8).LT.1.08) BALL=.TRUE. 301 IF (BALL) d1=d1-3 302 IF (BALL) V2=49 303 IF (BALL) GO TO 300 304 C 305 C * * * 50 * * * 306 50 BALL=.FALSE. 307 IF ( (J 1 - 3 ) .LE.O) GO TO 300 308 IF (M(d1).EO.1.AND,S(d1-3,8).GT.1.47.AND.S(d1-1,8).LT.1.08.AND.S 309 1 (d1-2,8) .LT. 1 .08.AND.(M(d1 - 1).EQ.3.OR.M(d1 - 1).EQ. 16.OR.M(d 1 - 1 ) . EQ 310 2 . 8 ) . AND.S(d1 + 1,8).LT. 1.08.AND.S(d1+2,8).LT. 1.08.AND.S(d1+3,8).GE. 31 1 3 S(d1-3,8).AND.S(d1+4,8).GT.1.08) BALL=.TRUE. 312 IF (BALL) d1=d1-3 313 IF (BALL) V2=50 314 IF (BALL) GO TO 300 315 C 316 C * * * 5 1 * + * 317 IF ((d1-5).LE.O) GO TO 60 318 BALL=.FALSE. 319 IF (S(d1 ,8) .LT. 1 .08.AND.S(d1, 1 ) .GT. 1 .01 .AND.M(d1-3) .EO. 15.AND.S(d1 320 1 -1,2).LE.0.75.AND.S(d1-5,2).LE.0.75.AND.S(d1+1,2).LE.0.75.AND.S(d 321 2 1-2,8).LT.2.01.AND.S(d1+1,8).LT.2.01.AND.S(d1+2,8).LT.2.01.AND.S( 322 3 1+3 , 1 ) .GT. 1 .01 .AND.S(d1+4, 1 ) .GT. 1.08) BALL=.TRUE. 323 IF (BALL) J1=d1-3 324 IF (BALL) V2=52 325 IF (BALL) GO TO 300 326 C 327 C . .. d1 = d1+2 328 C 329 C 330 C * * * 53 *** 331 60 BALL=.FALSE. 332 IF ((d1-3).LE.O) GO TO 300 333 IF (S(d1,8).LT. 1 .08.AND.S(d1 , 1 ) . LT . 1 .06.AND.S(d1+2,8) .GT. 1 .47.AND. 334 1 S(d1 + 1,8).LT. 1.08.AND.S(d1 - 1, 1).LE.0.69.AND.M(d1-1).NE.15.AND.S( 335 2 d1-2,8).LT.1 .08.AND.S(d1 -3,8).LT. 1.08.AND.S(d1-2, 1 ) . LT. 1.06.AND.S 336 3(d1-3, 1).LT. 1.06) BALL=.TRUE . 337 IF (BALL) d1=d1+2 338 IF (BALL) V2=53 339 IF (BALL) GO TO 300 340 C 34 1 C * * * 54 * * * 342 BALL=.FALSE . 343 IF (S(d1,1).LE.0.69.AND.M(d).NE.15.AND.S(d1+1.8).LT.1.08.AND.S(d1+ 344 1 2,8).GT. 1 .47.AND.S(d1-1, 1).LE.0.69.AND.M(d1 -1).NE. 15.AND.S(d1-2, 345 .2.8).LT.S(d1 + 2,8).AND.S(d1- 3,8) .LT. 1 .08) BALL=.TRUE. 346 IF (BALL) d1=d1+2 347 IF (BALL) V2=54 348 IF (BALL) GO TO 300 349 C 350 C *** 55 *** 00 351 BALL=.FALSE. 352 IF (S(J1,8).LT . 1 .08.AND.S(J1+1, 1).LE.0.69.AND.M(J1 + 1).NE. 15.AND. 353 1 S(J1+2.8).GT.1.08.AND.S(J1-1,8).LT.1.08.AND.S(J1-2,8).LT.S(J1+2,8 354 2 ).AND.S(<J 1-3,8).LE.S(J1+2,8).AND.S(d1-4,8),LE.S(d1+2,8)) BALL = 355 3 .TRUE. 356 IF (BALL) d1=d1+2 357 IF (BALL) V2 = 55 358 IF (BALL) GO TO 300 359 C 360 C * * * 56 ** + 361 IF ((J1-4).LE.0) GO TO 70 362 BALL=.FALSE. 363 IF (S(J1,8).LT.1.08.AND.S(J1,1).LT.1.06.AND.S(J1+1.8).LT.1.08.AND. 364 1 S(d1+2,8).GT.1.08.AND.S(d1+2,1).GT.1.01.AND.S(J1- 1 ,8) .LT. 1 .08.AND 365 2 .S(d1-1,2).GE.1.47.AND,S(J1-2,1).LE.0.69.AND.M(d1-3).EO.1.AND.S(d 366 3 1-4,2).GE.1.47) BALL=.TRUE. 367 IF (BALL) d1=d1+2 368 IF (BALL) V2=56 369 IF (BALL) GO TO 300 370 C 371 C *** 57 * * * 372 70 BALL=.FALSE . 373 IF ((d1-3).LE.O) GO TO 300 374 T1=0 375 T2 = 0 376 T5=0 377 T1=S(d1-3.1)+S(d1-2,1)+S(d1-1,1)+S(d1.1) 378 T2=S(d1-3,2)+S(d1-2.2)+S(d1-1,2)+S(d1,2) 379 T5=S(d1-3,5)+S(d1-2.5)+S(d1-1.5)+S(d1.5) 380 PRINT 75,T1,T2,T5 38 1 75 FORMATC ' ,30X, 'T1 ,T2,T5' ,3(F7 . 3) , ' STEP 57, d1 + 2 ,RMd1') 382 IF (T5.GT.T 1 .AND.T5.GT.T2.AND.S(d1 + 1 ,8) .LT. 1 .08.AND.S(d1 + 1 ,2) .GT . 383 1 1.38.AND.S(d1+2,8).GT.0.8 1.AND.S(d1+3,8).LT.1.08.AND.S(d1+4,8).LT 384 2 .1.08.AND.S(d1+3,2).GT.1.10.AND.S(d1+4.2).GT.1.10.AND.S(d1,1).LT. 385 3 1.06.AND.S(d1,5).GT. 1 .43.AND.S(d1-1,5).GT. 1.52.AND.S(d1-2,5).GT. 386 4 1.52) BALL=.TRUE. 387 IF (BALL) d1=d1+2 388 IF (BALL) V2=57 389 IF (BALL) GO TO 300 390 C 391 C . . . d1 = d1-2 392 C 393 C 394 C * * + 58 *** 395 BALL= . FALSE. 396 IF (S(d1,8).LE.1.08.AND.S(d1 - 1, 1).GT. 1 .01.AND.S(d1-1.8).LT.S(d1-2, 397 1 8).AND.S(d1-2,8).GT. 1 .47.AND.S(d1 -3,8).LT.S(d1-2,8).AND.S(d1 + 1.8) 398 2 .LT. 1 .08.AND,S(d1 + 2,8).LT.1.08.AND.S(d1+3,8).LT. 1 .08) BALL= .TRUE . 399 IF (BALL) d1=d1-2 400 IF (BALL) V2=58 401 IF (BALL) GO TO 300 402 C 403 C * + * 59 +** 404 BALL=.FALSE. 405 IF (S(Jl,8).LT.1.08.AND,S(J1.1).GT.1.01.AND.S(J1-2.8).GE.S(J1,8) 40G 1 .AND.S(J1-1,1).LT.S(J1-2,1).AND,S(J1+1,8).LT.1.47.AND.S(J1+2,8).L 407 2T.1.08.AND.(S(d 1 -3, 1).LE.0.69.OR.S(d1-3,8).LT. 1 .08).AND.(S(J1-2,1) 408 3 .GT. 1. 16.OR.M(J1- 1).NE. 15)) BALL= . TRUE . 409 IF (BALL) J1=J1-2 410 IF (BALL) V2=59 411 IF (BALL) GO TO 300 4 12 C 413 C * * * 6 0 * * * 414 BALL=.FALSE. 4 15 IF (S(J1,8).LT. 1.08.AND.S(J1-1,8).LT. 1.08.AND.S(J1-2,8).GT. 1.22 . AN 416 1D.S(J1+1,8).LT.1.08.AND.S(J1+2,8).GE.1.08.AND.S(J1+3,8).GT.2.01 417 2 .AND.S(J1-3.8).LT.S(J1-2,8).AND.S(J1-2,1).GT.0.69) BALL=.TRUE. 418 IF (BALL) J1=d1-2 419 IF (BALL) V2=60 420 IF (BALL) GO TO 300 421 C 422 C * * * g 1 * * * 423 BALL=.FALSE. 424 IF (S(J1.8).LT. 1.08.AND.S(J1. 1 ) .GT. 1.01 .AND.S(d1-2,8).GT.2.01 .AND. 425 1 S( J1-1,8).LT.S(J1-2.8).AND.S(J1-3,8).LE.S(J1-2,8).AND.S(J1+1,8). vo 426 2LE.S(J1-2,8).AND.S(J1+2.8).GE.1.08.AND.S(J1+3,8).GE.S(J1-2.8)) 427 3 BALL=.TRUE. 428 IF (BALL) J1=J1-2 429 IF (BALL) V2 = 61 430 IF (BALL) GO TO 300 431 C 432 C *** 62 *** 433 BALL=.FALSE. 434 IF(S(J1,8).GT.1.47.AND.S(J1-1,8).GT.1.47.AND.S(J1-2,8).GT.1.47.AN 435 1 D.S(J1+1,8).GT.1.47.AND.S(J1+2,8).LT.1.08.AND.S(J1+3,8).LT.1.08 436 2.AND.S(J1-3,8).LT. 1.08) BALL= . TRUE. 437 IF (BALL) J1=J1-2 438 IF (BALL) V2=62 439 IF (BALL) GO TO 300 440 C 441 C *** 63 *** 442 BALL=.FALSE. 443 IF(S(J1,8).GT.1.47.AND.M(J1-2) .EO. 1 .AND.S(J1 - 1 ,8) .LT. 1 .08.AND.S(J 444 1 1-3,8).LT. 1 .08.AND.S(J1 + 1,8).LT.S(J1-2,8).AND.S(J1+ 2 , 8).LT.S(d1-2 445 2 ,8) . AND.S(J1 + 3.8).LE.S(J1-2.8)) BALL=.TRUE. 446 IF (BALL) J1=J1-2 447 IF (BALL) V2=63 448 IF (BALL) GO TO 300 449 C 450 C *** 64 *** 451 BAL'L= . FALSE . 452 IF (M(J1).EO.7.AND.S(d1-2,8).GT.1.47.AND.S(d1-3,1).GT.0.69.AND.S( 453 1 d1-1,8).LT.1.08.AND.S(d1+1,8).LT.1.08.AND.S(d1+2,1).GT.1.01.AND.S 454 2 (J1-3.8) .LT. 1 .47) BALL= . TRUE . 455 IF (BALL) d1=d1-2 456 IF (BALL) V2=64 457 IF (BALL) GO TO 300 458 C 459 C . . J1 = d1+1 460 C 461 C 462 C * * * 65 *** 463 BALL=.FALSE. 464 "IF (S(d1,8).LE.1.08.AND.S(d1+1,8).GE.1.08.AND.S(d1+1,1).GT.1.01 465 1.AND.(S(d1+2,8).LT.S(d1 + 1 .8) .OR.S(d1 + 2.8) .LT. 1.47).AND.S(d1 + 3.8) 466 2.LT. 1 .08.AND.S(d1 - 1,8).LT. 1.08.AND.S(d1-2,8).LE. 1 .08.AND.S(d1-3.8 ) 467 3.LT. 1 .08.AND.S(d 1 +4,8 ) .LT . 1.08) BALL=.TRUE. 468 IF (BALL) d1=d1+1 469 IF (BALL) V2=65 470 IF (BALL) GO TO 300 47 1 C 472 C * * * 66 *** 473 BALL=.FALSE. 474 IF (S(d1 ,8) .LT. 1 .08.AND.S(d1 + 1,8).GT. 1 .47.AND.S(d 1+2,8 ) .LT.S(d1+1 , 475 1 8).AND.S(d1+3,8).LT.S(d1+1,8).AND.S(d1-1,8).LT.S(d1+1,8).AND.S(d1 476 2 -2,8) .LT.S(d1 + 1,8).AND.S(d1-3,8) .LT.S(d1 + 1 ,8)) BALL=.TRUE. 477 IF (BALL) d1=d1+1 478 IF (BALL) V2=66 479 IF (BALL) GO TO 300 480 C 481 C 482 C . . . . J1 = d1-1 483 C 484 C 485 C * * * 67 *** 486 BALL=.FALSE. 487 IF (S(d1,8) .LT . 1 .08.AND.S(d1-1,8).GT. 1.08.AND.S(d1-1, 1).GT. 1. 16.AN 488 1 D.S(d1-2,8).LT.S(d1-1,8).AND.S(d1+1,8).LT.1.08.AND.S(d1+2.8).LE. 489 2 S(d1-1,8).AND.S(d1-3,8) .LT. 1 .08) BALL=.TRUE. 490 IF (BALL) d1=d1-1 491 IF (BALL) V2=67 492 IF (BALL) GO TO 300 493 C 494 C * * * 68 '*** 495 BALL= . FALSE . 496 IF (S(d1 ,8).LT . 1 .08.AND.M(d1-1).EO. 15.AND.S(d1+1,8).LT.S(d1-1,8). 497 1 AND. S(d1+2,8) . LT . S(d1-1 ,8) . AND . S (d 1+3 . 8 ) . LT . S ( d 1 - 1 , 8 ) . AND.S(d1-"2, 498 2 8).LT.S(d1-1,8).AND,S(d1-3,8) .LT. 1.08.AND.S(d1, 1 ) .GT. 1 .01) BALL 499 4 =.TRUE. 500 IF (BALL) d1=d1-1 501 IF (BALL) V2 = 68 502 IF (BALL) GO TO 300 503 C 504 C *** 69 *** ' 505 BALL=.FALSE. 506 IF (S(J1.8).GE.1.08.AND. S ( d 1 , 1 ) .GT.1.01.AND.S(d1,8).LT.2.44.AND.S( 507 1 d1 + 1,8).LE.1 .08.AND.S(d1 + 2,8).GE. 1.08.AND.S(d1+ 3,8).LT.S(d1 - 1,8) 508 2 .AND.M(d1-1).EO.15.AND.S(d1-2,1).LE.O.69 .AND.(S(d1-3,1).LE.0.69 509 3 .OR . S(d1-3,8).LT. 1.08)) BALL=.TRUE. 510 IF (BALL) d1=J1-1 511 IF (BALL) V2=69 512 IF (BALL) GO TO 300 513 C 5 1 4 C * * * 7 0 * * * 515 BALL=.FALSE. 516 IF (M(d1).E0.7.AND.M(d1-1).EO. 15 . AND . (S(d1-2, 1 ) .LE.0.69.OR.S(d1-2, 517 1 8).LT. 1.08).AND.(S(d1-3, 1).LE.0.69.OR.S( d 1-3,8).LT. 1 .08).AND.S(d 518 2 1+1,8).GE.1.08.AND.S(d1+2,8).LT.1.08.AND.S(d1+3,8).GE.1.08) BALL 519 3 =.TRUE. 520 IF (BALL) d1=d1-1 521 IF (BALL) V2 = 70 522 IF (BALL) GO TO 300 523 C 524 C * * * 7 - | * * * 525 BALL=.FALSE. O 1 - 1 526 IF (S(d1,8) .LT. 1.08.AND.S(d1 + 1,8).LT. 1 .08.AND.S(d1 + 2,8).LT. 1.08.AN 527 1 D.S(d1+3,8).LT. 1 .08.AND.S(d1 - 1, 1).GT. 1. 16.AND.S(d1 - 1,8).GE. 1 .08. 528 2 AND.S(d1-2,8).LT. 1.08.AND.S(d1-3,8).LE.S(d1-1,8)) BALL= . TRUE . 529 IF (BALL) d1=d1-1 530 IF (BALL) V2=71 531 IF (BALL) GO TO 300 532 C 533 c **+ 72 +** 534 BALL=.FALSE. 535 IF(S(d1,8).GE.1.08.AND.S(d1-1,8).GT.S(d1,8).AND.S(d1 + 1 , 8).LT. 1.08 536 1 .AND.S(d1+2,8).LT.1.08.AND.S(d1+3,8).LT.1.08.AND.S (d1-2,1).LE. 537 2 0.69.AND.S(d1-3,8).LE.S(d1-1,8).AND.S(d1,1).GT.1.01) BALL=.TRUE. 538 IF (BALL) J 1 =J 1 - 1 539 IF (BALL) V2=72 540 IF (BALL) GO TO 300 541 C 542 C *** 73 *** 543 BALL=.FALSE. 544 IF (S(d1,8).GT.1.08.AND.S(d1,1).GT.1.01.AND.S(d1+1,8).LE.1.08.AND. 545 1 S(d1 + 2,8).LT. 1 .08.AND.S(d1+3,8).LT.S(d1 - 1,8).AND,M(J1-1).EO. 15.AN 546 2 D.(S(d1-2,1).LE.0.69.0R.S(d1-2,8).LT.S(d1-1,8)).AND. (S(d1-3,1).LE 547 3 .0.69.0R.S(d1-3,8).LT.1.08)) BALL=.TRUE. 548 IF (BALL) d1=d1-1 549 ' IF (BALL) V2=73 550 IF (BALL) GO TO 300 551 552 553 END OF N-BOUNDARY ADJUSTMENT. TO CALL SUBROUTINE MOJ2 FOR C-BOUNDA 554 RY ADJUSTMENT 555 556 300 CALL M0J2 557 RETURN 558 END nd of F i l e 1 2 C C 3 4 5 G 7 C C C C SUBROUTINE M0J2 8 9 c c BOUNDARY MOVE OF THE C-TERMINAL 10 c 1 1 c 12 c 13 c 14 c 15 c 16 c PURPOSE 17 c TO ADJUST THE C-TERMINAL RESIDUE BASED ON THE BOUNDARY CONFOR 18 c MAT IONAL PARAMETERS AND ON THE POTENTIAL OF TURN OR SHEET OF 19 c THE ADJACENT REGIONS 20 c 2 1 c 22 C ' 23 c 24 REAL S,T1,T2,A1,A2 ,T3,T4,T5,TT,P 25 INTEGER G,F.H,U,D,V1,V2,W, V3,V4,V5,V6.V7,V8.0 2G LOGICAL HELLO,BYE .BALL,MOVE 27 DIMENSION S(1000,20),M(1000),H(1000),D(1000,16),P(1000,10) 28 COMMON S.T1.T2.T3.T4,T5,TT,A 1,A2,P,F,H,U,D,W,M,M1,M2,M3,M4,M5,M6, 29 1L,I,K,L1,L2,NZ,NY,JA,JB,JC,JD,J1,J2,KM,N1,N2,NN,J,G,K3,V1,V2,V3,V4 30 2,V5,V6,V7,0,HELLO,BYE,BALL,MOVE 31 c 32 c 33 c DESCRIPTION OF PARAMETERS 34 c V1 - NUMBER OF BREAKERS IN THE PREDICTED HELIX BEFORE THE BOUN 35 c DARY ADJUSTMENT 36 c V2 - COUNTER USED IN N-BOUNDARY ADJUSTMENT 37 c V3 - COUNTER USED IN C-BOUNDARY ADJUSTMENT 38 c 39 c 40 c V2=80 WHEN THE N-TERMINAL ADJUSTMENT IS DUE TO STRONG B-TURN POTEN 4 1 c TIAL (THROUGH THE PROCEDURE OF REPEATING THE B-TURN CHECK). 42 c IF V2=0 NONE OF THE CONDITIONS LISTED IN THE N-TERMINAL ADJUSTMENT 43 c FIT THE CURRENTLY TESTED SEGMENT. IN OTHER WORDS J1 HAS NOT CHANGED 44 c 45 PRINT 1 46 1 FORMAT('O', 30X,'BOUNDARY ANALYSIS OF THE C-TERMINAL') 47 IF (.NOT. BALL.AND. V2.NE. 80) V2=0 48 c 49 c 50 c .... SITUATION WITH J2 CLOSE TO THE C- BOUNDARY 51 C 52 C TO TAKE INTO ACCOUNT THE POSITION OF J2 WHEN IT IS CLOSE TO THE C-53 C TERMINAL OF THE PROTEIN SINCE THERE IS LESS FREEDOM TO MOVE IT TO 54 C WARDS THIS END 55 C 56 C * * * \ * * * 57 BALL=.FALSE. 58 IF (02 .EO•NN.AND. S(02,9).GT. 1. 10.AND.S(J2, 1 ) .GT. 1 .01.AND.(S(J2,9) 59 1 .GT.S(02-1,9).OR.S(02-1 , 1 ) . LT.S(02, 1))) BALL =.TRUE. 60 IF (BALL) 02 = 02 6 1 IF (BALL) V3=1 62 IF (BALL) GO TO 300 63 C 64 C * * * 2 * * * 65 BALL=.FALSE . 66 IF ((02 + 3).GT.NN) GO TO 20 67 IF (S( J2 ,9) .GT .0.98 . AND .S(02,1).GT.0.69. AND. S(02+1 , 1 ) . LE .0.69 . AND . 68 1 S(J2+2, 1).LE.0.69.AND. S(02+3,9).LT. 1.57.AND. S(02- 1, 1).GT.0.69.AND 69 2 .S(J2-2,9).GT. 1 . 10.AND.S(02-3, 1 ) .GT. 1 . 16) BALL=.TRUE. 70 IF (BALL) 02 = 02 7 1 IF (BALL) V3 = 2 72 IF (BALL) GO TO 300 73 C 74 C * * * 3 * * + 75 BALL =.FALSE. 76 T1=0 77 T2=0 78 T1=S(J2,1) + S(J2+1,1)+S(J2+2,1 ) + S(J2+3, 1) 79 T2=S(02,2)+S(02+1,2)+S(J2+2,2)+S(J2+3,2) 80 PRINT 10.T1.T2 81 10 FORMAT(' ',30X,'T1,T2 ' ,2(F7 . 3 ) ,7X, ' STEP 3, 02 CLOSE TO 0') 82 IF (T2.GT.T1.AND.S(02,2).GT.1.38.AND.S(02+2,2).GT.1.38.AND.S(J2+1, 83 1 1).LE.0.69.AND.S(02,9).GT. 1 .20.AND.5(02-1. 1).GT. 1 . 16.AND.S(02-2. 84 2 2).LE.O.75) BALL =.TRUE. 85 IF (BALL) 02=02 86 IF (BALL) V3=3 87 IF (BALL) GO TO 300 88 C 89 C * * * 4 * * * 90 BALL=.FALSE. 91 IF ((02 + 4) .GT.NN) GO TO 20 92 IF (S(02,9).GT.1.08.AND.S(02-1,1).GT.1.16.AND.S(02-2,1).GT.1.16.AN 93 1 D . S(02+1, 1),GT.0.77.AND.S(02+2, 1 ) .GT. 1 .01.AND.S(02+2.9).GT.S(02+1 94 2,9) .AND.S(02 + 3,7) . GT . 1 .58.AND.S(02 + 4,7) .GT. 1 .58) BALL=.TRUE. 95 IF (BALL) 02=02+2 96 IF (BALL) V3=4 97 IF (BALL) GO TO 300 98 C 99 C * * * 5 * * * 100 20 BALL=.FALSE . 101 IF ((02+ 1 ) .GT.NN) GO TO GO 102 IF ((02+1).EQ.NN.AND.M(02+1).NE.15.AND.V1.LT.((02+1-01)/3).AND.S(0 103 1 2.9) .GT. 1 . 10.AND.S(J2-1,9).GT. 1. 10) BALL = . TRUE. 104 IF (BALL) 02=02+1 105 IF (BALL) V3 = 5 106 IF (BALL) GO TO 300 107 C 108 C *** g *** 109 BALL=.FALSE. 110 IF ((J2+2).GT.NN) GO TO 60 111 T1 =0 112 T2=0 113 T5=0 114 TT=0 115 T 1 = S(02-1 , 1) + S(02, 1 )+S(02+1 . 1)+S(02+2, 1 ) 116 T2=S(02-1,2)+S(02,2)+S(02+1.2)+S(02+2,2) 117 T5=S(J2-1,5)+S(02,5)+S(02+1,5)+S(J2+2,5) 118 TT=P(02-1,1 )*P(J2,2 )*P(02+1,3)*P(02 + 2,4) 119 PRINT 25,T1 ,T2,T5,TT 120 25 FORMAT( ' ' ,30X, 'T 1 ,T2,T5,TT' ,3(F7.3),F13.9, ' STEP 6, J2 CLOSE O') 12 1 IF (T5.GT.T1 .AND.T5.GT.T2.AND.TT.GT.0.00007500.AND.S(02-1,9).GT. 1. 122 1 57 .AND.S(J2-1, 9 ) . GT . S(02-2,9).AND.(S(J2-3, 1 ) . GT. 1 . 16.OR.S(02-3,9) 123 2.GT.1.20)) BALL=.TRUE. 124 IF (BALL) 02=02-1 I-- 125 IF (BALL) V3 = 6 O 126 . IF (BALL) GO TO 300 127 C 128 C 129 C 130 C THE DIFFERENT COMMENTS 02 =02,02 =J2+10,...,02=02-4 INDICATE THE EVE 131 C NTUAL POSITION OF J2 IF ITS ENVIRONMENT MEETS ONE OF THE CONDITIONS 132 C DESCRIBED BELOW 133 C 134 C : . . . . 02 = 02-10 135 C 136 C 137 IF ((02-10).LE.0) GO TO 50 138 IF ((02+3).GT.NN) GO TO 60 139 03=02 140 30 04=03+3 141 BALL=.FALSE. 142 T1=0 143 T2=0 144 T5=0 145 TT=0 146 DO 40 N=03,04 147 T1=T1+S(N,1) 148 T2=T2+S(N,2) 149 T5=T5+S(N,5) 150 40 CONTINUE 151 TT = P(03.1 )*P(03+1,2)*P(03+2,3)*P(03+3,4) 152 PRINT 45,T1,T2,T5,TT 153 45 FORMAT(' ',30X,'T1,T2,T5,TT',3(F7.3),F13.9,' STEP7, 02-10 , M0J2' 154 IF (T5.GT.T1.AND.T5.GT.T2.AND.TT.GE.0.00007500.AND.S(J3+1,1).LE.0. 155 1 69.AND.S(03+2,1).LE.0.69.AND.S(J3+3,1).LT.1.06.AND.S(03,1).LT.0. 156 2 98.AND.S(03-1,1).LT.0.98) 03=02-7 157 IF (T5.GT.T1.AND.T5.GT.T2.AND.TT.GE.O.00007500.AND.5(J3+1,1).LE.0. 158 1 69.AND.S(03+2,1).LE.0.69.AND.S(J3 + 3, 1 ) .LT. 1.06.AND.S(03, 1).LT.0. 159 2 98.AND.S(J3-1,1).LT.0.98) GO TO 30 160 IF (T5.GT.T1.AND.T5.GT.T2.AND.TT.GE.O.00007500.AND.03.EO.(02-7).AN 161 1 O.S(J2-8,8) .,LT . 1 . 10.AND.S(02-8 . 1 ) . LT .0.98 . AND.S(02-9,9) . LT . 1 . 10. A 162 2ND.S(02-10,9).GT.1.25.AND.S(02-10,1).GT.1.16) BALL =.TRUE. 163 IF (BALL) 02=02-10 164 IF (BALL) V3 = 7 165 IF (BALL) GO TO 300 166 C 167 C 02 = 02+10 168 C 169 C 170 C *** 8 +** 171 50 IF ((02+11).GT.NN) GO TO 60 172 BALL=. FALSE. 173 IF (M(02+1).EO.16.AND.M(J2).EQ•16.AND.M(J2+3).EQ.16.AND.M(02+8).EO 174 1 . 16 . AND.(P(J2+8, 1)*P(J2 + 9,2)*P(02 +10,3)*P(02+11,4)).GT.0.000100.A £ 175 2 ND.S(02-1, 1).GT, 1 . 16.AND.S(02+2, 1 ) .GT. 1 .01.AND.S(02 + 5, 1).GT. 1 .01 5^  176 3 .AND.S(02+6.1).GT.1.16.AND.S(02+4.1).GT.0.77.AND.S(02+7,1).GT.0. 177 4 77.AND.S(02-3,1).GT.1.13.AND.S(02-2,1).GT.1.11) BALL=.TRUE. 178 IF (BALL) 02=02+8 179 IF (BALL) V3 = 8 180 IF (BALL) GO TO 300 181 C 182 C 183 C *** g *** 184 BALL=.FALSE. 185 IF ((02+12).GT.NN) GO TO 60 186 IF (S(02,9).GT. 1 .57.AND . S(02-2, 1 ) .GT. 1 . 16.AND.S(02+10, 1 ) .GT. 1 . 16 187 1 .AND.S(02+11,7).GT. 1 .49.AND.S(02+12,7).GT. 1.58.AND.S(02 + 2, 1).GT. 1 188 2.16. AND.S(02 + 3, 1).GT. 1. 16.AND.S(02+6, 1).GT. 1. 16.AND.S(02 + 7, 1 ) .GT. 189 3 1.21.AND.S(02+8,9).GT. 1.20.AND.S(02 + 8, 1 ) .GT. 1.01.AND.S(02+9,7).GT 190 4.1. 57.AND.S(02+ 1 ,9).GT.0.98.AND.S(02+4,2).EQ.O.75.AND.S(02 + 5, 1). 191 5 GT.0.77) BALL=.TRUE. 192 IF (BALL) 02=02+10 193 IF (BALL) V3 = 9 194 IF (BALL) GO TO 300 195 C 196 C TO REPEAT THE B-TURN CHECK 197 C 198 C TO CHECK THE PRESENCE OF TURNS IN THE VICINITY OF THE HELIX BOUNDA 199 C RIES WHICH MAY FORCE THE PREDICTED BOUNDARIES TO BE MOVED TO A NEW 200 C POSITION. THIS PROCEDURE STARTS FROM POSITION 02-4 (1=0) TO 02+2 201 C (1 = 6) 202 C 203 60 1=0 204 LE=J2-4 205 70 LF=LE+3 206 IF ((LE+3).GT.NN) GO TO 210 207 HELLO=.FALSE. 208 C 209 C TO COMPARE PA (T1),PB (T2),AND PT (T5) AND TO CALCULATE THE PROBA 210 C BILITY OF B-TURN OCCURRENCE (TT) OF THE TETRAPEPTIDE LE-LF 21 1 C 212 T1=0 213 T2=0 214 T5=0 215 TT=0 216 DO 75 L = LE,LF 217 T1=T1+S(L,1) 2 18 T2=T2+S(L,2) 219 T5=T5+S(L,5) 220 75 CONTINUE 22 1 TT = P(LE, 1)*P(LE+1 ,2)*P(LE + 2,3)*P(LE + 3,4) 222 PRINT 78 , LE , T 1 ,T2,T5,TT,I 223 78 FORMAT(' ' , 10X , 'LE,T1,T2,T5.TT,I' . 15,3(F7.4,2X),F13.9,14,3X, 224 1 'B-TURN SEARCH AT C-TERMINAL') 225 IF (T5.GT.T1.AND.T5.GT.T2.AND.TT.GE.0.0O0O7500) HELLO=.TRUE. 226 C 227 C *** 1 * + * 228 IF ((J2+1).GT.NN) GO TO 80 229 IF (HELLO.AND.LE.EQ.(02+1).AND.S(J2,9).GT.1.10.AND.S(J2,1).GT.1.01 230 1 . AND.S(02+1 , 1 ) . LE . 0. 69 . AND .S(02 - 1 .9 ) . LE . S ( J2 , 9 ) . AND . S (<J2 - 1 , 1 ) . GT . 231 2 0.67.AND.((S(J2-2,5) + S(U2-1,5 ) + S(02,5 ) + S(02+ 1 ,5) ) .LT.(S(02-2, 1 ) + 232 3 S(02-1, 1) + S(02, 1) + S(02+1, 1) ) .OR.(P(d2-2, 1)*P(02-1,2)*P(02,3)*P(02 233 4 +1,4)).LT.0.00007500)) GO TO 10O 234 C 235 C * * * 2 * + * 236 IF (HELLO . AND. LE . EO . 02 . AND . S ( 02-1 , 9 ) . GT . 1 . 10. AND. S( 02- 1 , 1 ) . GT . 1 . 16 237 1 .AND.S(02,9).LT. 1 . 10.AND.S(02- 1, 1).GT.S(02, 1).AND.S(02+1, 1).LE.0. 238 2 69) GO TO 101 239 C 240 C * * * 3 * * * 24 1 80 IF (HELLO.AND.LE.EO.(02-1).AND .M(02- 1 ) . EO. 16.AND.S(02-2,9 ) .GT . 1 . 10 242 1 .AND.S(02-3,1).GT.1.16.AND.S(02,5).GT.1.19.AND.S(02+2,5).GT.1.19) 243 2 GO TO 101 244 C 245 C * * * 4 * + * 246 IF (HELLO.AND.LE.EO.(02-1).AND.S(02-2,9).GE.1.10.AND.(S(02-3,9).LT 247 1.S(02-2,9).OR.(S(02-3,9)-S(02-2,9)).LT.0.15).AND.S(02-1,9).LT.S(02 248 2 -2,9).AND.S(02+1,5).GT.1.19.AND.S(02+2,5).GT.1.19) GO TO 102 249 C 250 C * * * 5 *** 25 1 IF (HELLO.AND.LE.EO•(J2-2).AND.S(02-2,9).GT.S(J2-3,9).AND.S(02 - 3,2 252 1 ).LE.0.75.AND. S(02-2,1).GT.O.69.AND.S(02-5,2).LE.0.75) GO TO 102 253 C 254 C + * * g * * * 255 IF (HELLO.AND.LE.EO.(J2-2).AND. S(02-2,9).EO.0.98.AND.S(02 - 3, 1).GT 256 1 .1.16.AND.S(02-4, 1).GT. 1. 16.AND.5(J2-3,9).LT. 1.57.AND.S(02- 1 ,9) . 257 2 LT .5(02-2,9)) GO TO 102 258 C 25g C *** 7 *** 260 IF (HELLO.AND.LE.EQ.02.AND.(S(02,9).LT.O.98.OR.S(J2.2).GT.1.38).AN 261 1 D.(S(02- 1,2) .GT. 1 .60.OR.(S(02 - 1,9).LT. 1 . 10.AND.S(02- 1,2).GT. 1.38) 262 2 ).AND.S(02-2,9).GT.1.10.AND.S(J2-2,1).GT.1.16) GO TO 102 263 C 264 C *** 3 *** 265 IF (HELLO.AND.LE.EQ.(02-1).AND.S(02-1,9).LT.S(02-2 , 9).AND.S(02-2, 1 266 1 ) .GT. 1 . 16.AND.S(02-3, 1) .GT. 1 . 16.AND.S(02-1, 1) .LT.S(02-2, 1 ) ) GO 267 2 TO 102 268 C 269 C * * * g * * * 270 IF (HELLO.AND.LE.EQ.(02-2).AND.S(02-2,9).GT.1.10.AND.S(02-3,9).LT. 271 1 1.10.AND.S(02-4,9).LT.5(02-2,9)) GO TO 102 272 C 273 C * » * i o * * * 274 IF ((02+4).GT.NN) GO TO 90 00 275 IF (HELLO.AND.LE.EQ.(02-2).AND.M(02-2).EO.16.AND.S(02-3,9).GT.0.98 276 1 .AND.S(02-4,9).GT. 1 . 10.AND.S(02 + 2,2) .GT. 1 .38.AND.S(02- 1 ,2).GT. 1 .O 277 2 5.AND.S(02+3,2).GT.0.75.AND.S(02+4,2).GT.1.10) GO TO 102 278 C 279 C 280 90 IF (HELLO.AND.LE.EQ.02.AND.(P(02-3, 1)*P(02-2,2)*P(02-1 ,3)*P(02,4) ) 281 1 .GT.0.00007500.AND.S(02-4,9).GT.5(02-3,9).AND.S(02-4 , 9).GT. 1. 10 282 2 .AND.S(02-4,9).GT.5(02-5,9)) GO TO 104 283 C 284 C **+-12*** 285 IF (HELLO.AND.LE.EO.(02-3).AND.S(02-4. 1) . LT . 1.00.AND.S(02-3, 1).GT. 286 1 O.98.AND.S(02-4,9).GT.0.98.AND.S(02-4,9).LT.1.57.AND.S(02-2,7).GT 287 2 .1.06) GO TO 103 288 C 289 C *** 13 *** 290 IF (HELLO.AND.LE.EQ.(02- 1).AND.S(02-1 , 1 ) . LE.0.69.AND.S(02-2. 1).GT. 291 1 1 .01 .AND.S(02-2,9).GT.0.98.AND.S(02-3,9).LT. 1.57.AND.S(02- 1,5).GT 292 2 . 1 . 19.AND.S(02,5).GT.0.98.AND.S(02+1,5).GE. 1 . 56) GO TO 102 293 C 294 C * + * i ; 4 * * * 295 IF (HELLO.AND.LE.EQ.(02-1).AND.S(02-2,1).LE.O.69.AND.S(02-2,7).GT! 296 1 1.49.AND.S(02-3,9).GT.1.10.AND.S(02-3,1).GT.1.16) GO TO 103 297 C 298 C *** 15 *** 299 IF (HELLO.AND.LE.EO.(02-2).AND.S(02-3,9).GT.O.98.AND.S(d2-3,1).GT. 300 1 i .01.AND.S(02-4,9).LE.S(02-3,9).AND.(S(02-5,9)-S( 02-3,9)).LE.0.16 301 2 .AND.S(02- 1,9) .LT. 1.77.AND.S(02-2,9).LT. 1 .77.AND.S(02-1,5).GT .1.1 302 3 9 . AND.S(02-2,5).GT. 1 . 19) GO TO 103 303 C 304 C *** 16*** 305 IF (HELLO.AND.LE.EO.(02-3).AND.S(02-3,9).GT.1.57.AND.S(02-4,1).GT. 306 1 1 . 16.AND.S(02-2,7).GT. 1 . 24.AND.S(02-5, 1).GT. 1 . 16.AND.S(02- 1,1). 307 2 LE.0.69) GO TO 103 308 C 309 C *** 1 7 *** 310 IF (HELLO.AND.LE.EO.(02-2).AND.S(02-3,9).LT. 1. 10.AND.S(02-3, 1 ) . LE . 311 1 O.69.AND.S(02-4,9).GT.0.98.AND.S(02-4, 1) .GT. 1 .01 .AND. (S(02~5, 1 ) . 312 2 LT.S(02-4, 1 ) .OR . (S(02-5,9)-S(02-4,9)).LE.0. 15)) GO TO 104 313 C 314 C +** 18 *** 3 15 IF (HELLO .AND . LE.EO.(02-4).AND.S(02-4 , 1).GT. 1. 16 . AND.S(02-4,9).GT. 3 16 1 0.98.AND.S(02-5, 1 ) . LT . S(02-4, 1 ) .AND.S(02-6, 1 ) . LT.S(02-4, 1).AND. 317 2 S(02-3,9).LT.0.98) GO TO 104 318 C 319 C *** 19 *** 320 IF (HELLO.AND.LE.EO.(02-4).AND.S( J2-4, 1).GT.0.98.AND.S ( 02-5 , 9).LT . 321 1 1.1O.AND.S(02-6,9).LT.1.10) GO TO 104 322 C 3 2 3 c * * * 2 0 * * * 324 IF (HELLO.AND.LE.EO.(02-4).AND.S(02-5,9).GT.1.25.AND.S(02-5,1).GT. 325 1 1 . 16.AND.S(02-4,9).LT.5(02-5,9 ) .AND . 5(02-4 , 1).LT.S(02-5 , 1).AND.S( 326 2 02-6,9).LT.S(02-5,9)) GO TO 105 327 C 328 C *** 21 *** 329 IF ((02+2).GT.NN) GO TO 95 330 IF (HELLO.AND.LE.EQ.(02+1).AND,(S(02-3,1)+S(02-1,1)+S(02-1,1)+5(02 331 1,1 )+S(02+1, 1 )+S(02 + 2,1)).LT.(S(02-3,2)+S(02-2,2)+S(02-1,2)+S(02,2 332 2 )+S(02+1;2)+S(02+2,2)).AND.S(02-4,1).GT.1.16.AND.S(02-4,9).GT.1. 333 3 08.AND.S(02-5,9).GT.1.10) GO TO 104 334 C 335 C 336 95 IF (I.EO.O) GO TO 200 337 IF (I.EQ.1) GO TO 200 338 IF (I.EQ.2) GO TO 200 339 IF (I.EQ.3) GO TO 200 340 IF (I.EQ.4) GO TO 200 34 1 IF (I.EQ.5) GO TO 200 342 IF (I.EQ.6) GO TO 210 343 C 344 100 02=02 345 GO TO 110 346 101 02=02-1 347 GO TO 110 348 102 02=02-2 349 GO TO 110 350 103 02=02-3 o 3 5 1 GO TO 110 3 5 2 104 d 2 = d 2 - 4 3 5 3 GO TO 1 1 0 3 5 4 105 d 2 = d 2 - 5 3 5 5 GO TO 1 1 0 3 5 6 C 3 5 7 1 10 V3 = 8 0 3 5 8 GO TO 3 0 0 3 5 9 C 3 6 0 2 0 0 1 = 1 + 1 3 6 1 LE = LE+ 1 3 6 2 GO TO 7 0 3 6 3 C 3 6 4 c 3 6 5 c 3 6 6 c THE CURRENT P O S I T I O N OF J 2 MAY BE THE MOST F A V O R A B L E O N E , H E N C E I 3 6 7 c NEED TO ADJUST IT 3 6 8 c 3 6 9 c d 2 = J 2 3 7 0 c 3 7 1 c 3 7 2 c * * * 1Q * * * 3 7 3 2 10 B A L L = . F A L S E . 3 7 4 I F ( ( J 2 + 4 ) . G T . N N ) GO TO 2 2 0 3 7 5 T 1 = 0 3 7 6 T2=0 3 7 7 T 5 = 0 3 7 8 T 1 = S ( d 2 + 1 . 1 ) + S ( d 2 + 2 . 1 ) + S ( d 2 + 3 . 1 ) + S ( d 2 + 4 . 1 ) 3 7 9 T 2 = S ( d 2 + 1 , 2 ) + S ( d 2 + 2 , 2 ) + S ( d 2 + 3 . 2 ) + S ( d 2 + 4 , 2 ) 3 8 0 T 5 = S ( d 2 + 1 , 5 ) + S ( d 2 + 2 , 5 ) + S ( d 2 + 3 . 5 ) + S ( d 2 + 4 , 5 ) 3 8 1 P R I N T 2 1 5 , T 1 , T 2 , T 5 3 8 2 2 1 5 F O R M A T ( ' ' , 3 0 X . ' T 1 , T 2 , T 5 ' , 3 ( F 7 . 3 ) , ' S T E P 1 0 , <J2=J2 , M 0 J 2 3 8 3 I F ( T 5 . G T .T 1 . AND . T5 . GT . T2 . AND . S ( v J 2 , 9 ) .GT . 0 . 9 8 .AND . S (<J2 , 1 ) . GT 3 8 4 1 . A N D . S ( d 2 - 1 , 9 ) . G E . 1 . 5 7 . A N D . ( S ( J 2 - 2 . 1 ) .GT . 1 . 1 6 . O R . S ( J 2 - 2 , 9 ) . i 3 8 5 2 2 0 ) ) B A L L = . T R U E . 3 8 6 c 3 8 7 IF ( T 5 . G T . T 1 . A N D . T 5 . G T . T 2 . A N D . S ( d 2 + 1 , 1 ) . L E . 0 . 6 9 . A N D . S ( d 2 , 9 ) . I 3 8 8 1 5 7 . A N D . S ( J 2 - 1 , 9 ) . G T . 0 . 9 8 . A N D . S ( J 2 - 2 , 1 ) . G T . 1 . 16 ) B A L L = . T R U E 3 8 9 IF ( B A L L ) J 2 = J 2 3 9 0 IF ( B A L L ) V 3 = 1 0 3 9 1 I F ( B A L L ) GO TO 3 0 0 3 9 2 c ***+ 1 1 *** 3 9 3 B A L L = . F A L S E . 3 9 4 IF ( T 5 . G T . T 1 . A N D . T 5 . G T . T 2 . A N D . S ( d 2 , 9 ) . L T . 0 . 7 3 . A N D . S ( J 2 - 1 , 9 ) J 3 9 5 1 5 7 . A N D . S ( d 2 - 1 , 1 ) . G T . 1 . 0 1 . A N D . S ( d 2 - 2 , 9 ) . G T . 1 . 10) B A L L = . T R U E 3 9 6 I F ( B A L L ) d 2 = d 2 - 1 3 9 7 IF ( B A L L ) V3=11 3 9 8 I F ( B A L L ) GO TO 3 0 0 3 9 9 c 4 0 0 c * * + 12 * * * 401 BALL=.FALSE. 402 IF ((J2+6).GT.NN) GO TO 220 403 IF (S(J2 , 9).GT. 1. 10.AND.S(J2, 1 ) .GT. 1 .01.AND. S (<J2 - 1 . 9 ) . LT . S (<J2 , 9 ) . 404 1 AND . S(<J2 , 2) . GT .0. 93 . AND . S( J2+ 1 , 2 ) . GT . 1 . 05 . AND . S(J2+2 . 2 ) . GT . 1 . 38 . AN 405 2 D.S(J2+4,2).GT.O.75.AND.S(J2 + 5,2).GT. 1. 38.AND.S(J2+6,2).GT. 1 .05 ) 406 3 BALL=.TRUE. 407 IF (BALL) J2=J2 408 IF (BALL) V3=12 409 IF (BALL) GO TO 300 410 C 411 C ***13++* 412 220 IF ((J2+3).GT.NN) GO TO 230 413 BALL=.FALSE. 414 IF (S(J2,9).GT.1.10.AND.S(U2,1).GT.1.16.AND.S(J2+1,2).GT.1.38.AND. 4 15 1 S(J2- 1 , 2 ) . GT . 1 . 38 . AND ,S(<J2-2,2) . GT .1.38. AND . S( J2 + 3 . 2 ) . GT . 1 . 10. AND 416 2 . S(J2-3,2).GT. 1 .05) BALL=.TRUE. 417 IF (BALL) J2=J2 418 IF (BALL) V3=13 419 IF (BALL) GO TO 300 420 C 421 C *** 14 *** 422 230 BALL=.FALSE. 423 IF ((J2+1 ) .GT.NN) GO TO 270 424 IF (S(<J2.9).GT. 1 .57 . AND .M(J2+1).EO. 15.AND.S(J2-1,9).LT.S(J2,9) .AND h-i 425 1 . S( J2-2 , 9 ) . GT . 1 . 10. AND . (S( J2-3, 9 ) . GT . 1 . 10.OR . S( J2-3 , 1 ) . GT .0. 69 ) ) H 426 2 BALL=.TRUE. 427 IF (BALL) J2 = «J2 428 IF (BALL) V3=14 429 IF (BALL) GO TO 300 430 C 431 C *** 15 *** 432 BALL=.FALSE. 433 IF ((J2+5).GT.NN) GO TO 240 434 IF (M(J2).EO.16.AND.S(J2+1,1).LE.O.69.AND.S(U2+2,2).GT.1.38.AND. 4 35 1 S(J2+3,2).GT.1.38.AND.S(U2+4,2).GT.1.38.AND.S(J2+5.2).GT.1.38.AND 436 2 .S(J2-1,9).GT. 1 . 10.AND.S(J2-2,9).GT.1.10) BALL=.TRUE. 437 IF (BALL) U2=J2 438 IF (BALL) V3=15 439 IF (BALL) GO TO 300 440 C 44 1 C *** ng *** 442 240 BALL=.FALSE. 443 IF ((J2+4).GT.NN) GO TO 250 444 T1=0 445 T2=0 446 T1=S(U2+1. 1 ) + S(U2 + 2. 1 ) + S(J2 + 3, 1 ) + S(J2 + 4, 1) 447' " T2 = S(U2+1 , 2 )+ S ( J2 + 2 . 2 )+ S ( J2+3 , 2)+ S ( J2 + 4', 2 ) 448 PRINT 245,T1,T2 449 245 FORMATC ',30X,'T1,T2 ',2(F7.3),7X,' STEP 16 , J2=J2') 450 IF (T2 GT .T1 .AND.S(U2. 1).GT. 1. 16.AND.S(U2+1,9).LT . 1 . 10.AND.S(U2- 1 451 1 , 1 ) . LT.S(J2, 1).AND. S(02+2.2) .GT.0.75.AND.S(J2 + 3,2).GT. 1 .38.AND. 452 2 S(02+4,2).GT. 1 .38) BALL=.TRUE. 453 IF (BALL) 02 = 02 454 IF (BALL) V3=16 455 IF (BALL) GO TO 300 456 C 457 C *** -|7 *** 458 BALL=.FALSE. 459 IF (S(02, 1 ) .GT. 1 . 16.AND.S(02,9).GT. 1. 10.AND,S(02-1,9).GT. 1. 10.AND. 460 1 S(02+1,1).LE.0.69.AND.(S(J2+2,9).LT.1.10.OR.S(02 + 2,1).LT.1.06).AN 46 1 3 D.S(J2+3.9).LT . 1 . 10.AND.(S(J2+4,9).LT. 1. 10.OR.M(02 + 3).EO. 15) ) BA 462 4 LL= .TRUE. 463 IF (BALL) 02 = 02 464 IF (BALL) V3=17 465 IF (BALL) GO TO 300 466 C 467 C 468 C 02 = 02-1 469 C 470 C 47 1 C 18 *** 472 250 IF ((J2+2).GT.NN) GO TO 260 473 BALL =.FALSE. 474 IF ((P(J2 - 1 . 1)*P(02,2)*P(02+1,3)*P(J2 + 2.4)).GT.0.00007500.AND.S(02 475 1 -1,9).GT. 1 . 10.AND.S(02-1,1).GT. 1 . 16.AND.S(J2-2, 1).LT.S(02 -1 , 1 ) . AN 476 2D. S(02-2,1).GT.0.69.AND.S(J2,1).LT.1.06.AND.S(02.7).GT.0.84.AND. 477 3 S(02+1.7).GE. 1 .64) BALL=.TRUE. 478 IF (BALL) 02=02-1 479 IF (BALL) V3=18 480 IF (BALL) GO TO 300 48 1 C 482 C *** -jg *** 483 BALL=.FALSE. 484 IF ((02+3).GT.NN) GO TO 260 485 T1=0 486 T2=0 487 T5 = 0 488 T1=S(02, 1) + S(02+ 1 , 1 ) + S(02 + 2, 1) + S(02 + 3, 1 ) 489 T2 = S(02,2) + S(02+1.2) + S(02+2,2 ) + S(02 + 3.2) 490 T5=S(02,5)+S(02+1,5)+S(02+2,5)+S(02+3,5) 491 PRINT 255,T1.T2,T5 492 255 FORMAT(' ',30X, 'T1.T2.T5' ,3(F7.3), ' STEP 19 , 02-1 ,M002') 493 IF (T5.GT.T1 .AND.T5.GT.T2.AND.S(02-1,9).GE. 1.57.AND.S(02- 1 , 1).GT. 494 1 1.08.AND.S(02,9).LT.1.10.AND.S(02,2).GT.1.38) BALL=.TRUE. 495 C 496 IF (T5.GT,T1.AND.T5.GT.T2.AND,S(02,1).LE.0.69.AND.S(02-1,1).GT.1.1 497 1 6.AND.S(02-1,9).GT.1.10) BALL=.TRUE. 498 C 499 IF (T5.GT.T1 .AND.T5.GT ,T2.AND.S(02,9).LT. 1 . 10.AND.S(02, 1 ) . LT . 1 .01 500 1 .AND.S(02-1.9) .GE. 1 . 10.AND.S(02-1, 1).GT . 1 .01 ) BALL=.TRUE. 5 0 1 I F ( B A L L ) J 2 = J 2 - 1 5 0 2 I F ( B A L L ) V 3 = 1 9 5 0 3 I F ( B A L L ) GO TO 3 0 0 5 0 4 C 5 0 5 C * * * 2 0 * * * 5 0 6 B A L L = . F A L S E . 5 0 7 I F ( S( <J2 , 9 ) . LT . 1 . 1 0 . AND . S ( J 2 , 2 ) . GT . 1 . 38 . AND . S ( J 2 + 1 , 2 ) . GT . 1 . 3 8 . AND . 5 0 8 1 S ( , J2 + 2 , 2 ) . GT . 1 . 3 8 . AND . S( J 2 + 3 , 2 ) . GT . 0 . 7 5 . AND . S ( J 2 - 1 , 9 ) . GE . 1 . 57 . AND 5 0 9 2 . S ( d 2 - 2 , 9 ) . G T . 1 . 1 0 ) B A L L = . T R U E . 5 1 0 IF ( B A L L ) J 2 = J 2 - 1 51 1 I F ( B A L L ) V 3 = 2 0 5 1 2 I F ( B A L L ) GO TO 3 0 0 5 1 3 C 5 1 4 C *** 21 +•** 5 1 5 2 6 0 B A L L = . F A L S E . 5 1 6 I F ( ( J 2 + 1 ) . G T . N N ) GO TO 2 7 0 5 1 7 I F ( S ( J 2 , 1 ) . L E . 0 . 6 9 . A N D . M ( J 2 + 1 ) . E O . 1 5 . A N D . S (02 - 1 , 1 ) . G T . 1 . 0 1 . A N D . S ( 5 1 8 1 J 2 - 1 , 9 ) . G T . 1 . 1 0 . A N D . S ( U 2 - 2 . 9 ) . G E . 1 . 0 8 ) B A L L = . T R U E . 5 19 I F ( B A L L ) J 2 = J 2 - 1 5 2 0 I F ( B A L L ) V3=21 5 2 1 IF ( B A L L ) GO TO 3 0 0 5 2 2 C 5 2 3 C # * * 22 *** 5 2 4 B A L L = . F A L S E . 5 2 5 I F ( ( J 2 + 3 ) . G T . N N ) GO TO 2 7 0 5 2 6 I F ( S ( « J 2 , 9 ) . LT . 1 . 1 0 . A N D . S ( J 2 - 1 , 9 ) . G T . 1 . 1 0 . A N D . S ( U 2 - 1 , 1) . G T . 1 . 0 1 . A N 5 2 7 1 D . S(<J2 , 2 ) . GT . 1 . 3 8 . A N D . S ( J 2 + 1 , 2 ) . GT . 1 . 38 . AND . S ( U2 + 2 , 2 ) . GT . 0 . 9 3 . AND 5 2 8 2 . S ( J 2 + 3 , 2 ) . G T . 1 . 1 0 . A N D . S ( J 2 - 2 , 2 ) . G T . 1 . 3 8 ) B A L L = . T R U E . 5 2 9 I F ( B A L L ) u2=u2-1 5 3 0 I F ( B A L L ) V 3 = 2 2 5 3 1 I F ( B A L L ) GO TO 3 0 0 5 3 2 C 5 3 3 C 5 3 4 C . . . . J 2 = J2+1 5 3 5 C 5 3 6 C 5 3 7 c *** 2 3 *** 5 3 8 B A L L = . F A L S E . 5 3 9 IF ( ( J 2 + 4 ) . G T . N N ) GO TO 2 7 0 5 4 0 I F ( S(vJ2 . 9 ) . LT . 1 . 1 0 . AND . S ( J 2 + 1 , 9 ) . GT . 1 . 10 . AND . S(<J2+ 1 , 1 ) . GT . 1 . 0 1 . AN 5 4 1 1 D . S ( d 2 , 1 ) . G T . 1 . 0 1 . A N D . S ( J 2 - 1 , 1 ) . G T . 1 . 1 3 . A N D . S ( J 2 - 1 , 2 ) . L E . 0 . 7 5 . A N D 5 4 2 2 . S ( J 2 - 2 . 2 ) . L E . 0 . 7 5 . A N D . ( P ( J 2 + 1 . 1 ) * P ( U 2 + 2 . 2 ) * P ( U 2 + 3 , 3 ) * P ( J 2 + 4 . 4 ) ) 5 4 3 3 . G T . 0 . 0 0 0 1 0 0 . A N D . S ( J 2 - 2 , 1 ) . G T . 1 . 1 3 ) B A L L = . T R U E . 5 4 4 I F ( B A L L ) J 2 = d 2 + 1 5 4 5 IF ( B A L L ) V 3 = 2 3 5 4 6 I F ( B A L L ) GO TO 3 0 0 5 4 7 c 5 4 8 c *** 24 *** 5 4 9 B A L L = . F A L S E . 5 5 0 I F ( ( J 2 + 5 ) . G T . N N ) GO TO 2 7 0 551 T1=0 552 T2=0 553 T5=0 554 T1=S(J2+2, 1 )+S(J2+3 , 1 ) + S( J2+4 , 1 )+S(J2+5, 1 ) 555 T2=S(J2+2.2)+S(J2+3.2)+S(J2+4,2)+S(J2+5,2) 556 T5=S(J2+2,5)+S(J2+3,5)+S(J2+4,5)+S(J2+5,5) 557 PRINT 265.T1.T2.T5 558 265 FORMATC ' ,30X, 'T 1 ,T2,T5' ,3(F7 . 3 ) , ' STEP 24, J2+1 ,M0J2') 559 IF (T5.GT.T1.AND.T5.GT.T2 .AND.S(J2,9).GT.1.57.AND.S(J2+ 1 ,9 ) . 560 1 GT.1.20.AND.S(J2+1,1).GT.1.01) BALL =.TRUE. 561 IF (BALL) J2=J2+1 562 IF (BALL) V3=24 563 IF (BALL) GO TO 300 564 C 565 C 566 C 567 C TO CALL SUBROUTINE RMJ2 TO KEEP ON CHECKING FOR C-TERMINAL ADJUST 568 C MENT,RMJ2 IS A CONTINUATION OF THIS SUBROUTINE 569 C 570 270 CALL RMJ2 571 RETURN 572 C 573 574 C THE C-TERMINAL HAS BEEN ADJUSTED ACCORDING TO ONE OF THE SITUATIONS !_. 575 C MENTIONED ABOVE. TO PRINT OUT THE FINAL VALUES FOR J1.J2 AND TO RE H 576 C TURN TO SUBROUTINE ONE TO START THE WHOLE PROCEDURE AGAIN ^ 577 C 578 300 K3=J2 579 PRINT 301,J1,J2.V2.V3 580 301 FORMAT('0' ,20X,'EVENTUAL HELIX FROM J 1 : ' .15,5X. 'TO J2:',I5.14X, 581 1 ' *** V2,V3:',2(15),' ***<//) 582 RETURN 583 END End of F i l e 1 C 2 C 3 SUBROUTINE RMJ2 4 C 5 C 6 C 7 C 8 C 9 C RMJ2 = REMAINING OF MOVE OF J2 10 C 1 1 C 12 C 13 C 14 C 15 C 16 C PURPOSE 1 7 C TO KEEP ON CHECKING FOR OTHER POSSIBILITIES OF ADJUSTING THE C-18 C BOUNDARY OF THE PREDICTED HELIX 19 C 20 C 21 c 22 c 23 c REMARK 24 c ALL THE PARAMETERS STILL HAVE THE SAME DEFINITION AS IN THE PRE 25 c VIOUS SUBROUTINES 26 c 27 c 28 REAL S,T1,T2,A1,A2 ,T3,T4,T5,TT,P 29 INTEGER G,F,H,U,D.V1,V2.W, V3.V4,V5,V6,V7,V8,0 30 LOGICAL HELLO,BYE ,BALL,MOVE 3 1 DIMENSION S(1000,20),M(1000),H(1000),D(1000,16),P(1000,10) 32 COMMON S,T1,T2,T3,T4,T5,TT,A 1 ,A2,P,F,H,U,D,W,M,M1,M2,M3,M4,M5,M6, 33 1L.I,K,L1,L2.NZ,NY,JA,JB,JC,JD,J1.J2,KM,N1,N2,NN,J.G.K3,V1,V2,V3,V4 34 2,V5,V6,V7,Q.HELLO,BYE,BALL,MOVE 35 c 36 c 37 c .... J2 = J2-2 38 c 39 c 40 c *** 25 *** 41 BALL=.FALSE. 42 IF ((J2+2).GT.NN) GO TO 20 43 T1=0 44 T2=0 45 T5=0 46 T1=S(J2-1, 1 ) + S(J2, 1 ) + S(J2+1, 1 ) + S(J2+2, 1 ) 47 T2=S(J2-1,2)+S(J2,2)+S(J2+1,2)+S(J2+2,2) 48 T5=S(J2-1,5)+S(J2,5)+S(J2+1,5)+S(J2+2.5) 49 PRINT 5,T1,T2,T5 50 5 FORMAT(' ',30X,'T1,T2,T5',3(F7.3),' STEP 25, J2-2 , RMJ2') 51 IF (T5.GT.T1.AND.T5.GT.T2.AND.S(J2-2,9).GE. 1 . 57 .AND.S(J2-2.1).GT. 52 1 1 .08.AND.((S(J2-1, 1 ) . LT.S(J2-2,1).AND.S(J2-1.9).LT. 1 . 10).OR.S(J2-53 2 1,9).LE.S(J2-2,9)).AND.S(U2-1,5).GT. 1 . 19.AND.S(J2 + 2,5).GT. 1 .43.AN 54 3 D.S(J2+3.1).LT.1.06.AND.S(J2+4.1).LT.1.06) BALL=.TRUE. 55 IF (T5.GT.T1 .AND.T5.GT.T2.AND.S(J2- 1,9).LT.0.98.AND.S ( J2-2 . 9).GT. 56 1 1 . 10.AND.S(J2-2. 1 ) .GT.S(J2-1. 1 ) .AND.S(J2- 3,9).GT. 1 . 10.AND.S(J2.9) 57 2 .LT.0.98) BALL=.TRUE. 58 IF ((J2 + 3 ) .GT.NN) GO TO 10 59 IF (T1.LT.T2.AND.S(J2,2).GT.1.37.AND.S(J2-1,2).GT.1.37.AND.S(J2+1, 60 1 2) .GT. 1 .38.AND.S(U2-2, 1).GT. 1 . 16.AND.S(J2 + 3. 1 ) .LE.0.69) BALL = 61 3 .TRUE. 62 10 IF (BALL) J2=J2-2 63 IF (BALL) V3=25 64 IF (BALL) GO TO 300 65 C 66 C *** 26 *** 67 BALL=.FALSE. 68 IF (T5.GT.T 1 .AND.T5.GT.T2.AND.S(J2-3,9).GT. 1 . 10.AND.S(J2-3,1).GT. 69 1 1 . 16.AND.S(J2-2.9) .LT. 1. 10.AND.S(J2- 1,9).LT.S(02-3.9).AND.S(02-1, 70 2 1 ) . LT . 1 .01 . AND . S (<J2 , 5) . GT .1.52. AND . S( J2+1 ,5) . GT . 1 . 46 . AND . S(J2 - 1 , 5 7 1 3 ).GT.1.14) BALL=.TRUE. 72 IF (BALL) J2=J2-3 73 IF (BALL) V3=26 74 IF (BALL) GO TO 300 i _ ! 75 C l _ i 76 C *** 27 *** CTi 77 BALL=.FALSE. 78 IF ((J2+3).GT.NN) GO TO 20 79 IF (S(d2-2,9) .GT.S(U2,9) . AND . S( J2-2 , 9).GT.S(J2-3,9).AND.S(J2-1 ,2 ) 80 1 .GT. 1 .38.AND.S(J2+1 ,2) .GT. 1 .38.AND.S(U2 + 2,2 ) .GT. 1 .38.AND.S(J2 + 3,2 81 2 ) .GT. 1.38.AND.S(U2-2.2).LE.0.75) BALL= . TRUE. 82 IF (BALL) J2=J2-2 83 IF (BALL) V3=27 84 IF (BALL) GO TO 300 85 C 86 Q * * * 28 * * * 87 BALL=.FALSE. 88 T1=0 89 T2=0 90 T1=S(J2-1, 1 ) + S(J2, 1 ) + S(J2+1, 1 ) + S(J2 + 2. 1 ) + S(J2 + 3, 1) 91 T2=S(J2-1,2)+S(J2,2)+S(J2+1,2)+S(J2+2,2)+S(J2+3,2) 92 PRINT 15.T1.T2 93 15 FORMAT(' ',30X,'T1,T2 ' ,2(F7 . 3) ,7X. ' STEP 28. J2-2, RMJ2') 94 IF (T2.GT.T 1 .AND.S(J2- 1 ,2) .GT. 1 .38.AND.S(02-1.9) .LT. 1 . 10.AND.S(J2-95 12,9) .GT.O.98.AND.S(J2-2, 1).GT.1.01.AND.S(J2-3,9).LT.S(J2-2,9).AND 96 2 .S(J2,2).GT.1.38) BALL=.TRUE. 97 IF (BALL) J2=U2-2 98 IF (BALL) V3=28 99 IF (BALL) GO TO 300 100 C 101 C * + * 29 + * * 102 20 BALL =.FALSE. 103 IF ((J2+ 1 ) .GT.NN) GO TO 60 104 IF (S(J2.9) .LT.0.98.AND. M(U2+1) .EO. 1 5 . AND . S (02 - 2 . 9 ) . GT . 1 ,57.AND.S( 105 1 J2-1,2).GT. 1 .38.AND.S(J2-3,9).LT,S(J2-2.9)) BALL=.TRUE . 106 IF (BALL) J2=J2-2 107 IF (BALL) V3=29 108 IF (BALL) GO TO 300 109 C 1.10 C * * * 30 *** 1 1 1 BALL=.FALSE. 1 12 IF (S(J2-2,9) ,GE. 1 . 10.AND.S(J2- 1.2).GT. 1.38.AND.S(J2- 1,9 ) . LT . 1 . 10 1 13 1 .AND.M(J2+1).EQ.15.AND.S(J2,2).GT.0.75) BALL=.TRUE. 1 14 IF (BALL) J2=J2-2 1 15 IF (BALL) V3=30 1 16 IF (BALL) GO TO 300 1 17 C 1 18 C 1 19 C 120 C .... J2 = -J2 + 2 121 C 122 C 123 C + * * 31 * + * 124 BALL=.FALSE. 125 IF ((K+1).GT.KM) GO TO 30 126 IF ( S (02 , 9 ) . GT . 1.25. AND . S ( J2+2 , 9 ) . GT . 1 . 20 . AND . S( <J2+2 , 1 ) . GT . 1 .01 . A 127 1 ND.M(J2+1).NE. 15.AND.S(<J2-1,9).GE.S(02,9).AND. (U2 + 3).GE.H(K+1) ) 128 2 BALL=.TRUE. 129 IF (BALL) J2=J2+2 130 IF (BALL) V3=31 131 IF (BALL) GO TO 300 132 C 133 c * * * 32 * * * 134 BALL=.FALSE. 135 IF (S(U2,9).GT.1.10.AND.S(J2+2,9).GT.1.57.AND.M(J2+1).NE.15.AND.S 136 1 (02-1,9).LE.S(J2 + 2,9).AND.(J2 + 3).GE,H(K+1)) BALL=.TRUE . 137 IF (BALL) J2=U2+2 138 IF (BALL) V3 = 32 139 IF (BALL) GO TO 300 140 c 14 1 c * * * 33 *** 142 30 IF ((J2 + 6 ) .GT.NN) GO TO 40 143 BALL=.FALSE. 144 IF (S(U2.9).LT.1.25.AND.S(d2+4,9).GT.1.57.AND.S(J2+5,7).GT.1.49.AN 145 1 D.S(J2+1,1).GT.1.01.AND.S(J2+2,1).GT.1.16.AND.S(J2+3,1).GT.1.08 146 2 .AND.S(J2 + 3, 1 ) . LT . 1.57.AND.S(02+2,2).LT.0.87.AND.S(J2+6.2).LT.0.7 147 3 4.AND.S(J2- 1 , 1).GT.1.16) BALL=.TRUE. 148 IF (BALL) U2=U2+4 149 IF (BALL) V3=33 150 IF (BALL) GO TO 300 151 C 152 C ***34**+ 153 40 BALL=.FALSE. 154 IF ((K+1).GT.KM) GO TO 50 155 IF (S(02,9).GT.0.98.AND.S(<J2, 1).GT. 1 .01 .AND.S(02+2,9),GT.S(J2,9) 156 1 .AND.S(J2 + 2, 1) .GT. 1 . 16.AND.M(02+1) .NE. 15.AND.(02+3) .GE.H(K+1) ) 157 2 BALL =.TRUE . 158 IF (BALL) 02=02+2 159 IF (BALL) V3 = 34 160 IF (BALL) GO TO 300 161 C 162 C *** 35 +** 163 50 BALL=.FALSE. 164 IF ((02+4).GT.NN) GO TO 60 165 ' IF (S(02.9).GE.1.57.AND.S(J2+2,9).GT.1.10.AND.S(02 + 2,1).GT.1.16.AN 166 1 D . S(J2+1, 1).GT. 1.01.AND.S(J2+1,9) .GT.0.98.AND.S(02 + 3,9).LT . 1 . 10. 167 2 AND.S(02+4.1).LE.O.69) BALL =.TRUE. 168 IF (BALL) 02=02+2 169 IF (BALL) V3=35 170 IF (BALL) GO TO 300 17 1 C 172 C * * * 36 * * * 173 BALL=.FALSE. 174 IF ((02+6).GT.NN) GO TO 60 I—1 175 IF (S(02,9).GT. 1. 10.AND.S(02 + 2,9).GT. 1 . 10.AND.S(02 + 2, 1 ) .GT . 1 . 16 . AN M 176 1 D.M(02+1).NE.15.AND.(P(02+3,1)*P(02+4,2)*P(02+5,3)*P(02+6,4)).GT. 00 177 2 0.000100.AND.S(02- 1 .9) .LT. 1 . 10.AND.S(02-2.9) .GE. 1 .57) BALL=.TRUE. 178 IF (BALL) 02=02+2 179 IF (BALL) V3=36 180 IF (BALL) GO TO 300 181 C. 182 C *** 37 *** 183 BALL=.FALSE. 184 IF (S(02,9).GE.1.10.AND.S(02+2,9).GE.S(02,9).AND.M(02+1).NE.15.AND 185 1 .S(02-1, 1).GT. 1.06.AND.(P(02+3, 1)*P(02+4,2)*P(02+5,3)*P(02+6 , 4) ) 186 2 .GT.0.000100) BALL=.TRUE. 187 IF (BALL) 02=02+2 188 IF (BALL) V3=37 189 IF (BALL) GO TO 300 190 C 191 C *** 3g +** 192 BALL=.FALSE. 193 IF ((P(02+3,1)*P(02+4,2)*P(02+5,3)*P(02+6,4)).GT.0.00007500.AND.M( 194 1 02+ 1 ) .NE. 15.AND.S(02,9).GT.0.98.AND.S(02 + 2,9).GT. 1.24.AND.S(02 + 2. 195 2 1).GT. 1 .01 .AND.S(02-1,9).GT. 1 .57.AND.S(02 + 3.9).LT. 1. 10) BALL = 196 3 .TRUE. 197 IF (BALL) 02=02+2 198 IF (BALL) V3=38 199 IF (BALL) GO TO 300 200 C 201 C 202 C J2 = 02-3 203 C 204 C 205 C * + * 3 9 * * * 206 60 BALL =.FALSE . 207 IF (S(02,9).LT.1.10.AND.M(02-2).EO.15.AND.S(02-3,9).GT.0.98.AND.S( 208 1 02-4,9) .GT.0.98.AND.S(02+1,9).LT. 1 .77 .AND.S(02-3. 1 ) .GT. 1 . 16) 209 2 BALL=.TRUE. 210 IF (BALL) 02=02-3 21 1 IF (BALL) V3=39 212 IF (BALL) GO TO 300 213 C 2 14 C * * * 4 0 * * * 215 BALL=.FALSE. 2 16 IF ((02+1).GT.NN) GO TO 90 217 IF (S(02, 2) .GT . 1 . 19 .AND . S ( 02 - 1 , 2 ) . GT . 1 . 19 . AND . S ( 02-3 , 2 ) . GT . 1 . 38 . A 2 18 1 ND . S(02+1 ,2).GT. 1 .38.AND.S(02,9).LT. 1.24.AND.S(02-3,9).GT. 1 . 57 . AN 2 19 2 D.S(02-4,9).GT.1.10) BALL=.TRUE. 220 IF (BALL) 02=02-3 22 1 IF (BALL) V3=40 222 IF (BALL) GO TO 300 223 C 224 C * * * 4 -| * + * 225 BALL=.FALSE. 226 T1=0 227 T2=0 228 T5=0 229 T1=S(02-2,1) + S(02-1.1) + S(02,1 ) + S(02+1 , 1 ) 230 T2 = S(02-2,2) + S(02-1,2)+S(02,2 )+S(02+1,2) 23 1 T5=S(02-2,5)+S(02-1,5)+S(02,5)+S(02+1,5) 232 PRINT 65,T1,T2,T5 233 65 FORMAT( ' ' ,30X, 'T 1 ,T2,T5 ' ,3(F7 . 3 ) , ' STEP 41, 02-3 , RM02 ' ) 234 IF (T5.GT.T1 .AND.T5.GT.T2.AND.S(02-3,9).GT.0.98.AND.S ( 02-3, 1) .GT. 1 235 1 .01.AND.S(02-4,9).LT.1.77.AND.S(02-5,9).LT.1.77.AND.S(02-3,9).GT. 236 2 S(02-2,9).AND.S(02+2,5).GT.0.96.AND.S(02.5).GT.O.96.AND.S(02-1,5) 237 3 .GT.1.19) BALL=.TRUE . 238 IF (T5.GT.T1.AND.T5.GT.T2.AND.S(02-3,9).GE.1.10.AND.S(02-3,1).GT. 239 1 1.13.AND.S(02- 4,1).GT.0.69.AND.S(02-5,1).GT.1.16.AND.M(02+1).EO. 240 2 15.AND.S(02-2,7).GE. 1 .64.AND.S(02- 1,7).GT. 1.24.AND.S(02,9).LT. 1. 24 1 3 10) BALL=.TRUE. 242 IF (BALL) 02=02-3 243 IF (BALL) V3=41 244 IF (BALL) GO TO 300 245 C 246 C + * * 4 2 * + rr 247 BALL=.FALSE. 248 IF ((02+2).GT.NN) GO TO 90 249 IF (S(02,2) .GT. 1 .30.AND.S(02- 1,2).GT. 1 .30.AND.M(02-2).EO. 1.AND.S(0 250 1 2+1,2) GT.1.38.AND.M(02+2).EO.1.AND.S(02-3,9).GT.1.10)BALL=.TRUE. 251 IF (BALL) J2=J2-3 252 IF (BALL) V3=42 253 IF (BALL) GO TO 300 254 C 255 C 256 C ... J2 = J2 + 3 257 C 258 C 259 C * * * 43 .+ * * 260 BALL=.FALSE . 261 IF ((02+4).GT.NN) GO TO 80 262 IF (S(J2,9).LT. 1 . 10.AND.S(J2- 1 ,9).LT. 1 . 10.AND.S(U2 +1 ,9) .LT. 1 . 10.AN 263 1 D.S(J2+2,9).GT.0.98.AND.S(J2+3,9).GT.0.98.AND.S(J2 + 3. 1).GT. 1. 16. 264 2 AND.S(J2+1,1).GT.0.69) BALL=.TRUE. 265 IF (BALL) U2=J2+3 266 IF (BALL) V3=43 267 IF (BALL) GO TO 300 268 C 269 C *** 44 *** 270 BALL=.FALSE. 271 IF (S(J2,9).GT.1.25.AND.S(J2+3,9).GT.0.98.AND.S(J2+3,1).GT.1.16.AN 272 1 D.S(J2+1,9).LT.S(U2+3,9).AND.S(J2+2,9).LT.S(U2+3,9).AND.S(J2+4,7) 273 2 .GT. 1.58.AND . S(J2+1 . 1).GT.0.67.AND.S(J2 + 2, 1).GT.0.67) BALL=.TRUE . 274 IF (BALL) J2=U2+3 275 IF (BALL) V3=44 276 IF (BALL) GO TO 300 277 C 278 C + * * 4 5 * * * 279 BALL=.FALSE . 280 IF ( S (<J2 , 9 ) . GT . 1 . 20. AND. S(d2 + 3,9) . GT . 1 . 24 . AND . S( J2+3, 1 ) . GT . 1 . 01 . AN 281 1 D.S(J2+4,7).GT. 1 .58.AND.S(U2 + 5,7).GT. 1.58.AND.S(J2+1, 1 ) . LT.S(J2 + 3 282 2 ,1).AND.S(d2+2,9).LT.S(U2+3.9)) BALL=.TRUE. 283 IF (BALL) J2=J2+3 284 IF (BALL) V3=453 285 IF (BALL) GO TO 300 286 C 287 C *** 4g *** 288 BALL=.FALSE. 283 IF (S(U2,9).GT.0.98.AND.S(U2+3,9).GT.1.25.AND.S(U2+3,1).GT.1.16.AN 290 1 D . S(J2+2,9).LT.S(J2 + 3.9).AND.S(J2+1,9).LT.S(J2 + 3,9).AND.S(J2 + 4.7) 291 2 .GT. 1.58.AND.S(J2-1,9) .LT.S(J2+3,9) ) BALL=.TRUE. 292 IF (BALL) J2=J2+3 293 IF (BALL) V3=46 294 IF (BALL) GO TO 300 295 C 296 C *** 47 *** 297 BALL=.FALSE . 298 IF ((K+1).GT.KM) GO TO 70 299 IF (S(J2,9).LT . 1. 10.AND.S(02 + 3,9).GT. 1.57.AND.S(J2+2,9).GE.S(d2+3, 300 1 9) . AND.S(J2+1,9) .LT . 1. 10.AND,M(U2+1).NE. 15.AND.S(J2+4,7).GT.0.96 301 2 .AND.S(02-1,9).GT.0.98.AND.(02+3).GE.H(K+1)) BALL =.TRUE. 302 IF (BALL) 02=02+3 303 IF (BALL) V3=47 304 IF (BALL) GO TO 300 305 C 306 C *** 48 *** 307 BALL=.FALSE. 308 IF (S(02,9) .LT . 1.25.AND.S(02 + 3,9).GT.S(02,9 ).AND.S(J2 + 3, 1 ) . GT .1.16 309 1 .AND.(J2+4).GE.H(K+1).AND.M(02+1).NE.15.AND.S(J2+2,1).GT.0.69.AND 310 2 .S(02- 1 , 1 ) .GT.1.01) BALL=.TRUE. 311 IF (BALL) 02=02+3 312 IF (BALL) V3=48 313 IF (BALL) GO TO 300 314 C 315 C *** 49 *** 316 ' 70 BALL=.FALSE. 317 IF ((02+5).GT.NN) GO TO 80 318 IF (S(02,9).LT.1.25.AND.S(02+3,9).GT.S(J2.9).AND. S(02 + 3, 1).GT. 1 .08 319 1 .AND. S(02 + 2,9).LT.S(J2+3.9).AND.S(<J2+1, 1 ) . LT.S(02 + 3, 1).AND.S(02 + 4 320 2 , 1 ) .LE.0.69.AND.S(02+5.7) GT. 1 .58) BALL=.TRUE. 321 IF (BALL) 02=02+3 322 IF (BALL) V3 = 49 323 IF (BALL) GO TO 300 324 C ,_, 325 C *** 50 *** K) 326 BALL=.FALSE. 1 - 1 327 IF ( (K+1 ).. GT. KM) GO TO 80 328 IF (S(J2.9).GT. 1 .25.AND.S(J2+1, 1 ) .GT. 1 .01 .AND.S(02 + 2, 1).GT. 1.06.AN 329 1 D.S(02 + 3, 1) .GT. 1 . 16.AND.S(02 + 4, 1) .GT. 1 . 13.AND.S(02- 1 , 1 ) .GT. 1 . 16.A 330 2 ND.S(02-2, 1 ) . GT. 1.01.AND.S(02-3, 1 ) .GT. 1 . 16.AND.(02 + 5).GE.H(K+1)) 331 3 BALL =.TRUE. 332 IF (BALL) 02=02+3 333 IF (BALL) V3=50 334 IF (BALL) GO TO 300 335 C 336 C *** 51 *** 337 80 BALL=.FALSE. 338 IF ((02 + 3).GT.NN) GO TO 90 339 IF (S(J2.9).GT.1.57.AND.S(02+3.9).GE.S(02,9).AND.S(02+2.9).GE.S(02 340 1 ,9) . AND.S(02+1,9).LT. 1 .57.AND.S(02+4,9).LT. 1 .57.AND.M(02+1 ) .NE . 15 341 2 .AND.S(02+2.1).GT.1.16.AND.S(02+3,1).GT.1.16) BALL=.TRUE. 342 IF (BALL) 02=02+3 343 IF (BALL) V3=51 344 IF (BALL) GO TO 300 345 C 346 C *** 52 *** 347 BALL=.FALSE. 348 IF ( (K+1).GT.KM) GO TO 90 349 IF (S(02,9 ) .LT. 1 .25.AND.S(02 + 3.9) .GT.S(02,9).AND.S(02 + 3, 1).GT. 1 .08 350 1 .AND.S(02 + 2,9).LT.S(02 + 3,9).AND.S(02+1, 1 ) . LT.S(02 + 3, 1 ) .AND.S(02-1 351 2 ,9).LT.S(d2+3,9).AND.(J2+3).GE.H(K+1)) BALL=.TRUE . 352 IF (BALL) d2=d2+3 353 ' IF (BALL) V3 = 52 354 IF (BALL) GO TO 300 355 C 356 C 357 C d2 = J2-4 358 C 359 C 360 - C *** 53 *** 361 90 BALL=.FALSE. 362 IF ((J2-6) .LE.O) GO TO 100 363 IF ((P(J2-4,1)*P(d2-3,2)*P(d2-2,3)*P(d2-1,4)) .GT.0.00007500.AND. 364 1 S(J2-1,9) .LT.O.98.AND.S(02-2,9).LT.0.98.AND.M(d2-5).EO.12.AND.S(J 365 2 2-4,9).LT . 1.57.AND.S(J2-6,9).LT. 1 . 77) BALL=.TRUE. 366 IF (BALL) d2=d2-5 367 IF (BALL) V3 = 53 368 IF (BALL) GO TO 300 369 C 370 C *** 54 *** 37 1 BALL=.FALSE. 372 T1=0 373 T2=0 374 T5 = 0 375 T1=S(J2-4, 1 ) + S(J2-3, 1 ) + S(J2-2. 1)+S(d2-1, 1) 376 T2=S(J2-4, 2)+S(d2-3.2)+S(d2-2,2)+S(J2-1,2) 377 T5=S(J2-4. 5)+S(d2-3,5)+S(d2-2,5)+S(d2-1.5) 378 PRINT 95. T 1 , T2,T5 379 95 FORMAT(' ' ,30X, 'T1 ,T2,T5' ,3(F7.3) , ' STEP 54, J2-4 ,RMJ2' ) 380 IF (T5.GT. T1.AND.T5.GT.T2.AND.S(d2-5,9).GT.0.96.AND.S(J2-5,1).GT. 381 1 1.01.AND. S(d2-6.9).LT.S(J2-5.9) .AND.S(J2-6, 1 ) .LT.S(J2-5 , 1)) BALL 382 2 =.TRUE. 383 IF (BALL) J2=U2-5 384 IF (BALL) V3 = 54 385 IF (BALL) GO TO 300 386 C 387 C *** 55 *** 388 100 IF ((J2-5) .LE.0) GO TO 110 389 BALL=.FALSE. 390 T1=0 391 T2=0 392 T5 = 0 393 T1=S(u2-3, 1)+S(J2-2,1)+S(J2-1,1)+5(d2,1) 394 T2=S(J2-3. 2)+S(d2-2,2)+S(d2-1,2)+S(d2,2) 395 T5=S(J2-3, 5)+S(d2-2,5)+S(d2-1,5)+S(d2,5) 396 PRINT 105, T1.T2.T5 397 105 F0RMAT(' ' ,30X.'T1,T2,T5',3(F7.3),' STEP 55, d2-4 ,RMJ2') 398 IF (T5.GT. T1 .AND.T5.GT.T2 .AND.S(d2-3, 1).LE.0.69.AND.S(d2-4 . 1 ) 399 1 .GT.1.16. AND.S(d2-4,9).GT.1.10.AND.S(d2-5,1).GT.1.01.AND.S(d2-5,9 400 2 ).LT.S(d2 -4,9)) BALL= . TRUE . 401 C *** 12 *** 402 IF (T5 .GT .T1 . AND . T5 . GT . T2 . AND . S (<J2 -3 , 1 ) . LE .0.69 . AND . S( J2-4 , 1 ) . GT . 403 11.01.AND.S(J2-4,9).GT.0.96.AND.S(J2-5,9).GT.1.10) BALL=.TRUE. 404 IF (BALL) J2=J2-4 405 IF (BALL) V3=55 405 IF (BALL) GO TO 300 407 C 408 C 409 C .... J2 = <J2-5 4 10 C 4 1 1 C 4 1 2 C * * * 56 * * * 413 IF ((J2-7).LE.0) GO TO 110 4 14 BALL=.FALSE. 415 IF (S(02,2).GT.1.47.AND.S(J2-1,2).GT.1. 47.AND.S(J2-2,2).GT.1.37.AN 4 16 1 D.S(J2-4,2),GT. 1.47.AND.S(J2-3,2).GT. 1.47.AND.S(J2-5, 1) . GT . 1 . 1 1 . A 417 2 ND.S(J2-5.9).GT.1.01.AND.S(J2-5,2).LE.0.75.AND.S(U2-6,2).LE.0 . 75 4 18 3 .AND.S(02-7, 1).GT.1.11.AND.S(J2+1, 1).LE.0.69.AND.S(J2 + 2, 1 ).LE .0.6 4 19 4 9.AND.S(J2+3, 1).LE.0.69) BALL =.TRUE. 420 IF (BALL) J2=J2-5 421 IF (BALL) V3=56 422 IF (BALL) GO TO 300 423 C 424 C 425 C .... J2 •= J2 + 4 426 C 427 C 428 110 IF ((J2+5).GT.NN) GO TO 130 429 C 4 30 C * * * 57 * * * 431 BALL=.FALSE . 432 IF (S(J2,9) .LT. 1 . 10.AND.S(J2, 1).GT.0.69.AND,S(J2 + 4,9).GT.S(J2. 9) . A 433 1 ND.S(J2+1,9).LT.S(U2+4,9).AND.S(J2+2,9).LT.S(J2+4.9) 434 2 .AND.S(J2+5,9).LT.S(J2+4.9).AND.S(J2+1.1).GT.1.01.AND.S(U2+2 , O 435 • 3 .GT.1.08 .AND.M(J2+3).NE.15.AND.S(J2-1,9).GT.1.10.AND.S(J2+3, 9) . 436 4 LT.S(J2 + 4.9)) BALL= . TRUE. 437 IF (BALL) J2=J2+4 438 IF (BALL) V3=57 439 IF (BALL) GO TO 300 440 C 44 1 C *** 58 442 BALL=.FALSE. 443 IF (S(J2,9).LT. 1 .25.AND.S(J2 + 4,9).GT.S(U2,9).AND.S(J2 + 4, 1 ) .GT. 1.16 444 1 .AND.S(«J2+5,7) .GT. 1.58.AND.S(U2+4,9).GT.S(J2 + 3.9).AND.S(J2 + 3, 1) 445 2 . GT . 1 .01 . AND. S( J2 + 2 , 1 ) . GT . 0 . 69 . AND . S (<J2+ 1 , 1 ) . GT .0.67 . AND . S ( J2 -1,9 446 3 ).GT.1.10) BALL=.TRUE. 447 IF (BALL) U2=J2+4 448 IF (BALL) V3=58 449 IF (BALL) GO TO 300 450 C 451 C * * * 5 9 * + * 4 5 2 ' BAI_L= . FALSE . 4 5 3 I F ( S ( J 2 , 9 ) . L T . 1 . 1 0 . A N D . S ( J 2 , 1 ) . G T . 0 . 6 9 . A N D . S ( J 2 + 4 , 9 ) . G T . 1 . 0 8 . AND . 4 5 4 1 S( J2+4 , 1 ) . GT . 1 . 16 . AND . S(<J2 + 3 , 1 ) . GT . 0 . 69 . AND .S (U2+2 , 1 ) . GT . 0 . 69 . AND 4 5 5 2 . M ( J 2 + 1 ) . N E . 1 5 . A N D . S ( J 2 + 5 , 9 ) . L T . S ( J 2 + 4 , 9 ) . A N D . S ( J 2 + 2 , 9 ) . G T . 0 . 98 . AN 4 5 6 3 D . S ( U 2 + 3 , 9 ) . G T . 0 . 9 8 . A N D . S ( « J 2 - 1 , 9 ) . G T . 1 . 1 0 ) BALL= .TRUE . 4 5 7 I F ( B A L L ) J2=U2+4 4 5 8 I F ( B A L L ) V3=59 4 5 9 I F ( B A L L ) GO TO 3 0 0 4 6 0 C 46 1 C + * + 6 0 * * * 4 6 2 I F ( ( K + 1 ) . G T . K M ) GO TO 120 4 6 3 BALL= . FALSE . 4 64 T1=0 4 6 5 T2 = 0 4 6 6 T5 = 0 4 6 7 TT = 0 4 6 8 T1=S (J2+1 , 1 ) + S ( J 2 + 2 , 1) + S ( U 2 + 3, 1 )+S(U2+4, 1 ) 4 6 9 T2 = S ( J 2 + 1 , 2 ) + S ( J 2 + 2 ,2 )+ S ( J 2 + 3 , 2 )+ S ( J 2 + 4 , 2 ) 4 7 0 T 5 = S ( J 2 + 1 , 5 ) + S ( J 2 + 2 , 5 ) + S ( J 2 + 3 , 5 ) + S ( J 2 + 4 . 5 ) 471 T T = P ( J 2 + 1 , 1 ) * P ( d 2 + 2 , 2 ) * P ( U 2 + 3 , 3 ) * P ( J 2 + 4 , 4 ) 4 7 2 PR INT 1 1 5 , T 1 , T 2 , T 5 , T T 4 7 3 1 15 FORMAT( ' ' , 3 0 X , ' T 1 , T 2 , T 5 , T T ' , 3 ( F 7 . 3 ) , F 1 3 . 9 , ' STEP 6 0 , J2+4 , R M J 2 ' : 4 7 4 C 4 7 5 I F ( ( T 5 . L T . T 1 . O R . T 5 . L T . T 2 ) . A N D . T T . L T . 0 . 0 0 0 0 7 5 0 0 . A N D . S ( J 2 - 1 , 9 ) . GE . 1 . 4 7 6 1 1 0 . A N D . S ( J 2 , 9 ) . L T . 1 . 1 0 . A N D . S ( J 2 , 1 ) . G T . 0 . 6 9 . A N D . S ( J 2 + 4 , 9 ) . G T . 1 .08 4 7 7 2 . A N D . S ( U 2 + 4 , 1 ) . G T . 1 . 1 6 . A N D . S ( J 2 + 3 , 1 ) . G T . 0 . 6 9 . A N D . S ( J 2 + 2 , 1 ) . G T . 1 . 1 6 4 7 8 3 .AND.M(U2+1 ) .NE . 1 5 . A N D . ( U 2 + 5 ) . G E . H ( K + 1 ) ) BALL=.TRUE . 4 7 9 I F ( B A L L ) U2=J2+4 4 8 0 I F ( B A L L ) V3=60 481 IF ( B A L L ) GO TO 3 0 0 4 8 2 C 4 8 3 C * * * 61 * * * 484 B A L L = . F A L S E . 4 8 5 I F ( S ( J 2 . 9 ) . L T . 1 . 2 5 . A N D . S ( J 2 + 4 . 9 ) . G T . S ( U 2 , 9 ) . A N D . S ( J 2 + 4 , 1 ) .GT . 1 . 1 6 4 8 6 1 . A N D . S ( U 2 + 5 , 7 ) . G T . 1 . 2 4 . A N D . S ( J 2 + 1 , 1 ) . G T . 0 . 9 8 . A N D . S ( J 2 + 2 , 1 ) . G T . 1 . 0 4 8 7 2 1 . A N D . S ( J 2 + 3 , 1 ) . G T . 1 . 0 1 . A N D . S ( J 2 + 2 , 7 ) . L T . 0 . 9 6 . A N D . S ( J 2 + 3 , 7 ) . LT . 0 . 4 8 8 3 9 6 . A N D . ( J 2 + 4 ) , G E . H ( K + 1 ) . A N D . S ( J 2 - 1 , 9 ) . G T . 1 . 1 0 ) BALL= .TRUE . 4 8 9 I F ( B A L L ) U2=J2+4 4 9 0 I F ( B A L L ) V3=61 491 I F ( B A L L ) GO TO 3 0 0 4 9 2 C 4 9 3 C * + * 62 * * * 494 120 B A L L = . F A L S E . 4 9 5 I F ( ( U2+6 ) . GT . NN) GO TO 130 4 9 6 I F ( S ( J 2 , 9 ) . L T . 1 . 2 5 . A N D . S ( U 2 + 4 , 9 ) .GT. 1 . 5 7 . A N D . S ( J 2 + 5 , 7 ) . G T . 1. 49 . AN 497 1 D . S ( J 2 + 1 , 1 ) . G T . 1 . 0 1 . A N D . S ( J 2 + 2 . 9 ) . G E . S ( J 2 + 3 , 9 ) . A N D . S ( J 2 + 3 , 1 ) . L E . O 4 9 8 2 . 6 9 . A N D , M ( U 2 + 3 ) . N E . 1 5 . A N D . S ( J 2 + 6 , 7 ) . G T . 1 . 5 8 ) BALL= .TRUE . 4 9 9 I F ( B A L L ) J2=J2+4 5 0 0 I F ( B A L L ) V3=62 501 IF (BALL) GO TO 300 502 C 503 C *** 63 +** 504 BALL = . FALSE . 505 IF (S(J2.9).GE. 1 .57.AND.S(02, 1 ) .GT. 1. 16.AND.M(02+1).NE. 15.AND.S(J2 506 1 +2,9).GE.S(02,9).AND.S(02+3, 1 ) . GT . 1 . 16.AND.S(02+4, 1).GT. 1. 16.AND. 507 2 S(J2+4,9).GT. 1 . 10.AND.S(02+5,7).GT. 1 .58.AND.S(J2+6. 1) .LE.0.69) 508 3 BALL=.TRUE. 509 IF (BALL) 02=02+4 5 10 IF (BALL) V3=63 51 1 IF (BALL) GO TO 300 512 C 513 C *** g 4 *** 514 BALL =.FALSE. 515 IF (S(02,1). GT .1.13.AND.S(02,9) . GT . 1 . 10.AND.S(02-1 , 1).GT.1.16.AND. 5 16 1 S(J2-2,1).GT.1.16.AND.S(J2-4,2).LT.0.55.AND.S(02 + 4,t).GT.1.16.AND 517 2 .S(J2+5,1).LE.0.69.AND.S(J2+6.1).LE.0.69.AND.S(J2+3,1).GT.1.16.AN 518 3 D.S(02+2, 1).GT. 1 . 13.AND.S(02+2,2).LT.0.75.AND.M(J2+1) .NE. 15) 5 19 4 BALL=.TRUE. 520 IF (BALL) 02=02+4 521 IF (BALL) V3 = 64 522 IF (BALL) GO TO 300 523 C 524 C *** 65 *** 525 130 BALL=.FALSE. 526 IF ((02+4).GT.NN) GO TO 300 527 IF (S(02,9).LT.1.10.AND.S(02 +1,1).LE.O.69.AND.M(02+1).NE.15.AND.S( 528 1 02+2,1).LE.0.69.AND.M(02+2).NE.15.AND.S(02+3,9).GE.1.57.AND.S(J2+ 529 2 4. 1 ).GT. 1. 16.AND.S(J2 + 4.9).GT.0.98.AND.S(J2+3. 1 ) . GT. 1 .08.AND.S(d2 530 3 - 1 , 1 ) .GT. 1 . 16) BALL=.TRUE. 53 1 IF (BALL) 02=02+4 532 IF (BALL) V3=65 533 IF (BALL) GO TO 300 534 C 535 C .... 02 = J2+5 536 C 537 C 538 BALL=.FALSE . 539 IF ((02+6).GT.NN) GO TO 300 540 C 54 1 C *** 66 *** 542 IF (S(02,9).GT.0.98.AND.S(02-1,9).LE.S(J2,9).AND.S(02-2,9).GE.S(02 543 1 ,9).AND.S(02,1).GT.1.16.AND.S(02+5,9).GT.S(02.9).AND.S(02+5,1).GT 544 2 .1.01.AND.S(02+2,1).GT.1.16.AND.S(02+3,1).GT.1.01.AND.S(02+6,7).G 545 3 E. 1 .58.AND.S(02+4,2).LE.0.75) BALL =.TRUE . 546 IF (BALL) 02=02+5 547 IF (BALL) V3=66 548 IF (BALL) GO TO 300 549 C 550 C *** 67 *** 551 IF ((J2+7).GT.NN) GO TO 300 552 BALL=.FALSE. 553 IF (S(u2,9).GT.0.98.AND.S(J2+5,9).GT.1.57.AND.(J2+6).GE.H(K+1).AND 554 1 .M(J2+1) .NE. 15.AND.M(J2 + 2).NE. 15.AND.S(J2- 1, 1).GT.1.16.AND.S(J2 + 3 555 2 , 1 ) .GT. 1 .01 .AND.S(J2 + 4, 1).GT. 1.08.AND.S(J2+6, 1).GT. 1 . 16.AND.S(J2+ 555 3 7. 1 ) .GT. 1 . 16) BALL=.TRUE. 557 IF (BALL) J2=J2+5 558 IF (BALL) V3=67 559 IF (BALL) GO TO 300 560 C 561 C *#* 68 *** 562 BALL=.FALSE . 563 IF (S(U2,9).GT.1.10.AND.S(J2,1).GT.1.16.AND.S(J2-2, 1) .GT . 1 . 1 1.AND. 564 1 M(J2+1).EQ.M(J2 + 2).AND . S(J2+ 1 ,9).GT. 1 .24.AND.S(J2 + 5. 1).GT.1.16.AN 565 2 D.S(J2+5,9).GT. 1 . 10.AND.S(J2+6,7).GT. 1.58.AND.S(J2+4, 1).GT. 1 .01 566 3 .AND.S(J2+3.1).GT.0.77.AND.S(U2+7,2).GT.1.38) BALL=.TRUE. 567 IF (BALL) J2=J2+5 568 IF (BALL) V3=68 569 IF (BALL) GO TO 300 570 C 57 1 C . . . . J2 = J2+6 572 C 573 C 574 BALL=.FALSE. 575 IF ((J2+7).GT.NN) GO TO 300 576 C 577 C *** 69 *** 578 IF (S(J2, 1).GT. 1 . 16.AND.S(J2, 1 ) . LT. 1.25.AND.S(J2+6, 1).GT. 1 .00.AND. 579 1 S(U2 + 2,9).GT . 1.57.AND.S(J2 + 3, 1).GT. 1. 16.AND.S(J2+4.9).GT. 1.24.AND 580 2.S(U2+5,1).GT.0.69.AND.S(U2+6,2).LT.0.74.AND.S(J2+1,1).GT.0.69 581 3 .AND.S(J2+7, 1).LE.O.69) BALL= . TRUE . 582 IF (BALL) J2=J2+6 583 IF (BALL) V3=69 584 IF (BALL) GO TO 300 585 C 586 C * * * 7 0 * * * 587 BA L L =.FALSE. 588 IF (S(J2,9).GT.0.98.AND.S(U2, 1).GT.1.01.AND.S(U2 + 6,9).GT.S ( U2 , 9) 589 1 .AND.S(J2+6,1).GT.1.08.AND.S(J2+7,1).LE.0.69.AND.S(J2+2,9).GT.1.2 590 2 0.AND.S(J2+3,1).GT.1.16.AND.S(J2+4,1).GT.1.16.AND.S(U2+1,1).GT.0. 591 3 67.AND.S(J2 + 5, 1).GT.0.69.AND.S(J2+5,9).LT.S(J2+6.9).AND.S(J2 - 1 . 1 ) 592 4 .GT.1.01.AND.S(J2-2,1).GT.1.13) BALL=.TRUE. 593 IF (BALL) J2=d2+6 594 IF (BALL) V3=70 595 IF (BALL) GO TO 300 596 C 597 C 598 C 599 C V3=80 WHEN THE C-TERMINAL ADJUSTMENT IS DUE TO STRONG B-TURN POTEN 600 C TIAL (THROUGH THE PROCEDURE OF REPEATING THE B-TURN CHECK). 601 C IF V3=0 NONE OF THE CONDITIONS LISTED IN THE SUBROUTINES M0J2 AND 602 C RMJ2 FIT THE CURRENTLY TESTED SEGMENT. IN OTHER WORDS U2 HAS NOT 603 C CHANGED. 604 C 605 300 K3=J2 606 IF (.NOT. BALL.AND. V3.NE. 80) V3=0 607 C 608 C TO PRINT OUT THE FINAL VALUES FOR J1.U2. TO RETURN TO SUBROUTINE 609 C ONE TO START THE WHOLE PROCEDURE AGAIN. 610 C 61 1 PRINT 301 ,U1,J2,V2,V3 612 301 FORMAT('0',25X,'EVENTUAL HELIX FROM J1 : ' ,I 5,5X. 'TO J2:',I5.14X 613 •j ' * * * V2.V3: ' .2(15), ' ***'//) 614 RETURN 615 END End of F i l e to E - f f i c i e n c y o f the 3-sheet p r e d i c t i o n As i n d i c a t e d i n the p r e v i o u s s'ection s t r i c t adhe-rence to Chou and Fasman's s e t o f r u l e s l e d to the m i s s i n g o f a c e r t a i n number o f r e g i o n s and to some d i f f e r e n c e s between the b o u n d a r i e s o f p r e d i c t e d areas from t h i s s t u d y and those o f Chou and Fasman and X-ray a n a l y s i s (Table 6 ) . A n a l y s i s o f the r e s u l t s o b t a i n e d showed t h a t the o b s e r v a t i o n s made f o r the h e l i c a l s e a r c h c o u l d a l s o be a p p l i e d f o r 3-sheet. T h i s i n v o l v e d moving the b o u n d a r i e s J l and J2 to a more s u i t a b l e p o s i t i o n t h r o u g h c o n s i d e r a t i o n o f the boundary c o n f o r m a t i o -n a l parameters Pg N> P 3 C Pn3N a n < ^ Pn3C t b e n e i g h b c m r i n g r e s i d u e s . Some examples o f boundary adjustment f o r p r e d i c -t e d 3-sheet r e g i o n s are l i s t e d below: (1) J l = J l - 2: C o n c a n a v a l i n : 49-57 V a l G l y Thr A l a H i s H e 47 49 51 t I V a l (47) i s l i s t e d second f o r i t s P„,T and i t i s a s t r o n g 3-former. Hence, b e s i d e s the f a c t t h a t i t s presence, b a l ances. the b r e a k e r G l y (48) , i t a l s o ensures a v e r y s t a b l e 128 N-boundary t o the p r e d i c t e d -sheet. (2) J l = J l +3 g-Chymotrypsin: 36-42 Gin 'Asp Lys Thr Gly Phe H i s Phe I ! I I t I I L _ 34 36 38 40 i 1 B e s i d e s the good P ^ of the r e s i d u e Phe (39) , by moving J l to p o s i t i o n J l + 3 , Phe ( 3 9 ) , two 8-sheet b r e a k e r s , Lys (36) and G l y (38) are avoided,as w e l l a s , t h e t e t r a -p e p t i d e 35-38 which e x h i b i t s 8-turn p o t e n t i a l . (3) J2 = J2 + 3  Cytochrome b^: 73-76 Lys Thr Phe Phe" H e i G l y G l u Leu Pro Asp Asp 1 I I t r I I I I I ! _ _ 72 74 76 78 80 82 i 1 The r e g i o n 73-76 c o n t a i n s enough 8-sheet formers t o b a l a n c e the a d d i t i o n o f two b r e a k e r s , Gly (77) and G l u (78) . Leu has been ranked f i f t h f o r i t s P ^ and the r e s i d u e s Pro (80) , Asp (81) and Asp (82) p o s s e s s good P- R r ;. 129 (4) J2 = J2 - 3:-C o n c a n a v a l i n A: 25-32 Asp H e Lys Ser V a l Arg Ser Lys l L ! ! I > I t 28 30 32 34 A l t h o u g h H e 29 has a lower P g C than V a l 32, the new r e g i o n 25-29 s t i l l has a s t a b l e C-boundary and i s i t s e l f more s t a b l e because o f . e l i m i n a t i o n o f the two b r e a k e r s Lys 30, and Ser 31. In f a c t , ' r e g i o n 25-32 has 4 b r e a k e r s out o f 8 r e s i d u e s . (5) J2 = J 2 : C a r b o x y p e p t i d a s e A: 277-281 Tyr G l y Phe Leu Leu Pro A l a Ser G i n _ J ! ! t I ! t t L _ 277 279 281 283 285 t C o n s i d e r i n g i t s n e i g h b o u r i n g r e s i d u e s , Leu 281 appears t o be a good c h o i c e f o r the C-boundary s i n c e i t i s ranked f i f t h f o r i t s P ^ and i s a 3-former. The r e s i d u e s Pro 282 and Ser 284 e x h i b i t good Pn.g£ which may f a v o r the s t a b i l i z a t i o n o f the sheet C - t e r m i n a l . 1 3 0 These boundary a n a l y s e s f o r the B-sheet p r e d i c t i o n were e l a b o r a t e d i n two e x t r a s u b r o u t i n e s added to the end of the p r o p a g a t i o n p r o c e d u r e ( s u b r o u t i n e FOUR d e a l s w i t h the N-boundary adjustment and s u b r o u t i n e FIVE w i t h the C-bound-a r y a d j u s t m e n t ) . A g a i n , i t was: r e c o g n i z e d t h a t such a n a l y s e s were q u i t e t e d i o u s and d i d not always ensure c o m p l e t e l y s a t i s f y i n g r e s u l t s due to the c o m p l e x i t y of p r o t e i n a r r a n g e -ment . The n u c l e a t i o n p r o c e d u r e was a l s o s u b j e c t e d to some m o d i f i c a t i o n s t o reduce the number o f m i s s i n g r e s i d u e s . In most c a s e s , once an ar e a w i t h B-sheet p o t e n t i a l was l o c a t e d , the n u c l e a t i o n s e a r c h would s t a r t a g a i n from i t s ( C - t e r m i n a l + 1) r e s i d u e t o a v o i d r e p e t i t i o n i n the same are a ( c f . s u b r o u t i n e F I R S ) . However, f o r some p r o t e i n s (e.g. b o v i n e c o l o s t r u m i n h i b i t o r , g l u c a g o n , B l a c k Mamba T o x i n K and R u s s e l l ' s V i p e r venom), such a proced u r e r e -s u l t e d i n the o m i s s i o n o f some r e g i o n s (Table 6, p. 205). The problem was s o l v e d by . s t a r t i n g the s e a r c h a g a i n every time from the ( N - t e r m i n a l + 1) r e s i d u e o f the p r e v i o u s fragment. The major drawback o f such a pr o c e d u r e was the t e d i o u s r e p e t i t i o n o f the s e a r c h f o r h i g h m o l e c u l a r weight p r o t e i n s . The p r o t e i n s f o r which the new proced u r e improved the q u a l i t y o f the p r e d i c t i o n were: b o v i n e c o l o s t r u m i n h i b i t o r , g l u c a g o n , B l a c k Mamba T o x i n K and R u s s e l l ' s 131 Y i p e r Venom. These p r o t e i n s have m o l e c u l a r w e i g h t s of 7,511, 3,483, 6,566 and 6,850, r e s p e c t i v e l y , which are lower than those o f o t h e r p r o t e i n s used i n t h i s s t u d y . Hence i t i s p o s s i b l e t h a t i n l o w - m o l e c u l a r w e ight p r o t e i n s , s h o r t range i n t e r a c t i o n s between a d j a c e n t r e s i d u e s may l e a d to the f o r m a t i o n o f 3-sheets under c i r c u m s t a n c e s not e n c ountered i n b i g g e r p r o t e i n s . The r e q u i r e m e n t of l e s s than one t h i r d 3-sheet b r e a k e r s may sometimes provoke a s e c t i o n or a p r o t e i n w i t h 3 h's out o f 5 r e s i d u e s to be i g n o r e d i n the n u c l e a t i o n s e a r c h (e.g. a - c h y m o t r y p s i n 197-201, r i b o n u c l e a s e 116-124). In a d d i t i o n , the p r e s ence of Pro 198 and Pro 117 i n a - c h y m o t r y p s i n and r i b o n u c l e a s e , r e s p e c t i v e l y , i s u n f a v o r a -b l e to 3-sheet n u c l e a t i o n a c c o r d i n g to r u l e B . l . T h e r e f o r e , i n the m o d i f i e d program, two d i s t i n c t d e c i s i o n s were made: (1) f o r a - c h y m o t r y p s i n , once segment 197-201 has been c o n s i d e r e d as a p o s s i b l e 3-sheet, boundary a n a l y s i s a l l o w s s h i f t i n g o f the e n t i r e fragment to the r i g h t . The f i n a l v a l u e 199-204, b e s i d e s h a v i n g the advantage o f b e i n g c l o s e r to X-ray r e s u l t s (199-203), a l s o has b e t t e r P ^ (Leu) and P^ ,^ (Asn) . (2) f o r r i b o n u c l e a s e , i n s t e a d o f s h i f t i n g fragment 116-120, the a d d i t i o n o f an e x t r a t e t r a p e p t i d e (121-124) w i t h an a c c e p t a b l e 3-sheet p o t e n t i a l makes the presence 132 o f Pro 117 l e s s u n f a v o r a b l e to 8-sheet c o n f o r m a t i o n and i t e v e n t u a l l y l e a d s to the p r e d i c t i o n o f a B-sheet a r e a w i t h , • v e r y f a v o r a b l e P ^ N ( V a l ) and P ^ ( V a l ) . As Lys d i d not o c c u r o f t e n a t the N - t e r m i n a l o f a B-sheet s e c t i o n , the change of i t s assignment from a B-sheet b r e a k e r to a B-sheet former c o u l d not r e a d i l y be made because o f the p o s s i b l e r e s u l t o f erroneous p r e d i c t i o n s . However, i n the case of r i b o n u c l e a s e 61-65 i t was n e c e s s a r y to have Lys 61 e q u i v a l e n t to a hg ^ 3 N ( L y s ) = ^•^•^ s o t n a t t h i s s e c t i o n d i d not v i o l a t e the r e q u i r e m e n t o f two t h i r d s h's. The p r e s ence of a s t r o n g such as Asp c o u l d i n -t e r r u p t the p r e l i m i n a r y s e a r c h o f areas w i t h 8-sheet poten-t i a l (e.g. p a p a i n 4-9). T h i s d i s r u p t i o n r e s u l t e d i n an ina--b i l i t y t o s t a r t any n u c l e a t i o n p r o c e d u r e on the two fragments a r i s i n g from t h i s d i s r u p t i o n ( p a p a i n 3-6, 7-10). These two fragments c o u l d not by themselves meet the r e q u i r e m e n t of two t h i r d s h's. Hence i n such c o n d i t i o n s the n u c l e a t i o n r u l e may be s l i g h t l y m o d i f i e d so t h a t e v e n t u a l l y , w i t h the c o m b i n a t i o n o f boundary a n a l y s i s , one c o u l d s t i l l l o c a t e an a p p r o p r i a t e B-sheet a r e a . A somewhat s i m i l a r s i t u a t i o n was e n c ountered w i t h s u b t i l i s i n 44-51. The two a d j a c e n t fragments 42-45 and 49-52 c o u l d not be the s t a r t i n g p o i n t f o r 3-sheet f o r m a t i o n . They . were s e p a r a t e d by a s e c t i o n w i t h q u i t e low 8-sheet 133 i p o t e n t i a l ( G l y - G l y - A l a : < P g > = 0.76). N e v e r t h e l e s s the e n t i r e s e c t i o n 44-51, was d e t e c t e d as g-sheet by Chou and Fasman (1974b) and by X-ray d i f f r a c t i o n (Chou and Fasman, 1974b). I t a l s o has good end r e s i d u e s , V a l (44) and V a l ( 5 1 ) , and <P^> i s g r e a t e r than <Pa> (1.045 v e r s u s 1.040). In summary, by t a k i n g i n t o account the i m p o r t a n t c o n t r i b u t i o n o f the boundary c o n f o r m a t i o n a l parameters (sub-r o u t i n e s FOUR and FIVE) and the n e c e s s i t y o f a l l o w i n g more f l e x i b i l i t y t o the n u c l e a t i o n r u l e ( s u b r o u t i n e SECO) under the s p e c i f i c c o n d i t i o n s p r e v i o u s l y mentioned, the f o l l o w i n g program was adopted f o r the g-sheet s e a r c h . Only the d i f f e r -ent s u b r o u t i n e s are p r e s e n t e d here s i n c e the main program f o r g-sheet p r e d i c t i o n i s i d e n t i c a l to the one used f o r a-h e l i x s e a r c h , except t h a t the g-sheet boundary c o n f o r m a t i o -n a l parameters r e p l a c e those p e r t a i n i n g t o a - h e l i x charac-t e r i z a t i o n . 134 co cn 1 2 C C 3 4 5 6 7 c c c c SUBROUTINE FIRS 8 9 c c PRELIMINARY SEARCH FOR B-SHEET REGIONS 10 c 1 1 c 12 c '13 c 1 4 c 15 c 16 c PURPOSE 17 c PRELIMINARY SEARCH FOR B-SHEET REGIONS BY APPLYING RULE 2 : <PB> 18 c > 1 . 05 AND <PA> < <PB> 19 c 20 c 21 c 22 c 23 REAL S, T1.T2.A1.A2 ,T3,T4,T5,TT.P 24 INTEGER G,F,H,U,D,V1.V2,V3,V4,V5,V6,V7,V8.0 25 LOGICAL HELLO,BYE,BALL,MOVE 26 DIMENSION S(1000,10),M(1000),H(1000),D(1000,16),P(1000,10) 27 COMMON S.T1,T2,T3,T4,T5,TT,A1,A2,P ,V4,V5,V6,V7,V8,0,G,F,H,U ,D,NN, 28 1NW.KX,MA,MB,MC,MD,L,I,L1,L2,L3.J1,J2,N,K1,K2,V1,V2.IM.M,K3,K4,V3. 29 2BYE.BALL,HELLO,MOVE 30 c 31 c 32 c DESCRIPTION OF PARAMETERS 33 c H - BOUNDARY RESIDUES OF A PREDICTED REGION 34 c H(I) - N-TERMINAL RESIDUE 35 c H(I + D- C-TERMINAL RESIDUE 36 c MB - FIRST RESIDUE OF A SECTION TO BE CONSIDERED FOR THE PRE LI 37 c MINARY SEARCH BUT WILL CHANGE DURING N-PROPAGATION (MB-1) 38 c MA - FIRST RESIDUE OF A SECTION TO BE CONSIDERED FOR THE PRELI 39 c MINARY SEARCH BUT WILL CHANGE DURING C-PROPAGATION (MA+1) 40 c K 1 - FIRST RESIDUE OF A SECTION 'TO BE CONSIDERED FOR THE PRELI 41 c MINARY SEARCH 42 c K2 - LAST RESIDUE OF A SECTION TO BE CONSIDERED FOR THE PRELI 43 c MINARY SEARCH 44 c A1 - AVERAGE <PA> OF A SECTION 45 c A2 - AVERAGE <PB> OF A SECTION 46 c N - SWITCHING VALUE FOR DECISION MAKING 47 c N=1 N-PROPAGATION 48 c N=2 C-PROPAGATION 49 c I - COUNTER USED WITH THE ARRAY H TO STORE THE BOUNDARY RESI 50 c DUES OF PREDICTED REGIONS 51 C 52 C 53 C THE SEARCH WILL STOP WHEN THE LAST SEGMENT AT THE C-TERMINAL HAS 54 C ONLY 2 AMINO ACID RESIDUES. IT IS NOT LONG ENOUGH FOR THE B-SHEET 55 C STATE 56 C 57 10 I = 2 58 H(I) =0 59 H( I - 1 ) =0 60 NW = NN-2 6 1 MB = 1 62 MA = 1 63 LP = 1 64 20 N = 0 65 25 K2 = MA+2 66 HELLO=.FALSE. 67 IF (MB.EO.O) HELLO=.TRUE. 68 IF (HELLO) K1=H(I)+1 69 IF (.NOT.HELLO) K1=MB 70 C 7 1 C TO CALCULATE <PA>,<PB> FOR A POLYPEPTIDE CHAIN STARTING AT POSITION 72 C K1 AND ENDING AT POSITION K2 73 C 74 T1=0 75 T2=0 76 DO 30 MC=K1,K2 o\ 77 T1=T1+S(MC,1) 78 T2=T2+S(MC,2) 79 30 CONTINUE 80 A2=T2/(K2-K1+1) 81 A1=T1/(K2-K1+1) 82 C 83 C IF <PB> IS LESS THAN 1.05 THEN TO START THE SEARCH AGAIN FROM NEXT 84 C POSITION K1+1 85 C 86 IF (A2.LT.1.05-1.E-6) GO TO 35 87 c • 88 C TO START THE SEARCH AGAIN FROM NEXT POSITION MB+1 WHEN <PB> < <PA> 89 C EVEN IF <PB> > 1.05. THE SEARCH IS STOPPED WHEN THE LAST AMINO ACID 90 C ' RESIDUE HAS BEEN REACHED 91 C 92 IF (A 1 .GT.A2.AND.K2.EO.NN .AND.(K2+1-K1).EO.3) GO TO 70 93 IF (A 1 .GT.A2.AND.K2.EQ.NN .AND.(K2+1-K1).GT.3 ) GO TO 55 94 IF ( A 1 . GT . A2 . AND .K2 . NE . NN ) GO TO 35 95 C 96 C IF <PB> > <PA> AND <PB> > 1.05 TO CONTINUE THE PROPAGATION AT EI 97 C THER N- OR C-TERMINAL SIDE (N=1 INDICATES N-TERMINAL PROPAGATION, 98 C N=2 C-TERMINAL PROPAGATION) UNLESS WE REACHED THE LAST RESIDUE OF 99 C THE SEQUENCE (NN) 100 C 101 IF (N.E0.2 .AND. K2.E0.NN) GO TO 45 102 IF (N.E0.2 .AND. K2.NE.NN) GO TO 40 103 C 104 C TO START N-TERMINAL PROPAGATION WHEN <PB> > 1.05 AND <PB> > <PA> 105 C 106 MB = MB-1 107 N = 1 108 C 109 C AS LONG AS THE N-TERMINAL PROPAGATED PEPTIDE DOES NOT OVERLAP WITH 1 10 C THE PREVIOUS SHEET THE PEPTIDE CAN BE ELONGATED ON THAT SIDE,OTHER 1 1 1 C WISE TO SWITCH TO C-TERMINAL PROPAGATION 1 12 C 1 13 BYE =.FALSE. 1 14 IF (MB.EO.H(I)) BYE=.TRUE. 1 15 IF (BYE) N=2 1 16 IF (BYE) GO TO 40 1 17 C 1 18 C N-TERMINAL PROPAGATION IS STOPPED WHEN MB OR K1 = 1,TO SWITCH THEN 1 19 C TO C-TERMINAL PROPAGATION 120 C 121 BALL=.FALSE. 122 IF (MB.LE.H(1-1)) BALL =.TRUE. 123 IF (BALL) MB=MB+1 124 IF (BALL) MA=MA+1 125 IF (BALL) N=2 126 IF (MA.GT.NW). GO TO 45 127 IF (BALL) GO TO 25 128 IF (MB.GT.H(I-1)) GO TO 25 129 C 130 C TO START C-TERMINAL PROPAGATION WHEN IT IS STOPPED AT THE N-TERMIN 131 C AL SIDE. IF BOTH SIDES CANNOT BE ELONGATED ANYMORE THEN THE SEGMENT 132 C BEING ANALYZED SO FAR IS RECOGNIZED AS HAVING SHEET POTENTIAL 133 C 134 35 MB=MB+1 135 IF (N.E0.-2) GO TO 55 136 IF (N.EQ.1) N=2 137 40 MA = MA+1 138 IF (MA.LE.NW) GO TO 25 139 IF (MA.GT.NW) GO TO 70 140 C 14 1 C AFTER PRINTING OUT THE AREA WITH SHEET POTENTIAL THE SEARCH IS STOP 142 C PED BECAUSE WE GOT TO THE LAST RESIDUE IN THE SEQUENCE 143 C 144 45 1 = 1+1 145 H(I )=K1 146 1 = 1+1 147 H(I)=K2 148 PRINT 50,H(I-1),H(I) 149 50 FORMAT('0',30X,16,10X,16) 150 IM=I 15 1 GO TO 70 152 C 153 C TO PRINT OUT THE AREA WITH SHEET POTENTIAL (H(I - 1),H(I)) 154 C 155 55 1=1+1 156 H(I)=K1 157 1=1+1 158 H(I)=K2-1 159 PRINT 60.H(I-1),H(I ) 160 60 FORMAT('0'.30X,16,10X,16) 161 C 162 C TO START THE SEARCH AGAIN EITHER FROM (H(I-1) + 1) OR (H(I) + 1) 163 C 164 MB=H(I) + 1 165 MA=H(I) + 1 166 IM=I 167 IF (MA.LE.NW) GO TO 20 168 C 169 C TO PRINT OUT THE LAST VALUE OF THE COUNTER I (IM) WHICH WILL BE 170 C USED IN THE NEXT SUBROUTINE 17 1 C 172 70 PRINT 75,IM l _ i 173 75 FORMAT ( 'O' , 40X , ' IM ' ,14) LO 174 C 0 0 175 PRINT 90 176 90 FORMAT(12X,'SEARCH FOR ACTUAL SHEETS FROM THE POTENTIAL REGION 177 1S') 178 PRINT 95 179 95 FORMAT( ' ', 12X, ' 180 1.'//) 181 C 181.5 1 = 2 181.7 0 = 1 182 CALL SECO 183 RETURN 184 END End of F i l e SUBROUTINE SECO SEARCH FOR SHEET NUCLEATION PURPOSE SEARCH FOR NUCLEATING REGIONS WHICH SHOULD CONTAIN THREE BETA-FORMERS OUT OF FIVE RESIDUES REAL S,T1.T2.A1,A2 ,T3,T4,T5,TT,P INTEGER G,F,H.U.D.V1.V2,V3,V4,V5,V6,V7,V8,0 LOGICAL HELLO,BYE.BALL,MOVE DIMENSION S( 1000, 10),M(1000),H(1000),D(1000, 1G) ,P( 1000, 10) COMMON S,T1 ,T2.T3.T4,T5,TT,A 1 ,A2,P ,V4,V5,VG,V7,V8.0,G,F.H.U.D,NN, 1NW.KX,MA,MB,MC,MD,L,I,L1,L2,L3.J1.J2.N.K1,K2,V1,V2,IM.M.K3.K4,V3, 2BYE,BALL,HELLO,MOVE DESCRIPTION OF PARAMETERS G - FIRST RESIDUE OF THE 5 RESIDUE PEPTIDE SUBJECTED TO THE NUCLEATION SEARCH MA - FIFTH RESIDUE OF THE 5 RESIDUE PEPTIDE SUBJECTED TO THE NUCLEATION SEARCH 0 - SWITCHING VALUE FOR DECISION MAKING Q=1 THE CURRENT POTENTIAL AREA IS STILL LONG ENOUGH (> 3 RESIDUES) TO BE SUBJECTED TO THE NUCLEATION SEARCH 0=2 THE CURRENT POTENTIAL AREA IS TOO SHORT FOR ANOTHER SHEET SO TO START WITH THE NEXT POTENTIAL AREA REMARKS UNLESS NOTIFIED THE OTHER PARAMETERS STILL HAVE THE SAME DEFINITION IF 0=2 THE NUCLEATION SEARCH WILL START ON A NEW POTENTIAL AREA SI NCE THE PREVIOUS ONE HAD BEEN THOROUGHLY SCANNED THROUGH. EACH TI ME THAT I INCREASES BY. 1 THE NEXT POTENTIAL AREA WILL BE ANALYZED IF (Q.E0.2) GO TO 25 1 = 1+1 IF (I.GT.IM) GO TO 180 K1=H(I ) 51 1 = 1 + 1 52 K2=H(I) 53 G = K1 54 KX=K2-3 55 25 MA=G+4 56 IF (MA.GT.K2) MA=MA-1 57 C 58 C THE RESIDUE ASN CAN BE CONSIDERED AS A B-FORMER AT THE C-TERMINAL 59 C OF THE PEPTIDE CHAIN BECAUSE OF IT GOOD P.BC VALUE 60 C 61 N = G+1+(MA-G)/2 62 DO 30 L=N,MA 63 IF (M(L).E0.3) S(L,2)=1.05 64 30 CONTINUE 65 C 66 C TO COUNT THE DIFFERENT TYPES OF ASSIGNMENTS (T3) AND THE NUMBER OF 67 C BREAKERS (N) IN THE SECTION G-MA 68 C 69 T3=0 70 N = 0 7 1 DO 35 L=G,MA 72 S(L,3)=0 73 IF (S(L,2).GE.1.05) S(L.3)=1.0 74 T3=T3+S(L,3) 75 IF (S(L,2).LE.O.75) N = N+1 76 35 CONTINUE 77 PRINT 36,G.MA,T3,N 78 36 FORMAT(' ',10X.'G : ' ,14,5X, 'MA: ' ,14,5X, ' T3 : ' ,F7 . 4 , 5X , 'N :',I3, 79 1 8X,'SHEET NUCLEATION') 80 C 8 1 C 82 c IF THERE IS AT LEAST 3 HB AND LESS THAN 2 BB,THE NUCLEATION RULE 83 c IS SATISFIED. WE STILL HAVE TO CHECK FOR THE PRESENCE OF PRO OR 84 c GLU IN THE NUCLEATING SEGMENT (THEY ARE STRONG B-BREAKERS) 85 c 86 IF (T3.GE.3.0.AND.N.LT . 2) GO TO 60 87 c 88 c 89 c SOME MODIFICATIONS OF THE RULE WHICH TAKE INTO ACCOUNT THE PRESEN 90 c CE OF NEIGHBORING RESIDUES FAVORABLE TO SHEET NUCLEATION ALTHOUGH 91 c THE SEGMENT MAY CONTAIN MORE THAN ONE THIRD OF SHEET-BREAKERS 92 c 93 c 94 IF (T3.GE.3.0.AND.N.GE.2.AND.S(G,2).GE.1.05.AND.S(MA,9).GE.1.50 95 1.AND.S(MA-1,9).GE.1.50) GO TO 100 96 c 97 IF (T3.GE.3.0.AND.N.GE.2.AND.M(MA).EO.10.AND,M(G).EO.10) GO TO 100 98 c 99 IF (T3.GE.3.0.AND.N.GE.2.AND.M(MA).EO.19.AND.S(G,2).GE.1.05.AND. 100 1(M(G+1).EO.20.OR.M(G+2).EO.20.OR.M(G+3).EO.20)) GO TO 100 101 C 102 IF (T3 . GE.3.0.AND.N.GE.2.AND.S(MA.2).LE.0.75) GO TO 75 103 C 104 IF (S(G,2).LE.0.75.AND.T3.GE.3.0.AND.N.EO.2.AND.M(G+1).EO.15.AND. 105 1M(MA).EO.5.AND.M(MA-1 ) .EO.20.AND.M(MA-2).EO. 11) GOTO 100 106 C 107 IF (T3.GE.3.0.AND.N.GE.2.AND.5(G,2).LE.0.75) GO TO 90 108 C 109 IF (T3.GE.2.0.AND.N.LT.2.AND.M(G).EO.20.AND.M(G+2).EO.14) GO TO 1 10 1 120 1 1 1 C 1 12 IF (T3.GE.2.0.AND.N.EO.1.AND,M(G+2).EO.20.AND.M(G+4).EO.5.AND.M(G) 1 13 1.EO.12) GO TO 120 1 14 C 1 15 IF (M(G).EO.10.AND,M(MA+1).EO.20.AND.S(G+1,2).GE.0.93.AND.S(G+2.2) 1 16 1 .GE.0.75.AND.S(G+3,2).GE.0.75.AND.M(G-1).EO. 1 .AND.M(G-2).EQ. 1 ) 1 17 3 GO TO 130 1 18 C 1 19 IF ((G-4).LE.O.AND.(MA+2).GT.NN) GO TO 45 120 IF (T3.GE.2.0.AND.N.EO.1.AND.S(G-1,2).GE.0.54.AND.M(G-1).NE.15.AND 1 2 1 1 .S(G-2.2).GE.1.60.AND.S(G-3,2).GE.1.47.AND.S(G-4,2).LE.0.74.AND.S 122 2 (MA,2).LE.0.74.AND.S(MA-1,2).GT.0.93.AND.S(MA-3,2).GT.1.30.AND.S( 123 3 MA+1,2).LE.0.75.AND.S(MA+2,2).LE.0.83) GO TO 160 1 24 C 125 45 IF ((G+10).GT.NN.AND.(G-2).LE.O) GO TO 50 126 IF (T3.GE.2.0.AND.N.EO.1.AND.S(G+1,2).LE.0 .74.AND.S(G+2,8).GE.1.6 127 1 9.AND.S(G.8),LT.S(G+2,8).AND.M(G+3).EO.1.AND.S(G+4,2).GT.0.74.AND 128 2 .S(G+5,2).GT.0.74.AND.M(G+6).EQ.1.AND.S(G+7,2).GT.0.74.AND.S(G+8, 129 3 2).GT.0.93.AND.S(G+9,2).GE.1.60. AND.S(G+10.2).LE.0.74.AND. S(G-1, 130 4 2) .LE.0.74.AND.S(G-2,2) .LE.0.74) GO TO 170 131 C 132 50 IF ((G-5).LE.0.AND.(MA+2).GT.NN) GO TO 55 133 IF(T2.GE.2.0.AND.N.EO.2.AND.S(G-3,2).GE.1.60.AND.S(G-4,2).LE.0.75 134 1 .AND.S(G-5,2).LE.0.75.AND.S(G-2,2).GE.1.60.AND.M(G-1 ) . EQ . 1.AND. S( 135 2 G,2).GE.1.60.AND.S(G+1.2).GE.0.75.AND.M(G+2).EO.1.AND.S(G+3,2).GE 136 3 . 1 .60.AND.S(MA,2).LE.0.55.AND.S(MA+1,2).LE.0.75.AND.S(MA + 2,2 ) .LE. 137 4 0.75) GO TO 160 138 C 139 C 140 C IF THE SEGMENT UNDER CONSIDERATION CANNOT SATISFY ANY OF THE ABOVE 14 1 C CONDITIONS THEN THE SEARCH WILL START AGAIN FROM NEXT POSITION G+1 142 C 143 55 G = G+1 144 IF (G.LE.KX) GO TO 25 145 GO TO 20 146 c 147 c IF THERE IS NO GLU NOR PRO IN THE NUCLEATING SEGMENT THEN SUBROUTI 148 c NE THIR IS CALLED TO CARRY OUT THE PROPAGATION PROCEDURE 149 c 150 60 DO 61 L=G,MA 151 IF (M(L).E0.7 .OR .M(l_) .EQ. 15) GO TO 65 152 61 CONTINUE 153 CALL THIR 154 GO TO 10 155 C 156 C IN SOME INSTANCES,DESPITE THE PRESENCE OF PRO OR GLU THE NUCLEATING 157 C AREA REMAINS STABLE BECAUSE OF STRONG B-FORMER RESIDUES 158 C 159 65 IF (T3.GE.3.0.AND.N.EQ.1.AND.S(G,2).GE.1.30.AND.M(G).E0.M(G+2) 160 1.AND.M(G).E0.M(G+3).AND.(G-2).EQ.K3.AND.S(G-1,2).GE.0.75) GO TO 161 2 150 162 C 163 IF ((G+8).GT.NN) GO TO 70 164 IF (T3.GE.3.0.AND.N.EO.1.AND.S(G,8).GE.1.65.AND.S(G+1,2).GE.1.19. 165 1 AND.S(G-1,2).LE.0.75.AND.S(G+2,2).GE. 1 .30.AND.S(G+4,9).GE. 1 .50.AND 166 2 .S(G+5,9).GT.0.79.AND.S(G+6,9).GT.1.79.AND.S(G+7,2).LE.0.75.AND. 167 3 S(G+8,2).LE.O.75) GO TO 140 168 C 169 C 170 C NUCLEATION SEARCH STARTS AGAIN FROM NEXT POSITION G+1 171 C 172 70 G = L+1 173 IF (G.LE.KX) GO TO 25 174 GO TO 20 175 C 176 C 177 C TO START N-TERMINAL PROPAGATION WHEN THE PRESENCE OF A SHEET-BREA 178 C KER AT THE C-TERMINAL (MA) IMPEDES THE ELONGATION ON THAT SIDE 179 C 180 75 MV=MA-1 181 DO 76 L=G,MV 182 IF (M(L).E0.7.OR.M(L).EQ.15) GO TO 65 183 76 CONTINUE 184 80 BALL=.FALSE. 185 IF ((G-1).LE K3) GO TO 85 186 IF (S(G-1,2) GE.1.05) BALL=.TRUE. 187 IF (BALL) G=G-1 188 IF (BALL) GO TO 80 189 85 PRINT 86,G,MA 190 86 FORMAT('0' , 10X, 'PSEUDO-SHEET FROM G TO MA- 1' ,5X, 'G: ' ,15,5X, 'MA: ' , 191 115/) 192 J1=G 193 J2=MA-1 194 GO TO 115 195 c 196 c 197 c TO START C-TERMINAL PROPAGATION WHEN THE PRESENCE OF A SHEET-BREA 198 c KER AT THE N-TERMINAL (G) IMPEDES THE ELONGATION ON THAT SIDE 199 c 200 90 MU=G+1 LO 201 202 203 92 204 205 206 207 208 209 94 210 95 211 96 212 2 13 214 215 2 16 C 2 17 C 2 18 C I 2 19 C 220 C I 221 C 222 C 223 100 224 225 226 227 228 C 229 1 10 230 231 232 233 234 235 236 1 12 237 238 C 239 C 240 C \ 241 C I 242 C I 243 C I 244 C 245 C 246 1 15 247 1 18 248 249 250 GO TO 65 PSEUDO-SHEET FROM G+1 TO MA'.5X,'G: 15,5X,'MA: DO 92 L=MU,MA IF (M(L).EQ.7.OR.M(L).EQ.15) CONTINUE NV = MA +1 NU=MA+4 DO 94 L=NV,NU IF (S(L,2).GE.1.05) MA=MA+1 IF (S(L,2).LT. 1 .05) GO TO 95 CONTINUE PRINT 96,G,MA FORMAT('O'.10X, 115/) J1=G+1 J2=MA GO TO 115 N- THEN C-TERMINAL PROPAGATION BY ADDING ONE RESIDUE AT A TIME TO THE"NUCLEATING SEGMENT. IT IS DIFFERENT FROM THE PROCEDURE IN SUB ROUTINE THIR WHERE TETRAPEPTIDES INSTEAD OF SINGLE RESIDUES ARE CON SIDERED FOR ELONGATING THE SEGMENT BALL=.FALSE. IF ((G-1).LE.K3) GO TO 110 IF (S(G-1,2).GE.1.05) BALL=.TRUE. G = G- 1 IF (BALL) IF (BALL) GO TO 100 HELLO= . FALSE . IF (S(MA+1.2).GE.1.05) HELLO=.TRUE. IF (HELLO) IF (HELLO) J 1=G J2 = MA PRINT 112.J1.J2 FORMAT('0',10X. GO TO 115 MA = MA+1 GO TO 1 10 PSEUDO-SHEET FROM J1: I5,5X.'T0 J2:',I5/) WHEN THE PROPAGATION HAS BEEN STOPPED ON BOTH SIDES THEN SUBROUTINE FOUR IS CALLED FOR ADJUSTING THE BOUNDARIES TO THEIR MOST FAVORABLE POSITIONS. WHEN RETURNING FROM THE BOUNDARY ANALYSIS IF THE CURRENT POTENTIAL AREA IS NOT LONG ENOUGH FOR ANOTHER SHEET FRAGMENT THEN THE NEXT POTENTIAL AREA WILL BE ANALYZED (Q=1) CALL FOUR IF (J2.LT.KX) IF (J2.LT.KX) IF (J2.GE.KX) GO TO 10 G = J2+ 1 Q = 2 Q=1 r—1 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 28 1 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 End of ',I5,5X,'T0 J2: 15/) TO PRINT OUT THE NUCLEATING SEGMENTS WHICH DO NOT FOLLOW THE COM MON NUCLEATION RULE. SUBROUTINE FOUR IS THEN CALLED TO CARRY OUT THE BOUNDARY ADJUSTMENT 120 J1 = G J2 = MA PRINT 125.J1.J2 125 FORMAT('0'.10X,'PSEUDO-SHEET FROM J1 GO TO 115 130 J1=G-2 J2=MA+1 PRINT 125.J1.J2 GO TO 115 140 J1=G J2=MA+3 PRINT 125.J1.J2 GO TO 115 TO CHECK THE NUMBER OF B-BREAKERS (JC) WHICH SHOULD BE LESS THAN ONE THIRD OF THE LENGTH OF THE SEGMENT (JCC) 150 JC = 0 J2 = MA DO 155 L=J1,MA IF (S(L,2).LT.0.83) JC=JC+1 155 CONTINUE JCC=(MA+1-J1)/3 IF (JC.LE.2.AND.JC.LT.JCC) PRINT 125.J1.J2 GO TO 115 160 J1=G-3 J2=MA-1 PRINT 125.J1.J2 GO TO 118 170 180 185 J1=G+2 J2=MA+6 PRINT 125.J1.J2 GO TO 118 PRINT 185 FORMAT('O' RETURN END 'END OF PROGRAM') F i l e U l 1 C 2 C 3 SUBROUTINE THIR 4 C 5 C 6 C 7 C 8 C 9 C PROPAGATION OF THE BETA-SHEET 10 C 1 1 C 12 C 13 C ' 1 4 c 15 c PURPOSE 16 c TO ADD TO THE NUCLEATING FRAGMENT TETRAPEPTIDES WHICH HAVE <PB> 17 c > 1.00 AND WHICH SATISFY THE PROPAGATION SET OF RULES 1 8 c 19 c 20 c 21 REAL S,T1,T2,A1,A2 ,T3,T4,T5,TT,P 22 INTEGER G.F.H.U.D,V1,V2,V3,V4.V5,V6,V7.V8.0 23 LOGICAL HELLO,BYE,BALL,MOVE 24 DIMENSION S(1000,10),M(1000),H(1000),D(1000,16),P(1000,10) 25 COMMON S,T1,T2,T3.T4,T5,TT,A1,A2,P ,V4,V5,V6,V7,V8,0.G,F,H.U,D 26 1NW,KX,MA,MB,MC,MD,L,I,L1,L2,L3,J1,J2,N,K1,K2,V1,V2,IM,M,K3,K4, 27 2BYE,BALL.HELLO,MOVE 28 c 29 c 30 c DESCRIPTION OF PARAMETERS 31 c MB - WHETHER IT IS N- OR C-PROPAGATION JB WILL ALWAYS BE THE 32 c FIRST LEFT RESIDUE OF THE ADJACENT TETRAPEPTIDE 33 c MC - WHETHER IT IS N- OR C-PROPAGATION JC WILL ALWAYS BE THE 34 c FOURTH RESIDUE OF THE ADJACENT TETRAPEPTIDE 35 c K1 - N-TERMINAL RESIDUE OF THE CURRENT POTENTIAL AREA 36 c N2 - C-TERMINAL RESIDUE OF THE CURRENT POTENTIAL AREA 37 c F - SWITCHING VALUE FOR DECISION MAKING 38 c F=1 N-PROPAGATION 39 c F=2 C-PROPAGATION 40 c V1 - COUNTER 41 c V2 - COUNTER 42 c 43 c 44 c AS LONG AS MB BELONGS TO THE CURRENT POTENTIAL AREA THE N-PROPAGA 45 c TION CAN BE CARRIED OUT 46 c 47 10 V1=0 48 V2 = 0 49 V3 = 0 50 V4 = 0 5 1 V7=0 52 F =1 53 15 V1=V1+1 54 MB=G-(4*V1) 55 IF (MB.GT.O .AND.MB.GE.K1) GO TO 20 56 C 57 C TO SWITCH TO C-TERMINAL PROPAGATION WHEN THE N-TERMINAL SIDE IS STOP 58 C PED.THE VARIABLE MB THEN BECOMES THE FIRST RESIDUE IN THE TETRAPEP 59 C TIDE ADDED TO THE C-TERMINAL SIDE 60 C 61 IF (V1.E0.1) J1=G 62 IF (V1.NE.1) J1=G-4*(V1-1) * 63 F =2 64 20 T2=0 65 T1=0 66 IF (F . EO. 1) GO TO 25 67 IF (V2.NE.O) MB=MA+1+(4*V2) 68 IF (V2.E0.O) MB=MA+1 69 V2=V2 + 1 70 IF (MB.GT.K2) GO TO 50 7 1 25 MC=MB + 3 72 IF (MC.GT.K2 .AND. MB.LE.K2) GO TO 50 73 C 74 C CALCULATION OF THE PA.PB OF THE TETRAPEPTIDE MB-MC 75 C 76 DO 30 L=MB,MC CTi 77 T1=T1 + S(L, 1 ) 78 T2=T2+S(L,2) 79 30 CONTINUE 80 PRINT 35,MB,MC,T1,T2 81 35 FORMAT ( ' ' , 10X , ' MB : ' , 14 , 5X , ' MC : ' , I 4 , 5X , ' T 1 : ' , F7 . 4 , 5X , ' T2 : ' . F7 . 4., 82 1'SHEET PROPAGATION') 83 C 84 C IF PA > PB THEN TO SWITCH TO C-PROPAGATION IF N-PROPAGATION HAS 85 C BEEN CARRIED OUT,OTHERWISE TO START ELONGATING BOTH SIDES BY ONE 86 C RESIDUE AT A TIME 87 C 88 IF (T1 .GT.T2) GO TO 45 89 C 90 C IF PB > PA AND <PB> <1.00 TO TAKE INTO CONSIDERATION THE TYPES OF 91 C SHEET RESIDUES IN THE SEGMENT SINCE IT MAY STILL BE VALID FOR THE 92 C PROPAGATION 93 C 94 IF (T2.LT.4.0000) GO TO 130 95 C 96 C IF PRO OR GLU OCCURS IN THE PROPAGATED TETRAPEPTIDE THEN EITHER TO 97 C SWITCH FROM N-PROPAGATION TO C-PROPAGATION (F=2) OR TO START ELON 98 c GATING BOTH SIDES BY ONE RESIDUE AT A TIME 99 c 100 DO 40 L=MB,MC 101 IF (M(L).EQ.15.0R.M(L).EQ.7) GO TO 45 102 40 CONTINUE 103 GO TO 150 104 45 BALL=.FALSE. 105 IF (F.EO.1) BALL=.TRUE. 106 IF (BALL) J1=MB+4 107 IF (BALL) F=2 108 IF (BALL) GO TO 20 109 C 1 10 C 1 1 1 C ADDITION OF ONE RESIDUE (HB OR IB) AT A TIME TO THE N-TERMINAL SIDE 1 12 C WHEN ADDING IB TO EACH END TO CHECK IMMEDIATELY WHETHER THE RULE 1 13 C OF AT LEAST HALF OF FORMERS IS STILL SATISFIED OR NOT 1 14 C 1 15 50 L1=01 - 1 1 16 IF (L1 .LT.(G -4)) GO TO 55 1 17 IF (M(L1).EO.12) S(L1.2)=1.05 1 18 IF (S(L1,2),GE. 1 .05) J1=L 1 1 19 IF (S(L1,2).LE.O.93 .AND.S(L1,2).GE.0.83) J1=L1 120 IF (S(L1,2).GE.1.05 ) GO TO 50 121 C 122 C ADDITION OF ONE RESIDUE (HB OR IB) AT A TIME TO THE C-TERMINAL SIDE 123 C 1 24 55 J2=MB-1 125 60 L2=J2+1 126 IF (L2.GT.(MA + 4 ) ) GO TO 65 127 IF (M(L2).E0.3) S(L2,2)=1.05 128 IF (S(L2.2).GE.1.05) J2=L2 129 IF (S(L2,2).LE.O.93 .AND.S(L2,2).GE.0.83) J2=L2 130 IF (S(L2,2).GE.1.05) GO TO 60 131 C 132 C TO COUNT THE NUMBER OF SHEET-FORMERS IN THE ENTIRE SHEET AREA 133 C TO COMPARE THE ACTUAL NUMBER OF FORMERS (T4) TO ITS THEORITICAL 134 C ONE (TT : EQUAL TO AT LEAST ONE HALF OF THE SECTION) 135 C 136 65 T4 = 0 137 DO 70 L=J1,J2 138 S(L,4)=0 139 IF (S(L,2) .GE.1.05) S(L,4)=1.0 140 T4=T4+S(L,4) 141 70 CONTINUE 142 TT = (J2-U1+1) / 2.0 143 PRINT 75,J1,J2,T4, TT 144 75 FORMAT ( ' ' , 10X, 'U1 : ' , I4.5X , 'U2 : ' , 14, 5X , ' T4 : ' , F7 .4 , 5X , ' TT : ' , F7 .4 145 1 4X, 'ACTUAL AND THEORIT. H FORMERS FROM J1 TO <J2 ' ) 146 C 147 C IF THE RULE OF MORE THAN HALF OF SHEET-FORMERS IS SATISFIED THEN 148 C TO KEEP ON ADDING HB OR IB TO EACH SIDE OF THE SHEET SECTION 149 c 150 IF (T4.GE.TT .AND. S(J1 - 1.2).LE.0.75 ) GO TO 80 151 IF (T4.GE.TT .AND. S(J1 - 1,2).GT.0.75.AND.L1 .GE.(G -4)) GO TO 50 152 80 IF (T4.GE.TT .AND. S(J2 + 1,2).GT.0.75.AND.L2.LE.(MA+4)) GO TO 60 153 IF((T4.GE.TT .AND. S(J2+1,2).LE.O.75) . OR . (T4 . GE.TT.AND.S(J2+1 ,: 154 1GT.0.75.AND.L2.GT.(MA+4))) GO TO 115 155 C 156 C IF THE RULE IS NOT SATISFIED THEN TO TAKE AWAY RESIDUES WHICH ARE 157 C NOT HB SO THAT EVENTUALLY THERE IS ENOUGH HB IN THE SECTION 158 C 159 85 IF (S(J2,2).LT.1.05) GO TO 90 ' 160 IF (S(J1,2).LT.1.05) GO TO 95 161 90 J2=J2-1 162 IF (S(J2+1,2).LT.1.05) GO TO 100 163 95 J1=J 1 + 1 164 IF (S(J1-1,2),LT.1.05) GO TO 100 165 C 166 C EVERY TIME A RESIDUE IS TAKEN AWAY THE RULE OF MORE THAN HALF OF 167 C SHEET-FORMERS IS CHECKED AGAIN ON THE SHORTENED SECTION 168 C 169 100 T4=0 170 DO 105 L=J1,J2 171 S(L,4)=0 172 IF (S(L,2).GE.1.05) S(L,4)=1.0 173 T4=T4+S(L,4) 174 105 CONTINUE 175 TT=(J2-J1+1)/2.0 176 PRINT 75, J1,J2.T4.TT 177 IF (T4.GE.TT) GO TO 115 178 IF (T4.LT.TT) GO TO 85 179 115 PRINT 120.J1.J2 180 120 FORMAT('0'. 10X, 'PSEUDO-SHEET FROM J1: ' ,15.5X, 'TO J2:',I5/) 181 C 182 C WHEN THE PROPAGATION IS TERMINATED ON BOTH SIDES TO CALL SUBROUTINE 183 C FOUR FOR THE BOUNDARY ADJUSTMENT 184 c 185 125 CALL FOUR 186 IF (J2.LT.KX) G=J2+1 187 IF (J2.LT.KX) 0=2 188 IF (J2.LT.KX) RETURN 189 0=1 190 RETURN 191 c 192 c 193 c PRESENCE OF B-BREAKER OR OF CHARGED RESIDUE (ARG.LYS) IS NOT FAVO 194 c RABLE TO PROPAGATED TETRAPEPTIDES WITH <PB> '< 1.00. SO EITHER TO 195 c SWITCH TO C-PROPAGATION OR TO START ADDING HB OR IB TO EACH SIDE 196 c OF THE SHEET AREA 197 c 198 130 DO 135 L = MB, MC 199 IF (S(L,2).LE.0.75) GO TO 45 200 135 CONTINUE 201 DO 140 L=MB,MC 202 IF (M(L).E0.2 .OR. M(L).E0.9) GO TO 45 203 140 CONTINUE 204 C 205 C IF THE TETRAPEPTIDE WITH <PB> <1.00 ONLY HAS IB THEN IT CANNOT BE 206 C ADDED TO THE PROPAGATED SHEET 207 C 208 L3=0 209 DO 145 L=MB,MC 210 IF (M(L).EQ.3 .OR. M(L).E0.1) L3=L3+1 211 145 CONTINUE 212 IF (L3.E0.4) GO TO 45 2 13 C 2 14 C 215 C ... TO CHECK THE NUMBER OF BREAKERS IN THE ENTIRE POLYPEPTIDE ... 216 C 2 17 C TO COUNT THE NUMBER OF BB IN THE ENTIRE SECTION (V8). IT SHOULD NOT 218 C BE GREATER THAN ONE THIRD OF THE LENGTH (V6). IF V8 IS LESS THAN V6 219 C THEN THE SECTION IS CONSIDERED TO BE VALID AND SUBROUTINE FOUR IS 220 C CALLED TO CARRY OUT THE BOUNDARY ADJUSTMENT. IF NOT EITHER HB OR IB IS 221 C ADDED TO BOTH SIDES TO SATISFY THE REQUIREMENT OR C-PROPAGATION 222 C .WILL REPLACE N-PROPAGATION ._, 223 C ^ 224 C DESCRIPTION OF PARAMETERS 225 C V3 - COUNTER 226 C V4 - COUNTER 227 C MB - N-TERMINAL OF THE SHEET REGION 228 C MD - C-TERMINAL OF THE SHEET REGION 229 C 230 150 V6 = 0 231 V8=0 232 IF (F . EQ. 1) GO TO 155 233 MB=MB-5-(4+V4) 234 155 MD=MB+8+(4*V3) 235 V3=V3+1 236 V4=V4+1 237 V6=(MD-MB+1)/3 238 DO 160 L=MB.MD 239 IF (S(L,2).LE.0.75) V8=V8+1 240 160 CONTINUE 241 C 242 PRINT 165,MB,MD.V6,V8 243 165 FORMAT(' ' , 10X, 'MB: ' ,14,5X, 'MD: ' , 14 , 5X , ' V6 : ' , 17,5X, 'V8: ' ,I 3 , 8X, 244 1'THEORITIC. AND ACTUAL tt BREAKERS FROM MB TO MD' ) 245 IF (V8.LT.V6.AND.F.EQ.1) GO TO 170 246 IF (V8.LT.V6.AND.F.EQ.2) GO TO 180 247 V7=V2 248 IF (F.EQ.2) MB=MB+5+(4*V7) 249 IF (F.EQ.2) GO TO 50 250 F=2 251 J1=MB+4 252 GO TO 20 253 C 254 C 255 C TO PRINT OUT THE POSSIBLE SHEET AREAS THEN TO CALL SUBROUTINE FOUR 256 C FOR THE BOUNDARY ADJUSTMENT 257 C 258 170 J2 = MA 259 J1=MB 260 PRINT 120.J1.J2 261 GO TO 125 262 180 J1=G 263 J2=G+8 264 PRINT 120.J1.J2 265 GO TO 125 266 END End of F i l e ( J l O 1 c 2 C 3 SUBROUTINE FOUR 4 C 5 C G C 7 C 8 C 9 C BOUNDARY MOVE OF THE N-TERMINAL 10 C 11 C 12 C 13 C 14 C 15 C PURPOSE 16 C TO FIND OUT THE MOST FAVORABLE N-BOUNDARY RESIDUE FOR THE PREDIC 17 C TED SHEET BASED ON THE BOUNDARY CONFORMATIONAL PARAMETERS OF THE 18 C ADJACENT RESIDUES 19 C 20 C 21 C 22 REAL S,T1,T2,A 1 ,A2 ,T3,T4,T5,TT,P H 23 INTEGER G,F,H,U,D,V1,V2,V3,V4,V5,V6,V7,V8,0 <-n 24 LOGICAL HELLO, BYE , BALL, MOVE 1 - 1 25 DIMENSION S(1000,1O),M(1000),H(1000),D(1000,16),P(1000.1O) 26 COMMON S.T1,T2,T3,T4,T5,TT,A 1,A2,P ,V4,V5,V6,V7,V8,0,G,F,H,U,D,NN, 27 1NW,KX,MA,MB,MC,MD,L,I,L1,L2,L3,J1,J2,N,K1,K2,V1,V2,IM,M,K3,K4,V3, 28 2BYE.BALL,HELLO,MOVE 29 C 30 C 31 C DESCRIPTION OF"PARAMETERS 32 C V8 - ACTUAL NUMBER OF BREAKERS IN THE PREDICTED SHEET 33 C K3 - C-TERMINAL RESIDUE OF THE PREVIOUS PREDICTED SHEET 34 C V2 - COUNTER USED IN THE N-BOUNDARY ADJUSTMENT 35 C V3 - COUNTER USED IN THE C-BOUNDARY ADJUSTMENT 36 C 37 C 38 V2 = 0 39 V3 = 0 40 C 41 C 42 C J1 = J1 43 C 44 C 45 C THE POSITION J1 APPEARS TO BE THE MOST FAVORABLE COMPARED TO ITS 46 C ADJACENT RESIDUES,NO NEED TO ADJUST IT. 47 C 48 C 49 BALL=.FALSE. 50 IF (M(J1).EO. 1.AND.M(J1 + 1).EO. 1.AND.S(J1- 1.8).LT. 1 .07.AND.S(J1-2, 51 18 ) . LT. 1 .07.AND.M(J1+2 ) .EO. 10) BALL=.TRUE. 52 IF (BALL) 01=01 53 IF (BALL) V2=1 54 IF (BALL) GO TO 200 55 C 56 C # * * 2 * * * 57 BALL = .FALSE. 58 IF (M(01).EQ.1.AND.S(01-1,2).LT.1.05.AND.M(01+1).EQ.11) BALL = 59 1 .TRUE. 60 IF (BALL) 01 = U1 61 IF (BALL) V2=2 62 IF (BALL) GO TO 200 63 C 64 C * * * 3 * * * 65 BALL=.FALSE. 66 IF (M( 01).EO.1.AND.S(J1-1.2).LT.1.05.AND.V8.EO.1.AND.S(J1+2,8). 67 1LT.1.69.AND.(J2-J1).GE.8) BALL =.TRUE. 68 IF (BALL) 01 = J1 69 IF (BALL) V2=3 70 IF (BALL) GO TO 200 71 C 72 C * * * 4 * + * 73 BALL =.FALSE. 74 IF (M(J1).EO.1.AND.S(d1-1,2).LE.0.75.AND.S(J1+1,8).GE.1.30.AND. 75 1S(01+1,8).LT.1.69) BALL=.TRUE. 76 IF (BALL) J1=J1 77 IF (BALL) V2 = 4 78 IF (BALL) GO TO 200 79 C 80 C 81 C MOVE OF J1 82 C 83 84 C THE POSITION OF J1 IS LESS FAVORABLE THAN THAT OF ITS ADJACENT RE 85 C SIDUES 86 C 87 C * * * 5 * * * 88 BALL=.FALSE. 89 IF (S(J1,2).GT.0.89.AND.V8.EO.0.AND.M(J1 - 1).EO. 1 .AND.(J2-J1).GE.8' 90 1 BALL=.TRUE. 91 IF (BALL) 01=01-1 92 IF (BALL) V2=5 93 IF (BALL) GO TO 200 94 C 95 C * + * £ * * * 96 BALL=.FALSE. 97 IF (M(01).EQ.12 .AND.S(01-1,2).LT.0.74.AND.S(01+1,8).LT.1.30. 98 1 AND . S( J1 + 2, 2 ) . LE'.O. 75 . AND . S ( 0 1+ 3 , 8 ) . GE . 1 . 50 . AND :(S(01-2,8)-S(01+3. 99 28) ) . LT.0.20) BALL = . TRUE. 100 IF (BALL) 01=01+3 101 IF (BALL) V2 = 6 102 IF (BALL) GO TO 200 103 C 104 C *** 7 *** 105 BALL=.FALSE. 10G IF (S(d1,8).LT.1.50.AND.S(d1+1,8).LE.S(d1-2,8).AND .S(d1-2,8).GE. 107 11. 50.AND.S(d1-1,2).LT.0.74.AND.(J2-J1 + 3).GT.8.AND. ( d1 - 2).GE.K3) 108 3BALL=.TRUE. 109 IF (BALL) d1=d1-2 110 IF (BALL) V2=7 111 IF (BALL) GO TO 200 112 C 113 Q + * * g * * * 114 BALL=.FALSE. 115 IF(S(d1.2).LT.1.05.AND.S(d1-1.2).LT.1.05.AND.S(d1-2,2).LT.1.05 116 1 .AND.S(d1-3,8).LT. 1 .65.AND.S(d1 + 1.8).GE. 1.07) BALL=.TRUE . 117 IF (BALL) d1=d1+1 118 IF (BALL) V2=8 1 19 IF (BALL) GO TO 200 120 C 121 C *+*9**+ 122 BALL=.FALSE. ,_, 123 IF ((S(d1 + 1,8 )-S(d1,8) ) .GT.0.20.AND.(M(d1-1).EO. 15.OR.M(d1-1).EO. (jl 124 17.OR,M(d1- 1).EO.4).AND.(d2-d1+2).LE.8.AND.S ( d1 -2 , 8) . LT . 1.69.AND. CO 125 2S(d1 ,8).LT. 1 .07) BALL =.TRUE. 126 IF (BALL) d1=d1+1 127 IF (BALL) V2=9 128 IF (BALL) GO TO 200 129 C 130 C *** 10 *** 131 BALL=.FALSE. 132 IF (S(d1 ,2) . LT . 1 .05.AND.S(d1 - 1,2).LT. 1 .05.AND.S(d1-2,8) .LT. 1 .65 133 1.AND.S(d1+1,8).GE.1.07) BALL=.TRUE. 134 IF (BALL) J1=d1+1 135 IF (BALL) V2=10 136 IF (BALL) GO TO 200 137 C 138 C *** 11 *** 139 BALL=.FALSE. 140 IF (S(d1,2).LT.1.05.AND.M(J1+1).EO.1.AND.(M(d1+2).EQ.11.0R.S(d1+2, 141 12).GE. 1.30).AND.S (d1 - 1.2).LT.O.83) BALL=.TRUE. 142 IF (BALL) d1=d1+1 143 IF (BALL) V2=11 144 IF (BALL) GO TO 200 145 C 146 C *** 12 **.* 147 BALL=.FALSE. 148 IF(S(d1,2).LT.1 .05.AND.S(d1 - 1,2).LT. 1 .05.AND.S(d1 -2,8).GE. 1 .69 149 1.AND.S(d1+1,8).LT.1.65.AND.(d1-2).GT.K3) BALL=.TRUE. 150 IF (BALL) d1=d1-2 151 IF (BALL) V2=12 152 IF (BALL) GO TO 200 153 C 154 C *** 13 *** 155 BALL=.FALSE. 156 IF (S(d1,8).GE.1.07.AND.S(d1-2.8).GE. 1 .65.AND.S(d1-1,2).LT.0.74 157 1.AND . (J2-J1 + 3).GT.8.AND.(d1-2).GT.K3) BALL= . TRUE. 158 IF (BALL) d1=d1-2 159 IF (BALL) V2=13 160 IF (BALL) GO TO 200 161 C 162 C * * * 14+** 163 BALL=.FALSE. 164 IF (S(d1,8).GE.1 .07.AND.S(J1-2,8) .GT.S(J1 ,8) .AND.S(J1-1 ,2) .GE . 165 10.74 . AND . ( J1.-2) . GT . K3 . AND . ( S ( J 1-2 , 8 )-S( d1 ,8) ) .GE .0.50) BALL = 166 2.TRUE. 167 IF (BALL) J1=J1-2 168 IF (BALL) V2=14 169 IF (BALL) GO TO 200 170 C 171 6 *** 15**+ 172 BALL=.FALSE. ,_, 173 IF ((S(J1+3,8)-S(J1,8)).GE.0.35 .AND.S(d1+1,8).LT.1.07.AND.S(d1+2, U l 174 18).LT.1.07.AND.S(d1-1,8).LT.1.07.AND.S(d1-2,8).LT,S(d1+3.8)) BALL= >fc» 175 2.TRUE. 176 IF (BALL) d1=d1+3 177 IF (BALL) V2=15 178 IF (BALL) GO TO 200 179 C 1.80 C *** 16*** 181 BALL=.FALSE. 182 IF (S(d1.8).GE.1.07.AND.S(d1-2,8).GT.S(d1,8).AND.S(d1-1,2).GE. 183 10.74 .AND.(d1-2).GT.K3) BALL=.TRUE. 184 IF (BALL) d1=d1-2 185 IF (BALL) V2=16 186 IF (BALL) GO TO 200 187 C 188 C *** 17 *** 189 BALL=.FALSE. 190 IF (S(d1.8).GE.1.07.AND.S(d1-2,8).GT.S(d1,8).AND.(S(d1-1,2).GE.0. 191 174.OR.M(d1-1).EO.4).AND.(d2-d1+3).GE.8.AND.(J1-2).GT.K3) BALL= 192 2 .TRUE. 193 IF (BALL) d1=d1-2 194 IF (BALL) V2=17 195 IF (BALL) GO TO 200 196 C 197 C *** 18 *** 198 BALL=.FALSE. 199 IF (S(d1,2).LT.1.05.AND.S(d1-1,2).LT.1.05.AND.S(d1+1,8).GE.1.07 200 1.AND.(d1-2).LE.K3) BALL=.TRUE. 2 0 1 I F ( B A L L ) J 1 = J 1 + 1 2 0 2 I F ( B A L L ) V2=18 2 0 3 I F ( B A L L ) GO TO 2 0 0 2 0 4 C 2 0 5 C *** 19 *** 2 0 6 B A L L = . F A L S E . 2 0 7 I F ( S ( J 1 , 2 ) . LT . 1 . 0 5 . AND . S( <J 1 + 1 , 2 ) . LT . 1 . 0 5 .AND . (M( J 1 - 1 ) . EO . 15 . OR . M( 2 0 8 1 J 1 - 1 ) . E O . 7 . O R . M ( J 1 - 1 ) . E O . 4 ) . A N D . S ( J 1 + 2 , 8 ) . G E . 1 . 0 7 ) B A L L = . T R U E . 2 0 9 I F ( B A L L ) d1=d1+2 2 1 0 I F ( B A L L ) V 2 = 1 9 2 1 1 I F ( B A L L ) GO TO 2 0 0 212 C 2 1 3 C * * * 2 0 * * * 2 1 4 B A L L = . F A L S E . 2 1 5 I F ( S(vJ 1 - 1 , 2 ) . LT . 1 . 0 5 . AND . S( <J 1 - 2 . 8 ) . LT . 1 . 0 7 . AND . S ( d 1 + 1 , 2 ) . LT . 1 . 0 5 2 1 6 1 . A N D . ( S ( d 1 + 2 , 8 ) - S ( J 1 , 8 ) ) . G E . 0 . 5 5 . A N D . S ( d 1 + 2 , 8 ) . G E . 1 . 0 7 ) B A L L = 2 1 7 2 . T R U E . 2 1 8 I F ( B A L L ) d1=d1+2 2 1 9 I F ( B A L L ) V 2 = 2 0 2 2 0 I F ( B A L L ) GO TO 2 0 0 2 2 1 C 2 2 2 C * * * 2 1 *++ ^ 2 2 3 B A L L = . F A L S E . 2 2 4 I F ( S ( d 1 , 2 ) . LT . 1 . 0 5 . AND . S ( d 1 + 1 , 2 ) . LT . 1 . 0 5 . AND. ( S( d 1 + 2 . 8 ) - S ( d 1 - 1 , 8 ) 2 2 5 1 ) . G T . 0 . 2 5 . A N D . S ( d 1 + 2 , 8 ) . G E . 1 . 5 0 ) B A L L = . T R U E . 2 2 6 IF ( B A L L ) d1=d1+2 2 2 7 I F ( B A L L ) V2=21 2 2 8 IF ( B A L L ) GO TO 2 0 0 2 2 9 C 2 3 0 C *** 2 2 *** 2 3 1 B A L L = . F A L S E . 2 3 2 IF ( M ( G ) . E O . 1 9 . A N D . S ( G - 1 , 8 ) . G E . 1 . 6 9 . A N D . M ( G + 1 ) . E O . 4 . A N D . S ( G + 2 . 8 ) . L 2 3 3 1 T . S ( G - 1 . 8 ) ) B A L L = . T R U E . 2 3 4 IF ( B A L L ) d 1 = d 1 - 1 2 3 5 IF ( B A L L ) V 2 = 2 2 2 3 6 IF ( B A L L ) GO TO 2 0 0 2 3 7 C 2 3 8 C *** 2 3 *** 2 3 9 B A L L = . F A L S E . 2 4 0 IF ( S ( d 1 + 2 . 8 ) . G T . S ( d 1 , 8 ) . A N D . ( M ( d1 + 1) . EO . 1 5 . O R . M ( d 1 + 1 ) . E O . 7 . O R . 2 4 1 1 M ( d 1 + 1 ) . E O . 4 ) . A N D . S ( d 1 + 2 , 8 ) . G E . 1 . 0 7 . A N D . S ( d 1 , 8 ) . L T . 1 . 4 2 ) B A L L = 2 4 2 2 . T R U E . 2 4 3 I F ( B A L L ) d1=d1+2 2 4 4 IF ( B A L L ) V 2 = 2 3 2 4 5 I F ( B A L L ) GO TO 2 0 0 2 4 6 C 2 4 7 C * * * 24 * * * 2 4 8 B A L L = . F A L S E . 2 4 9 I F ( S ( d 1 . 2 ) . L T . 1 . 0 5 . A N D . S ( d 1 + 1 , 2 ) . L E . 0 . 7 5 . A N D . S ( d 1 - 1 . 2 ) . L T . 1 . 0 5 2 5 0 1 . A N D . S ( d 1 + 2 . 8 ) . G E . 1 . 0 7 ) B A L L = . TRUE . 251 IF (BALL) d1=d1+2 252 IF (BALL) V2=24 253 IF (BALL) GO TO 200 254 C 255 C *** 25 *** 256 BALL=.FALSE. 257 IF (S(J1 . 8 ) . LT . 1 .07 . AND . S (d 1 - 1 , 8 ) . LT . 1 . 07 . AND . S(d1 -2,8).LT. 1 .65 258 1.AND.S(d1+1,8).GE.1.07) BALL=.TRUE. 259 IF (BALL) d1=d1+1 260 IF (BALL) V2=25 261 IF (BALL) GO TO 200 262 C 263 C *** 26 *** 264 BALL=.FALSE. 265 IF (S(d1.8).GE . 1 .07.AND.S(d1 -2,8).GE. 1.07.AND.S(d1- 1.2).GE.0.75 266 1.AND.S(d1,8).LE.S(d1-2.8).AND.M(d1+1).EO.20.AND.M(d1+3).EO.20) 267 2 BALL=.TRUE. 268 IF (BALL) d1=d1-2 269 IF (BALL) V2=26 270 IF (BALL) GO TO 200 271 C 272 C *** 27 *** 273 BALL=.FALSE. 274 IF((S(d1+1,8)-S(d1,8)).GT.0.20.AND.(S(d1-1.8)-S(d1,8)).LT.0.20 275 1 .AND.S(d1 + 1.8).GE. 1 .07.AND. (d1-2) . LE.K3) BALL=.TRUE. 276 IF (BALL) d1=d1+1 277 IF (BALL) V2=27 278 IF (BALL) GO TO 200 279 C 280 C *** 28 *** 281 BALL=.FALSE. 282 IF ((S(d1+3,8)-S(d1 ,8) ).GE.0.35 .AND.S(d1 + 1,8).LT. 1.07.AND.S(d1+2, 283 18) . LT. 1.07.AND.S(d1- 1 ,8).LT. 1.07.ANDS(d1-2,8).LT.S(d1+3,8).AND. 284 2(d1-2).LE.K3) BALL=.TRUE. 285 IF (BALL) d1=d1+3 286 IF (BALL) V2=28 287 IF (BALL) GO TO 20O 288 C 289 C *** 29 +** 290 BALL=.FALSE. 291 IF (S(d1 .8) .LT. 1 .07.AND.(d1- 1).LE.K3.AND.S(d1 + 1 ,8) .LT. 1 .07.AND. 292 1S(d1+2,8).LT.1.07.AND.S(d1+3,8).GE.1.07) BALL=.TRUE. 293 IF (BALL) d1=d1+3 294 IF (BALL) V2=29 295 IF (BALL) GO TO 200 296 C 297 C *** 30 *** 298 BALL=.FALSE. 299 IF(((S(d1+1,2).LT.0.74.AND.S(d1+2,8).LT.1.07).OR.(S(d1+1.8).LT. 300 11.07.AND.S(d1+2,2).LT.0.74)).AND.S(d1+3.8).GE.1.07.AND.S(d1,8).LE. 301 21.65) BALL =.TRUE. 302 IF (BALL) d1=d1+3 303 IF (BALL) V2=30 304 IF (BALL) GO TO 200 305 C 306 C *** 31 *** 307 BALL=.FALSE. 308 IF (S(d1,8).GE.1 .69 .AND. S(d1 -2.8).GE. 1 .69.AND.S(J1+1,8).LT.S(J1-2, 309 18) . AND . S(d1- 1 ,2) . LT .0. 74 .AND . (d2-d1+ 3).GE.7. AND . (d 1 - 2 ) . GT . K3 ) 310 2 BALL=.TRUE. 311 IF (BALL) d1=d1-2 312 IF (BALL) V2=31 313 IF (BALL) GO TO 200 314 C 315 C *** 32 *** .316 BALL=.FALSE. 317 IF (S(d1,2).LT.0.83.AND.S(d1+1,8) .GE . 1.07.AND.(S(d1 + 1,8)-S(d1-1,8) 318 2).GT.0.30.AND.S(d1-1,8).LT.1.30) BALL=.TRUE. 319 IF (BALL) d1=d1+1 320 IF (BALL) V2 = 32 321 IF (BALL) GO TO 200 322 - C 323 C *** 33 *** 324 LK=d1-3 (-J 325 IF (LK.LE.O) GO TO 100 U l 326 V8=0 327 DO 50 L=LK,d2 328 IF (S(L, 1).LE.0.75) . V8 = V8+1 329 50 CONTINUE 330 LY=(d2+1-LK)/3 331 C 332 BALL=.FALSE. 333 IF (V8.LE.LY.AND.M(d1).EQ.6 .AND.M(d1 - 1).EO.4.AND.S(d1 -2,2).GE. 334 10.75.AND.S(d1-3,2).GE.1.30.AND.S(d1-3,8).GE.1.30) BALL=.TRUE. 335 IF (BALL) J1=d1-3 336 IF (BALL) V2=33 337 IF (BALL) GO TO 200 338 C 339 C *** 34 *** 340 BALL=. FALSE. 34 1 IF (S(d1,8) .GE. 1.69.AND.S(d1-3.8).E0.1.94.AND.S(d1-1,2) GE.0.74 342 1.AND.S(d1-2,2).GT.0.75.AND.S(d1+1,8).LT.S(d1-3,8).AND.N.LE.LY) 343 2 BALL=.TRUE. 344 IF (BALL) J1=d1-3 345 IF (BALL) V2=34 346 IF (BALL) GO TO 200 347 C 348 C 349 C d1 = d1 350 C 351 C 352 C *** 35 *** 353 100 BALL = . FALSE . 354 IF (S(d1,8).GE.1. 50 . AND .5(01-1,8).LT. 1 . 50. AND . S( J 1-2 , 8 ) . LT . 1 . 50 355 1 . AND . S(<J1 + 1 , 8) . GE . 1 . 07 ) BALL = . TRUE . 356 IF (BALL) d1=J1 357 IF (BALL) V2=35 358 IF (BALL) GO TO 200 359 C 360 C *** 36 *** 361 BALL=.FALSE. 362 IF (S(d1,8).GE. 1 .07.AND.S(d1-1,2).LE.0.75.AND.S(d1-2,8).LT.S( J1,8) 363 1 .AND.S(d1+1,8).LT.S(d1,8).AND.S(J1+2,8) .LT . S(d1.8).AND.S(J1 + 1 ,2) 364 2.GE.0.74.AND.S(d1+2,2).GE.0.74) BA LL =.TRUE. 365 IF (BALL) d1=d1 366 IF (BALL) V2=36 367 IF (BALL) GO TO 200 368 C 369 C *** 37 *** 370 BALL=.FALSE. 371 IF (S(d1 .8) .GE. 1 .07.AND.S(d1+1.8).GE.1 .07.AND.(S(J1+1,8)-S(d1.8)) 372 1 .LT.0.20.AND. S ( J 1 - 1 , 2 ) .LT. 1 .05.AND.S(d1 -2,2) .LT. 1 .05) BALL=.TRUE. 373 IF (BALL) d1=d1 374 IF (BALL) V2=37 375 IF (BALL) GO TO 200 376 C 377 C *** 38 *** 378 ' BALL=.FALSE. 379 IF ((M(d1-1).E0.15.0R.M(d1-1).E0.7.0R.M(d1-1).E0.4).AND.(d2-d1+2) 380 1 .LE . 8.AND.(S(d1 + 1,8)-S(J1,8)).LT.O.20.AND.S(d1,8).GE. 1 .07) BALL = 381 2.TRUE. 382 IF (BALL) d1=d1 383 IF (BALL) V2=38 384 IF (BALL) GO TO 200 385 C 386 C *** 39 *** 387 BALL=.FALSE. 388 IF ((J1-1).LE.K3.AND.S(d1,8).GE.1.07.AND(S(d1+1,8)-S(d1,8)).LT. 389 10.20) BALL= . TRUE. 390 IF (BALL) d1=d1 391 IF (BALL) V2=39 392 IF (BALL) GO TO 200 393 C 394 C *** 40 +** 395 BALL=.FALSE. 396 IF (S(d1,8).GE.1.07.AND.(S(d1+1,8)-S(d1,8)).LT.O.20.AND.S(d1-2,2) 397 1.LT.1.05.AND.S(d1-1,2).LT.1.05.AND.S(d1+2,8).LT.S(d1.8).AND.S(d1+1 398 2,2 ) .GE.0.74.AND.S(d1+2,2).GE.0.74) BALL=.TRUE. 399 IF (BALL) d1=d1 400 IF (BALL) V2=40 401 IF (BALL) GO TO 200 402 C 403 C 404 C TO CALL SUBROUTINE FIVE TO CARRY OUT THE ADJUSTMENT OF THE C-BOUN 405 C DARY 406 C 407 200 CALL FIVE 408 RETURN 409 END End of F i l e U l 1 C 2 C 3 SUBROUTINE FIVE 4 C 5 C G C 7 C 8 C 9 C BOUNDARY MOVE OF THE C-TERMINAL 10 C 1 1 C 12 C 13 C 14 c 15 c PURPOSE 1G c TO ADJUST THE C-TERMINAL RESIDUE BASED ON THE BOUNDARY CONFOR 17 c MAT IONAL PARAMETERS OF THE ADJACENT RESIDUES 18 c 19 c 20 c -21 REAL S,T1,T2,A1,A2 ,T3,T4,T5,TT,P 22 INTEGER G,F,H,U,D,V1,V2, V3,V4,V5,V6,V7,V8,0 23 LOGICAL HELLO,BYE ,BALL,MOVE H 24 DIMENSION S(1000,10),M(1000),H(1000),D(1000,16),P(1000,10) 25 COMMON S,T1,T2,T3,T4,T5,TT,A1,A2,P ,V4,V5,V6,V7,V8,0.G,F,H,U,D,NN, o 2G 1NW,KX,MA,MB.MC,MD,L,I,L1,L2,L3,J1,J2,N,K1,K2,V1,V2,IM,M,K3,K4,V3, 27 2BYE,BALL,HELLO,MOVE 28 c 29 c 30 c ... TO CHECK THE NUMBER OF BREAKERS IN THE SECTIONS J1-J2 + 4,J1 -J2 + 3 ... 3 1 c 32 c DESCRIPTION OF PARAMETERS 33 c V8 - ACTUAL NUMBER OF BREAKERS IN THE SEGMENT J1 TO J2+4 34 c JJ - THEORITICAL NUMBER OF BREAKERS IN THE SECTION J1 TO J2+4 35 c MM - ACTUAL NUMBER OF BREAKERS IN THE SEGMENT J1 TO J2+3 3G c JM - THEORITICAL NUMBER OF BREAKERS IN THE SECTION J1 TO J2+3 37 c K3 - C-TERMINAL RESIDUE OF THE PREVIOUS PREDICTED SHEET 38 c 39 J3=J2+4 40 V8=0 41 DO 90 JC=J1,J3 42 IF (S(JC,2).LE.O.75) V8=V8+1 43 90 CONTINUE 44 JJ=(J3+1-J1)/3 45 c 4G J5=J2+3 47 MM=0 48 DO 102 JC=J1,J5 49 IF (S(JC,2).LE.0.75) MM=MM+1 50 102 CONTINUE 51 OM=(05+1-01 )/3 52 C 53 C 54 C . 02 = 02 55 C 56 C 57 C * * * 1 * * * 58 BYE= . FALSE. 59 IF (M(02).EQ.1 . AND.S(J2+1,2).LT. 1.05.AND.S(02-1,2).GE. 1 .47) BYE = 60 1 .TRUE. 6 1 IF (BYE) 02=02 62 IF (BYE) V3=1 63 IF (BYE) GO TO 300 64 C 65 c * * * 2 * * * 66 BYE =.FALSE. 67 IF (S(02,9).GE.1.11.AND.M(02).EQ.5.AND.M(02-1).EO.1.AND.S(02-2,2) 68 1 .GE. 1.30.AND.S(02+1,2 ) .LT . 1 .05) BYE= .TRUE . 69 IF (BYE) 02=02 70 IF (BYE) V3=2 7 1 IF (BYE) GO TO 300 72 c 73 c * * * 3 * * * 74 BYE =.FALSE. 75 IF (M(02).EQ. 1.AND.S(02- 1,9).LT. 1 . 79.AND.T3.EO.3.0.AND.N.EQ.0.AND 76 1 (02+1-01).EO.5) BY E =.TRUE. 77 IF (BYE) 02=02 78 IF (BYE) V3=3 79 IF (BYE) GO TO 300 80 . c 81 c * * * 4 * * * 82 BYE= . FALSE. 83 IF (M(02-1).EQ.19.AND.M(02-2).EQ.20.AND.M(02-3).EQ.13.AND.S(02,2) 84 1.GE.0.75) BYE=.TRUE . 85 IF (BYE) 02=02 86 IF (BYE) V3=4 87 IF (BYE) GO TO 300 88 c 89 c. 90 c MOVE OF 02 91 c 92 c 93 c 94 c * * * 6 *** 95 BYE = . FALSE. 96 IF (S(02,2).GE. 1 .05.AND.S(02+1,9).LT. 1. 11 .AND.S(02 + 2,9) .LT . 1 . 1 1 97 1.AND.S(02+3,9).GE.1.96.AND.((M(02+1).EQ.4.AND.S(02+2,2).GE.0.74) 98 2.OR.(M(02+2).EQ.4.AND.S(02+1,2).GE.0.74)).AND.(02-01+5).GE.7.AND. 99 3MM.LE.0M) BY E =.TRUE. 100 IF (BYE) 02=02+3 101 IF (BYE) V3=6 102 IF (BYE) GO TO 300 103 C 104 C **+7**+ 105 BYE=.FALSE. 106 IF (S(J2,9).LT.1.11.AND.S(d2-1,9).GT.S(d2,9 ) .AND.S(d2+1,9).LT.1.11 107 1.AND.S(J2+2.9).LT. 1. 1 1 .AND.S(d2- 2,9)LE.S(d2-1,9)) BYE =.TRUE. 108 IF (BYE) d2=d2-1 109 IF (BYE) V3 = 7 1 10 IF (BYE) GO TO 300 111 C 112 C * * * 8 * * * 113 BYE=.FALSE. 114 IF (S( J2 + 3 , 9) .GE . 1 .96 . AND . S ( J2 + 2 , 2 ) . GE . 1 .05 . AND . S ( <J2 . 9 ) . LT . 1 . 1 1 115 1.AND. S(d2-1 ,9) .LT. 1 . 1 1.AND.S(J2-2,9).LE.S(J2+3.9).AND. S(02+1,9). 116 2 LT. 1. 11.AND.M(d2+1).NE. 15.AND.M(d2 +1).NE.7.AND.M(J2+1).NE.4.AMD. 117 3MM.LE.dM) 8YE=.TRUE. 118 IF (BYE) d2=d2+3 119 IF (BYE) V3=8 120 IF (BYE) GO TO 300 121 C 122 C *** g *** 123 BYE=.FALSE. 124 IF (S(d2,9).GE. 1. 11.AND.S(d2+3,9).GE.S(d2,9).AND.S(d2-1 ,9).LE. 125 1S(d2 + 3,9).AND.M(d2+1 ) .NE. 15.AND.M(d2+1).NE.4.AND.M(d2+1).NE.7.AND. to 126 2M(d2 + 2).NE. 15.AND.M(d2 + 2).NE.4.AND.M(d2+2).NE.7.AND.(S(d2- 1,2).GE. 127 30.74 .AND.S(d2-2,2).GE.0.74).AND.MM . LT.dM) BYE= . TRUE. 128 IF (BYE) d2=d2+3 129 IF (BYE) V3=9 130 IF (BYE) GO TO 300 131 C 132 C * + * i o * + * 133 BYE=.FALSE. 134 IF (S(d2,9).GE.1.11.AND.S(J2-1,9).LT.1.11.AND.S(d2+4,2).GE.1.05.AN 135 1D.S(d2+1,2) .GE.0.74.AND.S(d2+2,2).GE.0.74.AND.S( d2+3 , 2) .GE .0. 74 136 2.AND.S(d2-1,2).GE.0.74.AND.(S(d2-2,9)-S(d2,9)).LT.0.60.AND.V8.LE. 137 3dd.AND.S(d2+2,9).LT.1.50) BYE=.TRUE. 138 IF (BYE) d2=d2+4 139 IF (BYE) V3=10 140 IF (BYE) GO TO 300 14 1 C 142 C *** 11 * * * 143 BYE=.FALSE. 144 IF ((d2+5).GT.NN) GO TO 100 145 IF (S(d2,9).GE. 1. 11.AND.S(d2- 1,9).GE. 1.50.AND.S(d2 + 4,9).GT . 1 . 1 1 146 1.AND.S(d2+5,9).GT.S(d2+4,9).AND.S(d2+1,2).GT.0.74.AND.S(d2+2,2 ) 147 2.GT.0.74.AND.S(d2+3,2).GT.0.74.AND.(S(d2-1,9)-S(d2+5,9)).LT.0.30 148 3.AND.V8.LE. ((d2 + 6-d1)/3) ) BYE=.TRUE. 149 IF (BYE) d2=d2+5 150 IF (BYE) V3=11 15 1 IF (BYE) GO TO 300 152 C 153 C *** 12 *** 154 100 BYE=.FALSE. 155 IF (S(J2,2).LE.0.75.AND.S(J2-1,2).LE.0.75.AND.M(J2-2).EQ.19.AND. 156 1(S(d2-2,9)-S(u2+1,9)).GE.0.84) BYE=.TRUE. 157 IF (BYE) J2=J2-2 158 IF (BYE) V3=12 159 IF (BYE) GO TO 300 160 C 161 C *** 13 *** 162 BYE=.FALSE. 163 IF (S(J2 - 1 ,9) . LT. 1. 11 .AND.S(U2+1,9).LT. 1 . 11 .AND.S(J2-2,9).GT.S(J2, 164 19) .AND.S(J2-2,9).GE. 1 .79.AND.(J2-2).GT.J1) BYE = . TRUE. 165 IF (BYE) J2=J2-2 166 IF (BYE) V3=13 167 IF (BYE) GO TO 300 168 C 169 C *** 14 '*** 170 BYE=.FALSE. 17 1 IF (S(J2,9) .LT. 1 . 11.AND.S(J2+1,9).GE.1 . 11.AND.(S(J2-1,9)-S(J2+1,9) 172 1).LE.O.60) BYE=.TRUE. 173 IF (BYE) J2=J2+1 174 IF (BYE) V3=14 175 IF (BYE) GO TO 300 176 C 177 C *** 15 *** 178 BYE=.FALSE. 179 IF (S(d2,9).LT .1.11 .AND.S(J2+1,9).GE. 1.11 .AND.(S(J2-1,9)-S(J2+1,9). 180 D.GT.0.60) BYE =.TRUE. 181 IF (BYE) J2=J2-1 182 IF (BYE) V3=15 183 IF (BYE) GO TO 300 184 C 185 C *** 16 *** 186 BYE=.FALSE. 187 IF (S(J2.9) .LE. 1 . 11.AND.S(J2- 1,9).LT. 1. 11 .AND.S(U2-2,9).LT. 1. 11 188 1 .AND.S(J2+1 ,9 ) .LT. 1 . 11 .AND.S(U2 + 2,9) .LT. 1 . 11 .AND. (S(J2-3,9) .GE. 1 . 189 211 .OR.M(J2-3).EQ. 19).AND.(J2-3).GT.J1.AND.S(J2 + 3.9).LT. 1 .96) BYE = 190 3.TRUE. 191 IF (BYE) J2=J2-3 192 IF (BYE) V3=16 193 IF (BYE) GO TO 300 194 C 195 C *** 17 *** 196 BYE=.FALSE. 197 IF ( S (<J2 - 1 , 9 ) . GE . 1 . 79 . AND . ( S ( J2 - 1 , 9 )-S (J2 . 9 ) ) . GE . 0 . 70 . AND . S ( J2+1 , 198 19) . LT . 1 . 11.AND.S(J2-2.9).LT.S(J2-1,9)) BYE= .TRUE. 199 IF (BYE) J2=J2-1 200 IF (BYE) V3=17 201 IF (BYE) GO TO 300 202 C 203 C *** 18 * + * 204 BYE=.FALSE. 205 IF (S(J2-1,9).LT.1.11.AND.S(02+1,9).GT.S(J2.9).AND.S (<J2 , 9).GE. 1. 11 206 1) BY E =.TRUE. 207 IF (BYE) J2=J2+1 208 IF (BYE) GO TO 300 209 C 21Q C * * * 1 9 * * * 211 BYE=.FALSE. 212 IF ( (S(U2-1,9).LT. 1 . 1 1 .OR.S(d2-1 ,9) . LE. S(J2+1.9)).AND.S(J2+1,9) 213 1.GT.S(d2,9).AND.S(d2,9).GE.1.11) BYE =.TRUE. 214 IF (BYE) d2=d2+1 215 IF (BYE) V3=19 216 IF (BYE) GO TO 300 2 17 C 218 C * * * 20 * * * 219 BYE=.FALSE. 220 IF (S(U2+2,9).GE.S(J2,9).AND.(S(J2,9).GE.1.11.OR.M(J2+2).EO.5) 22 1 1 .AND.(M(d2 +1) .NE.15.AND.M(U2+1) .NE.7) .AND. S(d2 + 2,9).GT.S(d2+1,9)) 222 2 BYE= .TRUE. 223 IF (BYE) J2=J2+2 ^ 224 IF (BYE) V3 = 20 ,y\ 225 IF (BYE) GO TO 300 >J> 226 C 227 C * * * 2 1 * * * 228 BYE=. FALSE. 229 IF (S(d2,2) .LT. 1.05.AND,S(J2+1,2).LT. 1.05.AND.S(J2- 1,9).GT.S(J2 + 2. 230 19) .A ND.S(J 2 -1,9).G E. 1 . 11) BY E =.TRUE. 231 IF (BYE) d2=d2-1 232 IF (BYE) V3=21 233 IF (BYE) GO TO 300 234 C 235 Q *** 22 * ** 236 BYE=.FALSE. 237 IF (S(d2 , 2) . LT . 1 .05. AND . S ( J2 - 2 , 9 ) . GT . S (J2 - 1 . 9 ) . AND . S («J2 - 2 , 9 ) .GE . 238 11 .07.AND.S(d2+1,9).LT. 1 . 11 .AND.S(U2+2,9).LT. 1. 11 .AND.(J 2-2) .GT.J1) 239 2BYE =.TRUE. 240 IF (BYE) J2=J2-2 241 IF (BYE) V3=22 242 IF (BYE) GO TO 300 243 C 244 C *** 23 *** 245 BYE=. FALSE. 246 IF (S(d2,9) .GE. 1 . 11 .AND.(S(J2+1,2).GE.0.74.OR,M(J2+1) !E0.4).AND. 247 1S(J2+2.9).GE. 1 . 11 .AND.S(U2- 1,9).GE. 1. 11 .AND.S(U2,9).LT. 1 .96) BYE 248 2=.TRUE. 249 IF (BYE) U2=J2+2 250 IF (BYE) V3=23 251 IF (BYE) GO TO 300 252 C 253 C *** 24 *** 254 BYE=.FALSE. 255 IF (S(J2,2) .GE. 1 .05.AND.S(02 + 3,9).GE. 1.79.AND. S(-J2+2, 2).GE. 1.05 255 1.AND.S(J2-1,2).GE.1.05.AND. (J2-J1 + 5) .GE.7.AND.(M(J2+1).EO.7 .OR. 257 2M(J2+1).EO.4).AND.MM.LE.JM ) BYE=.TRUE. 258 IF (BYE) J2=U2+3 259 IF (BYE) V3=24 260 IF (BYE) GO TO 300 261 C 262 C *** 25 +*+ 263 BYE=.FALSE. 264 ' IF ((J2-U1+1).LE.5.AND.T3.GE.3.0.AND.N.LE.1.AND.M(U2+1).EO.4.AND. 265 1S(J2+2.9).GE.1.11.AND.S(J2+3,9).GE.1.11.AND.S(U2+1,2).GE.1.05.AND. 266 2S(U2+3,2).GE.1.05.AND.MM.LE.JM) BYE =.TRUE. 267 IF (BYE) J2=J2+3 268 IF (BYE) V3=25 269 IF (BYE) GO TO 300 270 C 27 1 C * * * 2 6 * * * 272 BYE=.FALSE. H 273 IF (S(J2,9) . LT. 1 . 11 .AND.S(J2+1,9).LT. 1. 1 1 . AND.(U2+2).GT.NN.AND. <^  274 1S(J2-1.9).GE.1.11) BYE=.TRUE. ^ 275 IF (BYE) <J2 = J2-1 276 IF (BYE) V3 = 26 277 IF (BYE) GO TO 300 278 C 279 C * * * 2 7 * * * 280 BYE=. FALSE. 281 IF (S(J2,9).LT.1.11.AND.S(J2+1.9).LT.1.11.AND.S(J2+2,9).GE.1.79.AN 282 1D.S(J2-2,9).LT.S(U2 + 2,9)) BYE= . TRUE. 283 IF (BYE) U2=J2+2 284 IF (BYE) V3=27 285 IF (BYE) GO TO 300 286 C 287 C *#*28*** 288 BYE=.FALSE. 289 IF ( S ( J2 , 9 ) . GE . 1 . 79 . AND . S ( U2 - 1 , 9 ) . GE . 1 . 79 . AND . S ( <J2 - 2 . 9 ) . GE . 1 . 79 290 1.AND.S(J2-3.9).GE.1.79.AND.M(J2+1).EO.1.AND,M(J2+2).EO.1) BYE= 291 2.TRUE. 292 IF (BYE) J2=d2+2 293 IF (BYE) V3=28 294 IF (BYE) GO TO 300 295 C 296 C *** 29 *** 297 BYE=.FALSE. 298 IF (M(J2).EO.5.AND.S(U2-1,9).GE.1.79.AND.MM.LE.JM.AND.S(U2-2,9).GE 299 1.1.27.AND.S(J2 + 3,9) .GE. 1 .21 .AND.S( <J2+1 ,9).GE.0.74.AND.S(U2 + 2,2) .GE 300 2.0.74) BYE =.TRUE. 301 IF (BYE) J2=J2+3 302 IF (BYE) V3=29 303 IF (BYE) GO TO 300 304 C 305 • C *** 30 *** 30G BYE=.FALSE. 307 IF (S(J2,2).GE.1 .GO.AND.S(J2- 1,2 ) .GE. 1.60.AND.S(02-2,2).GE. 1.38 . AN 308 1D.MM.LE.JM.AND.S(J2+1,2).GE.0.75.AND.(M(U2+2).EQ.7.OR.M(J2+2) . EQ . 309 24).AND.S(J2 + 3,9).GE . 1 .27 ) BYE =.TRUE. 310 IF (BYE) J2=U2+3 311 IF (BYE) V3=30 312 IF (BYE) GO TO 300 313 C 314 c ***31 315 BYE=.FALSE.' 316 IF (M(J2).EQ.20.AND.M(J2+4).EO.20.AND.M(J2-2).EQ.20.AND.S(J2+1,2) 317 1.GE.0.75.AND.S(J2 + 2,2).GE.0.93.AND.S(J2 + 3,2).GE.0.75) BYE=.TRUE . 318 IF (BYE) J2=J2+4 319 IF (BYE) V3=31 320 IF (BYE) GO TO 300 321 C 322 C 323 C J2 = 02 324 C 325 C 326 C 327 C * + * 32 * + * 328 BYE=.FALSE. 329 IF (S(02,9).GE. 1. 11 .AND.S(J2-1,9).LT. 1. 11 .AND.S(J2+1,9).LT. 1. 1 1 330 1.AND.S(J2-2,9).LE.S(d2,9)) BY E =.TRUE. 331 IF (BYE) J2=d2 332 IF (BYE) V3=32 333 IF (BYE) GO TO 300 334 C 335 C *** 33 *** 336 BYE=.FALSE. 337 IF (S(J2,9).GE.1.11.AND.S(J2+1,9).LT.1.11.AND.S(02+2,9).LT.S(U2,9) 338 1 . AND . S(d2- 1 ,9) . LE . S(J2 ,9) . AND . S( J2-2 ,9) . LT .1.11) BYE = . TRUE . 339 IF (BYE) U2=J2 340 IF (BYE) V3=33 341 IF (BYE) GO TO 300 342 C 343 C *** 34 *** 344 BYE=.FALSE. 345 IF (S(J2,9).GE. 1 .27.AND.S(U2+1 ,9) .LT. 1 . 11.AND.(S(U2 + 2,9) . LT . 1 . 1 1 346 1.OR.S(J2+2,9).LT.S(02,9)).AND.S(J2-1,9).LE.S(J2,9).AND.S(J2-2,9) 347 2.LE.S(d2,9)) BYE= . TRUE. 348 IF (BYE) J2=U2 349 IF (BYE) V3=34 350 IF (BYE) GO TO 300 351 C 352 C 353 354 355 356 357 358 359 C 360 C 361 362 363 364 365 366 367 C 368 C 369 370 37 1 H 372 G\ 373 374 375 C 376 c 377 c 378 c 379 c 380 381 382 383 384 385 End of F i l e BYE= . FALSE . IF (S(d2,9).GE. 1 . 11 .AND.(d2-2).LE.d1.AND.S(d2- 1,9).LT . 1 . 1 1 .AND. 1S(J2+1,9).LT.1.11.AND.S(d2+2.9).LT.1.11) BYE=.TRUE. IF (BYE) d2 = d2 IF (BYE) V3 = 35 IF (BYE) GO TO 300 * + + 3^ * + + BYE= . FALSE . IF (S(J2,9).GE. 1.27.AND.S(J2-1,9).GE. 1.21 .AND.S(J2-2,9).GE . 1 . 2 1 1.AND.S(J2+1,9).LT.1.11.AND.S(J2+2,9).LT.1.11) BYE=.TRUE. IF (BYE) d2 = d2 IF (BYE) V3=36 IF (BYE) GO TO 300 BYE=.FALSE. IF (S(02,9).GE. 1 . 11 .AND.S(d2+ 1,9) . LT . 1 . 1 1 .AND.S(J2+2,9).LT. 1 . 11 1.AND.(d2-1).LE.d1) BY E =.TRUE. IF (BYE) J2=J2 IF (BYE) V3 = 37 IF (BYE) GO TO 300 TO PRINT OUT THE FINAL VALUES d1,02 OF THE PREDICTED SHEET. THEN TO RETURN TO SUBROUTINE FIRS TO START THE SEARCH AGAIN 300 K3=d2 PRINT 301,d1,d2,V2.V3 301 FORMAT('0' .25X,'EVENTUAL SHEET FROM d1: ' ,15,5X, 'TO d2:',I5,14X. <,/ *** V2.V3 :',2I5,' ***'//) RETURN . END E f f i c i e n c y o f the 8-turn p r e d i c t i o n A l t h o u g h some s m a l l d i f f e r e n c e s e x i s t e d between the r e s u l t s i n t h i s s t u d y and those r e p o r t e d by Chou and Fasman (1977, 1979) (e.g. c a r b o n i c anhydrase 71-74, 109-112; a - c h y m o t r y p s i n 148-151; a-hemoglobin 81-84; t h e r m o l y s i n 19-22, 43-46), i n g e n e r a l the r e s u l t s i n t h i s s tudy agreed v e r y w e l l w i t h those o f Chou and Fasman (1977, 1979). T h e r e f o r e , n o m o d i f i c a t i o n was needed f o r 8-turn p r e d i c t i o n . The program used f o r 8-turn p r e d i c t i o n c o n s i s t e d o f the main program and one s u b r o u t i n e . The s u b r o u t i n e was the o n l y p a r t p r e s e n t e d i n t h i s s t u d y because the main program was s i m i l a r to the one used f o r a - h e l i x and 8-sheet s e a r c h . 168 1 C 2 C 3 SUBROUTINE TURN 4 C 5 C 6 C 7 c : 8 C PURPOSE 9 C TO LOCATE B-TURNS BY APPLYING THE RULE: <PA> < <PT> > <PB> 10 C AND THE PROBABILITY OF TURN OCCURRENCE SHOULD BE GREATER THAN 11 C 0.000075. AND FOR 2 ADJACENT TURNS THE ONE WITH THE HIGHEST PRO 12 C BABILITY OF OCCURRENCE WILL BE CHOSEN 13 C 14 C 15 C 16 . INTEGER G.F.H.U.D 17 REAL S.T1,T2,A1,A2 .T3 , T4,T5,TT,PRB,P.PRBO,A3 18 LOGICAL HELLO.BYE.BALL 19 DIMENSION S(1000,8),M(1000).H(100) .D(100.16),P(1000.8) 20 COMMON S,T1,T2,A1,A2,T3.T4,T5.TT.PRB.P.G.F.H.U.D.M,IM.I 21 1 NN , NW,N,K,J,MC,HELLO,BYE,BALL 22 C 23 C 24 C DESCRIPTION OF PARAMETERS 25 C I - COUNTER 26 C H - ARRAY TO STORE THE BOUNDARY VALUES OF TURNS 27 C H(I) - N-BOUNDARY VALUE 28 C H(I+1) - C-BOUNDARY VALUE 29 C MB - FIRST RESIDUE OF A TETRAPEPTIDE (=K1) 30 C K2 - FOURTH RESIDUE OF A TETRAPEPTIDE (=K1+3) 31 C A 1 - AVERAGE PA OF A TETRAPEPTIDE 32 C A2 - AVERAGE PB OF A TETRAPEPTIDE 33 C A3 - AVERAGE PT OF A TETRAPEPTIDE 34 C PRB - PROBABILITY OF B-TURN OCCURRENCE 35 C PRBO - PROBABILITY OF B-TURN OCCURRENCE OF THE ADJACENT 36 C PEPTIDE STARTING AT K1-1 37 C 38 C 39 10 1 = 1 40 ' H(I)=0 41 NW = NN-3 I 42 MB = 1 43 20 K2 = MB+3 44 K 1 = MB 45 PRB =0 46 T 1 = 047 T2 = 0 48 T3 = 0 49 A1 = 0 50 A2 = 0 51 A3=0 52 C 53 C TO CALCULATE THE AVERAGE PA,PB,PT OF A TETRAPEPTIDE 54 C 55 DO 25 MC=K1,K2 56 T1=T1+S(MC, 1 ) 57 T2=T2+S(MC,2) 58 T3=T3+S(MC,6) 59 25 CONTINUE 60 A1=Tl/4 .0 61 A2 = T2/4 .0 62 A3 = T3/4 .0 63 PRB = P(K 1 , '1 )*P(K1 + 1 , 2)*P(K 1+2 , 3)*P(K2 , 4 ) 64 PRINT 30,A1,A2.A3,PRB,MB 65 30 FORMAT ( ' ' , 10X, 'A 1: ' ,F6.3 , 5X , ' A2 : ' ,F6.3,5X, 'A3: ' ,F6.3,5X, 'PRB: ' ,F 1 66 1 3.10,18) 67 IF ((A3.GT.A2.AND.A3.GT.A1).AND.(PRB.GT.0.000075).AND.A3.GT . 1.0000 68 1 O) GO TO 50 69 40 MB = MB+ 1 70 IF (MB.LE.NW) GO TO 20 7 1 IF (MB.GT.NW) GO TO 70 72 50 1 = 1+1 73 H(I )=K1 74 1 = 1 + 1 75 H(I)=K2 76 PRINT 55,H(I-1),H(I) 77 55 FORMAT('0' . 10X, 'POTENTIAL BETA-TURN' ,5X,14,5X,14) 78 C 79 C 80 C TO CHECK FOR' THE POSSIBLE PRESENCE OF AN ADJACENT TURN 81 C 82 IF (I.LE.3) GO TO 60 83 IF (K1.EO.(H(I-3)+1 ) ) GO TO 80 84 C 85 60 MB=K1+1 86 IM=I 87 IF (MB.LE.NW) GO TO 20 88 70 PRINT 75,IM 89 75 FORMAT('0',10X.'END OF PROGRAM',5X,16) 90 GO TO 90 91 C 92 C 93 C TO CALCULATE THE PROBABILITY OF OCCURRENCE OF THE ADJACENT TURN 94 C 95 80 KO=H(1-3) 96 PRBO=0 97 PRBO=P(KO,1)*P(K0+1,2)*P(KO+2,3)*P(K0+3,4) 98 IF (PRBO.GT.PRB) PRINT 85,PRBO,PRB,K1,KO 99 85 FORMAT('0',20X,'PRBO:',F11.8,4X,'PRB:',F11.8,6X,'B-TURN NOT AT'.15 100 1 ,' BUT AT',15,/) 101 IF (PRBO.LT.PRB) PRINT 88,PRBO,PRB,KO,K1 102 88 FORMAT('0' ,20X, 'PRBO: ' , F 1 1 . 8 . 4X, 'PRB: ' .F 1 1 .8,6X, 'B-TURN NOT AT' ,15 103 1 ,' BUT AT',15,/) 104 GO TO GO 105 C 106 90 RETURN 107 END End of F i l e . E f f i c i e n c y o f the r e s o l u t i o n o f o v e r l a p p i n g a- and g- areas In g e n e r a l , the p r o c e d u r e o u t l i n e d by Chou and Fasman (1978a, 1978b ) was e f f e c t i v e to s o l v e the dilemma. In the p r e s e n t program, i f more than h a l f o f the c o n d i t i o n s t e s t e d (P a> P^ >; c h a r a c t e r a n a l y s i s ; boundary a n a l y s i s ; r a t i o o f h e l i x l e n g t h to 8 - s h e e t l e n g t h ) f a v o r e d one o f the c o n f o r -m a t i o n s , then t h i s c o n f o r m a t i o n would be adopted. However, i t happened t h a t some cases c o u l d not be e a s i l y s o l v e d because both c o n f o r m a t i o n s ( a - h e l i x and 8 - s h e e t ) were e q u a l l y f a v o r e d . A l t h o u g h the c a l c u l a t i o n s showed t h a t < P a > < < P g > ' the o v e r l a p p i n g s e c t i o n may c o n t a i n more H^ than H^, or l e s s B a than B^. T h i s may be e x p l a i n e d by the h i g h e r v a l u e s o f 8 - s h e e t c o n f o r m a t i o n a l parameters compared to h e l i x ; , thus, they compensate the lower number o f o c c u r r e n c e o f H^ i n the o v e r l a p p i n g r e g i o n s . For ambiguous s i t u a t i o n s (e.g. p a p a i n 26-33, r i b o n u c l e a s e 49-59, myo g l o b i n 100-119, lysozyme 107-114, s u b t i l i s i n 269-275, t h e r m o l y s i n 138-150, t h e r m o l y s i n 160-175, t h e r m o l y s i n 175-180, t h e r m o l y s i n 261-274, t h e r m o l y s i n 234-246), more w e i g h t was g i v e n t o f a c t o r s such as: a) p r e s e n c e o f a n t i p a r a l l e l 8 - s h e e t s . A c c o r d i n g to r u l e 3 f o r s o l v i n g o v e r l a p p i n g a r e a s , a n t i p a r a l l e l 8 - s h e e t s are p r e f e r e n t i a l l y p r e d i c t e d due to i n t e r a c t i o n s which enhance c o n f o r m a t i o n a l s t a b i l i t y . Thus, i n case a n t i p a r a l l e l 8 - s h e e t s are a b s e n t , 172 p r e f e r e n c e f o r l o n g a - h e l i x over s h o r t e r 8 - s h e e t i s one o f the major f a c t o r s t o be c o n s i d e r e d ; e s p e c i a l l y when the h e l i c a l c o n f o r m a t i o n i s s u p p o r t e d by o n l y h a l f or l e s s than h a l f o f the c o n d i t i o n s t e s t e d . b) r a t i o o f h e l i x l e n g t h to -sheet l e n g t h (R^ _> 2.0) and c) c h a r a c t e r a n a l y s i s ( t o take i n t o account the d i f f e r e n t t ypes o f r e s i d u e s , f o r m e r , i n d i f f e r e n t t o , or b r e a k e r o f a- and 8 - c o n f o r m a t i o n ) . S t a p h y l o c o c c a l n u c l e a s e 13-18, 30-39; c o n c a n a v a l i n 125-133; r i b o n u c l e a s e 94-110; a - c h y m o t r y p s i n 85-91; p a p a i n 161-166 a r e examples o f a n t i p a r a l l e l 8 - s h e e t s b e i n g p r e d i c t e d i n s t e a d o f l o n g e r h e l i c e s , a l t h o u g h these r e g i o n s a l s o e x h i b i t good p o t e n t i a l f o r h e l i c a l c o n f o r m a t i o n . The r e f e r e n c e t o known p r o t e i n s i n the p r e d i c t i o n of unknown ones i s v e r y u s e f u l , e s p e c i a l l y when some homolo-gy e x i s t s between the known and unknown p r o t e i n s (Argos et a l . , 1976). T h i s was observed i n the p r e s e n t study f o r the p r e d i c t i o n o f p r o t e i n a s e i n h i b i t o r s . The f o l l o w i n g program was w r i t t e n t o a s s e s s the d i f f e r e n t i m p o r t a n t f a c t o r s c o n t r i b u t i n g to the r e s o l u t i o n o f o v e r l a p p i n g a- and 8 - r e g i o n s . An e x t r a p a r t to r e a d p a i r s o f o v e r l a p p i n g h e l i c e s and 8 - s h e e t s was added to the main program common to the s e a r c h o f a - h e l i x , 8 - s h e e t and 8 - t u r n . 173 1 c 2 C 3 C EXTRA PART FOR OVERLAPPING AREAS 4 C 5 C TO READ IN PAIRS OF OVERLAPPING HELIX AND SHEETS 6 C 7 C 9 C DESCRIPTION OF PARAMETERS 10 C NR - NUMBER OF LINES OF DATA (16 DATA PER LINE) 11 C NT - TOTAL NUMBER OF DATA 12 C AH - ARRAY TO STORE THE HELICAL VALUES 13 C AH(I) - N-TERMINAL VALUE 14 C AH(I+1) - C-TERMINAL VALUE 15 C SH - ARRAY TO STORE THE SHEET VALUES 16 C SH(I) - N-TERMINAL VALUE 17 C SH(I+1) - C-TERMINAL VALUE 18 C 19 C 20 PRINT 35 21 35 FORMAT('PAIRS OF OVERLAPPING HELICES AND SHEETS') 22 PRINT 36 23 36 FORMAT( ' ' , ' .'....'/) 24 READ(5,40) NT,NR !~J 25 40 F0RMAT(6X, I4.6X, 14) ^ 26 41 F0RMAT(16I5) 27 WRITE (6,42) ((R(J,K),K=1 , 16 ) ,U =1.NR) 28 42 FORMAT(' ',1615) 29 . IM=NT/2 30 C 31 1 = 1 32 DO 52 J= 1 , NR 33 DO 51 K=1,16,2 34 AH(I)=R(J,K) 35 IF (AH(I).EO.O) GO TO 54 36 1 = 1 + 1 37 51 CONTINUE 38 52 CONTINUE 39 C 40 54 1=1 4 1 DO 56 J=1,NR 42 DO 55 K=2,16,2 43 SH(I)=R(J,K) 44 IF (SH(I).EQ.O) GO TO 60 45 1=1+1 46 • 55 CONTINUE 47 56 CONTINUE 48 C 49 C TO CALL SUBROUTINE 0LA1 TO CARRY OUT THE COMPARISON OF PA,PB OF 50 C EACH REGION AND THAT OF THEIR OVERLAPPING AREA 51 C < o _1 CL O a < h- z o l/"> UJ o to CM ro 1 LO «-LO LO LO LO 0 "U c UJ 1 7 -0 cn 1 C 2 C 3 C 4 SUBROUTINE 0LA1 5 • C S C 0LA1 - PROCEDURE OF OVERLAPPING ff 1 7 C 8 C g c 10 C PURPOSE 1 1 c TO COMPARE THE AVERAGE PA, PB OF THE PREDICTED HELIX (H1-H2),0F THE 1 2 c SHEET (S1-S2),AND OF THEIR OVERLAPPING AREA AND TO CALCULATE THE 13 c RATIO HELIX LENGTH/SHEET LENGTH 14 15 c c 16 c 17 REAL A1,A2,S,T1,T2,TTH,TTS,P,HN,HC,NHN,NHC,SN,SC,NSN,NSC,HHF,HF, 18 1 IIH.IH.BH.BBH.SSF,SF,IS,BS,BBS 19 INTEGER H1 .H2.S1 .S2.AH.SH.IT1, IT2.D.R 20 DIMENSION S(1000,20),AH(1000),SH(1000),M(1000),R(1000,16),D(1000, 21 1 16),P(1000,10) 22 COMMON A1,A2,S.T1 ,T2,TTH,TTS,P,HN,HC,NHN,NHC,SN,SC,NSN,NSC,HHF,HF 23 1 ,IIH.IH.BH.BBH,SSF,SF,IS.BS.BBS.HI,H2,S1,S2.AH,SH.IT1 . IT2,D.R.NR, 24 2 NT.NN.N.M.IM,I,K,J 25 c 26 c 27 c DESCRIPTION OF PARAMETERS 28 c I - COUNTER 29 c H1 - N-TERMINAL OF THE PREDICTED HELIX 30 c H2 - C-TERMINAL OF THE PREDICTED HELIX 31 c S1 - N-TERMINAL OF THE PREDICTED SHEET 32 c S2 - C-TERMINAL OF THE PREDICTED SHEET 33 c LH - HELIX LENGTH 34 c LS - SHEET LENGTH 35 c A1 - AVERAGE PA OF A SECTION 36 c A2 - AVERAGE PB OF A SECTION 37 c 38 c 39 c EVERY TIME I INCREASES BY 1 A NEW SET OF OVERLAPPING HELIX AND SH 40 c EET IS SUBJECTED TO THE ANALYSIS 41 c 42 1 = 1 43 1 1=1+1 44 IF (I,GT.IM) GO TO 300 45 c 46 H1=AH(I-1) 47 H2=AH(I) 48 S1=SH(I-1) 49 S2=SH(I) 50 LH=H2-H1+1 51 LS=S2-S1+1 52 A1=LH/LS 53 PRINT 5,LH,LS,A1 ' 54 5 FORMAT('-',20X. ' * * * COMPARISON OF THEIR LENGTH + * *' ,5X, 'L-HELIX 55 1 14,3X, 'L-SHEET ' : ' ,14,5X, 'RATIO = LH/LS: ' ,F4. 1) 56 PRINT 8 57 8 FORMAT('0',30X, ****** COMPARISON OF P-HELIX AND P-SHEET *+***') 58 C 59 K= 1 60 GO TO 110 61 10 IF (A1.GT.A2) PRINT 11,H1,H2,A1 ,A2 62 1 1 FORMAT('0'.15X, 'H1 : ',14,3X,'H2 :',14,5X,'A1:',F6.3,3X,'A2:',F6 63 1 10X,'A1 > A2 FROM H1 TO H2 ' ) 64 IF (A1.LT.-A2) PRINT 12,H1,H2,A1,A2 65 12 FORMAT('0',15X,'H1 : ' ,I4,3X, 'H2 : ' ,14,5X, 'A 1 : ' ,F6.3,3X, 'A2: ' .F6 66 1 10X,'A1 < A2 FROM H1 TO H2' ) 67 C 68 K = 2 69 GO TO 120 70 20 IF (A1.GT.A2) PRINT 21 ,S1 ,S2, A1 ,A2 7 1 2 1 FORMAT('0'.15X, 'S1 : ' ,I4.3X, 'S2 : ' .I4.5X, 'A1 : ' .F6.3.3X, 'A2: ' ,F6 72 1 10X,'A1 > A2 FROM S1 TO S2' ) 73 IF (A1.LT.A2) PRINT 22,S1 ,S2,A1 ,A2 74 22 FORMAT('0' . 15X, 'S1 : ' ,14,3X, 'S2 : ' ,14,5X, 'A1 : ' ,F6.3,3X, 'A2: ' ,F6 75 1 10X.'A1 < A2 FROM S1 TO S2' ) 76 C 77 IF (SH(I-1).LT. AH(I- 1).AND.SH(I).GT.AH(I-1).AND.SH(I).LT.AH(I)) 78 1 K = 3 79 IF (SH(I-I).LT. AH( I- 1).AND.SH(I).GT.AH(1-1).AND.SH(I).LT.AH(I) ) 80 1 GO TO 130 81 C 82 IF (AH(I-I).LT. SH( I- 1).AND.AH(I).GT.SH(1-1).AND.AH(I).LT.SH(I ) ) 83 1 K = 4 84 IF (AH(I-1).LT. SH( I- 1) .AND.AH(I) .GT.SH(I-1).AND.AH( I) .LT.SH(I)) 85 1 GO TO 140 86 C 87 C TO CALL SUBROUTINE 0LA2 TO ANALYZE THE TYPES OF RESIDUES WITHIN 88 C EACH SECTION 89 C 90 50 CALL 0LA2 91 GO TO 1 92 C 93 C 94 1 10 L1=H1 95 L2=H2 96 GO TO 200 97 120 L1=S1 98 L2 = S2 99 GO TO 200 100 130 L1=AH(I-1) 101 L2=5H(I) 102 GO TO 200 103 140 L1=SH(I-1) 104 L2=AH(I) 105 GO TO 200 106 C 107 C TO CALCULATE PA,PB OF THE REGION L1-L2 108 C 109 200 A 1=0 110 A2=0 111 T1=0 112 T2=0 113 DO 210 L=L1,L2 114 T1=T1+S(L,1) 115 T2=T2+S(L,2) 116 210 CONTINUE 117 A1=T1/(L2+1-L1) 118 A2=T2/(L2+1-L1) 119 C 120 IF (K.EQ.1) GO TO 10 121 IF (K.EQ.2) GO TO 20 ~0 122 IF (K.EQ.3) GO TO 230 0 0 123 IF (K.EQ.4) GO TO 240 124 C 125 230 PRINT 232 126 232 FORMAT( 'O' ,25X, '*** P-HELIX AND P-SHEET OF INTERS. AREA : H1 TO S2 127 1 ***') 128 IF (A1.GT.A2) PRINT 233. L1, L2.A1.A2 1 29 233 FORMAT('0' . 15X. 'OL1 : ' , 14,3X, '0L2: ' ,14,5X, 'A 1: ' .F6.3,3X, ' A2 : ' .F6.3, 130 1 10X,'A1 > A2 FROM H1 TO S2'./) 131 IF (A1.LT.A2) PRINT 234, L1, L2.A1.A2 132 234 FORMAT('0' . 15X. 'OL1 : ' .14,3X, '0L2: ',14,5X, 'A 1: ',F6.3,3X, 'A2 : ' .F6.3, 133 1 10X,'A1 < A2 FROM H1-T0 S2',/) 134 GO TO 50 135 C 136 240 PRINT 242 137 242 FORMAT('0' ,25X, '*** P-HELIX AND P-SHEET OF INTERS. AREA : S1 TO H2 138 1 *** ' ) 139 IF (A1.GT.A2) PRINT 243, L1, L2,A1,A2 140 243 FORMAT('0' , 15X, 'OL1 : ' , 14,3X, '0L2: ' . 14,5X, 'A 1 : ' .F6.3,3X, ' A2 : ' ,F6.3, 141 1 10X,'A1 > A2 FROM S1 TO H2'./) 142 IF (A1.LT.A2) PRINT 244, L1, L2.A1.A2 143 244 FORMAT('0' . 15X, 'OL1 : ' . 14 , 3X , '0L2: ' , 14 , 5X , ' A 1 : '.F6.3,3X, 'A2 : ' ,F6 . 3 , 144 1 10X.'A1 < A2 FROM S1 TO H2',/) 145 GO TO 50 146 C 147 300 PRINT 305 148 305 FORMAT('0',1OX,'END OF PROGRAM') 149 RETURN 150 END End of f i l e SUBROUTINE 0LA2 OLA2 - PROCEDURE OF OVERLAPPING H 2 PURPOSE TO COMPARE THE TYPES OF RESIDUES (BREAKER,FORMER,INDIFFERENT) CONTAINED IN THE PREDICTED HELIX (H1-H2).THE SHEET (S1-S2),AND IN THEIR OVERLAPPING AREA • REAL A 1,A2,S.T1 ,T2,TTH,TTS,P,HN,HC,NHN,NHC,SN,SC,NSN,NSC.HHF,HF, 1 IIH,IH.BH.BBH,SSF,SF,IS,BS.BBS INTEGER H1,H2,S1,S2,AH,SH,IT1,IT2.D.R DIMENSION S(1000,20),AH(1000),SH(1000),M(1000),R(1000,16),D(1000, 1 16),P(1000,10) COMMON A 1 , A2 , S . T 1 , T2 , TTH. TTS . P , HN , HC , NHN . NHC , SN-, SC , NSN, NSC , HHF , HF 1 ,IIH,IH.BH.BBH,SSF,SF,IS.BS,BBS,H1,H2,S1.S2,AH,SH,IT1,IT2,D,R.NR. 2 NT.NN.N.M.IM.I.K.d DESCRIPTION OF PARAMETERS HHF - COUNTER FOR STRONG HELIX-FORMER HF - COUNTER FOR HELIX-FORMER IIH - COUNTER FOR WEAK HELIX-FORMER IH - COUNTER FOR HELIX-INDIFFERENT BH - COUNTER FOR HELIX-BREAKER BBH - COUNTER FOR STRONG HELIX-BREAKER SSF - COUNTER FOR STRONG SHEET-FORMER SF - COUNTER FOR SHEET-FORMER IS - COUNTER FOR SHEET-INDIFFERENT BS - COUNTER FOR SHEET-BREAKER BBS - COUNTER FOR STRONG SHEET-BREAKER TTH - TOTAL OF THE DIFFERENT HELIX COUNTERS BBH TTS - TOTAL OF THE DIFFERENT SHEET COUNTERS K - COUNTER =HHF+HF+IIH+IH+BH+ PRINT 5 5 FORMAT('0',32X,'*** COMPARISON OF ASSIGNMENTS TYPES ***'/) K=1 GO TO 1 10 10 IF (TTH.GT.TTS) PRINT 13,H1,H2,TTH,TTS 13 FORMAT('O' ,15X, 'H1 :',I4.3X,'H2 : ' , 14,5X, 'TTH: ' .F6.3.3X, 'TTS: ' ,F6. 51 1 3,10X,'TTH > TTS FROM H1 TO H2'/) 52 IF ( T T H . L T . T T S ) PRINT 14,H1,H2,TTH,TTS 53 14 FORMAT('0'.15X, 'H1 : ' , I 4 . 3 X , 'H2 : ' , I 4 . 5 X . 'TTH:', F 6 . 3 . 3 X , 'TTS: ' , 54 1 3,10X,'TTH < TTS FROM H1 TO H2'/) 55 C 56 K = 2 57 GO TO 120 58 20 IF (TTH.GT.TTS) PRINT 23,S1 ,S2,TTH,TTS 59 23 FORMAT('0',15X,'S1 : ' , I 4 , 3 X , ' S 2 : ' , I 4 , 5 X , 'TTH:'. F 6 . 3 . 3 X , ' T T S : ' , 6 0 1 3,10X,'TTH > TTS FROM S1 TO S2'/) 61 I F ( T T H . L T . T T S ) PRINT 24.S1,S2.TTH,TTS 62 24 FORMAT('0',15X, 'S1 : ' , I 4 . 3 X , 'S2 : ' ,14,5X, 'TTH:', F 6 . 3 , 3 X , 'TTS: ' , 63 1 3,10X,'TTH < TTS FROM S1 TO S2'/) 64 C 65 C TO CHECK THE BOUNDARIES OF THE OVERLAPPING AREA. IN CASE B-SHEET 66 C I S CONTAINED WITHIN A - H E L I X NO NEED TO CARRY OUT THE : A N A L Y S I S FOR 67 C THE : OVERLAPPING AREA AGAIN. 68 C 69 I F ( S H ( I - 1 ) . L T . A H ( I - 1 ) . A N D . S H ( I ) . G T . A H ( I - 1).AND. S H ( I ) . L T . A H ( I ) ) 70 1 K = 3 71 I F ( S H ( I - I ) . L T . A H ( I - 1 ) . A N D . S H ( I ) . G T . A H ( I - 1).AND. S H ( I ) . L T . A H ( I ) ) 1—1 72 1 GO TO 130 00 73 C o 74 75 I F ( A H ( I - I ) . L T . 1 K = 4 S H ( I - 1 ) . A N D . A H ( I ) . G T . S H ( I - 1).AND. A H ( I ) . L T . S H ( I ) ) 76 I F ( A H ( I - I ) . L T . S H ( I - 1 ) . A N D . A H ( I ) . G T . S H ( I - 1).AND. A H ( I ) . L T . S H ( I ) ) 77 1 GO TO 140 78 C 79 c TO CALL SUBROUTINE 0 L A 3 TO CARRY OUT THE BOUNDARY A N A L Y S I S OF EACH 8 0 c REGION 8 1 c 82 5 0 C A L L 0 L A 3 83 RETURN 84 c 85 i i o L 1 =H1 86 L2 = H2 87 GO TO 200 88 120 L 1 = S 1 89 L2 = S2 9 0 GO TO 200 91 130 L 1 = A H ( I - 1 ) 92 L 2 = S H ( I ) 93 GO TO 200 94 140 L 1 = S H ( I - 1 ) 95 L 2 = A H ( I ) 96 GO TO 200 97 c 98 c TO CALCULATE THE DIFFERENT TYPES OF RESIDUES IN THE REGION L 1 - L 2 99 C 100 2 0 0 HHF =0 101 HF=0 102 IIH=0 103 IH=0 104 BH=0 105 BBH=0 106 SSF=0 107 SF=0 108 IS=0 109 IS=0 110 BS=0 111 BBS=0 112 TTH=0 113 TTS=0 114 C 115 DO 210 L = L1,L2 116 IF ( S ( L , 1 ) .GT.1.16) HHF=HHF+2.00 117 IF (S(L, 1).GT. 1.01 .AND.S(L, 1) .LE. 1 . 16) HF=HF+1.00 118 IF (S(L, 1).GT.0.98.AND.S(L. 1 ) . LE . 1.01) IIH=IIH+0.50 119 IF (S(L,1).GT.0.69.AND.S(L,1).LE.0.98) IH=IH+0.25 120 IF (S(L,1).GT.0.57.AND.S(L,1).LE.0.69) BH=BH-0.50 121 IF (S(L, 1).LE.0.57) BBH=BBH-1.00 H 122 IF (S(L,2).GT.1.38) SSF=SSF+2.00 CO 123 IF (S(L,2).GT.0.93.AND.S(L,2).LE.1.38) SF=SF+1.00 H 124 IF (S(L,2).GT.0.75.AND.S(L,2).LE.O.93) IS=IS+0.25 125 IF (S(L,2).GT.0.55.AND.S(L,2).LE.O.75) BS=BS~0.50 126 IF (S(L,2).LE.O.55) BBS=BBS-1.00 127 210 CONTINUE 128 TTH = HHF + HF +11H+1H+BH+BBH 129 TTS=SSF+SF+0.0+IS+BS+BBS 130 PRINT 211 131 211 FORMATC ',11X,'HHF',6X,'HF',5X,'IIH',6X,'IH',6X,'BH',5X,'BBH',5X. 132 1 'SSF' ,SX, 'SF' ,6X, 'IS' .6X, 'BS' ,5X, 'BBS') 133 PRINT 212,HHF,HF,IIH,IH.BH.BBH,SSF.SF,IS,BS,BBS 134 212 FORMAT(' ',10X,11(F5.2.3X)) 135 C 136 IF (K.EO.1) GO TO 10 137 IF (K.EQ.2) GO TO 20 138 IF (K.EQ.3) GO TO 230 139 IF (K.EQ.4) GO TO 240 140 C 141 230 PRINT 231 142 231 FORMAT( '0' ,28X. '*** ASSIGNM. TYPES IN OVERL. AREAS : H1 TO S2 *** 143 1 ' ) 144 IF (TTH.GT.TTS) PRINT 235, L1, L2,TTH,TTS 145 235 FORMAT('0' , 15X, 'OL1: ' , 14 , 3X , ' 0L2 : ' ,14,5X. 'TTH: '.F6.3.3X. 'TTS: ' ,F6. 146 1 3,10X,'TTH > TTS FROM H1 TO S2'/) 147 IF (TTH.LT.TTS) PRINT 236, L1, L2,TTH,TTS 148 236 FORMAT('0' , 15X, 'OL 1 : ' ,14,3X, '0L2 : ' ,14,5X. 'TTH: ' .F6 . 3 , 3X , 'TTS : ' . F6 . 149 1 3,10X.'TTH < TTS FROM H1 TO S2'/) 150 GO TO 50 151 C 152 240 PRINT 24 1 153 241 FORMAT('O' ,28X, '*** ASSIGNM. TYPES IN OVERL. AREAS : S1 TO H2 *** 154 1 ' ) 155 IF (TTH.GT.TTS) PRINT 245, L1, L2,TTH,TTS 156 245 FORMAT( 'O' , 15X, 'OL1 : ' ,14,3X, '0L2: ' , I 4,5X, 'TTH: ' ,F6.3,3X, 'TTS : ' ,F6. 157 1 3,10X,'TTH > TTS FROM S1 TO H2'/) 158 IF (TTH.LT.TTS) PRINT 246, LI, L2,TTH,TTS 159 246 FORMAT('0' , 15X, 'OL1 : ' ,14,3X, '0L2 : ' , 14 , 5X , 'TTH: ' ,F6 . 3,3X , 'TTS : ' ,F6. 160 1 3.10X,'TTH < TTS FROM S1 TO H2'/) 161 GO TO 50 162 END End of F i l e 00 1 1 2 C 3 C 4 SUBROUTINE OLA3 5 C 6 C 0LA3 - PROCEDURE OF OVERLAPPING H 3 7 C 8 C 9 C 10 C PURPOSE 11 C TO COMPARE THE SUM OF THE BOUNDARY CONFORMATIONAL PARAMETERS OF 12 C THE PREDICTED HELIX AND SHEET. ONLY THE 3 RESIDUES BELONGING TO 13 C THE BOUNDARIES OF EACH SECTION AND THOSE 3 ADJACENT TO THE BOUN 14 C DARIES ARE CONSIDERED 15 C 16 C 17 C 18 REALA1.A2.S,T1,T2,TTH,TTS,P,HN,HC,NHN,NHC,SN.SC,NSN,NSC.HHF,HF, 19 1 11H,IH,BH,BBH,SSF,SF,IS,BS,BBS 20 INTEGER H1,H2,S1,S2,AH,SH,IT1,IT2,D,R 21 DIMENSION S(1000,20),AH(1000).SH(1000),M(1000),R(1000.16),D(1000, 22 1 16 ) ,P(1000, 10) 23 COMMON A1,A2.S.T1,T2,TTH.TTS,P,HN.HC,NHN,NHC.SN,SC.NSN,NSC,HHF,HF 24 1 ,IIH,IH,BH.BBH,SSF,SF,IS,BS,BBS,H1,H2.S1,S2,AH.SH,IT1,IT2.D,R.NR. 25 2 NT.NN.N.M.IM,I,K,J 26 C 27 C 28 C DESCRIPTION OF PARAMETERS 29 C HN - SUM OF THE BOUNDARY CONFORMATIONAL PARAMETERS OF THE 3 RE 30 C SIDUES BELONGING TO THE HELIX N-TERMINAL 3 1 C HC - SUM OF THE BOUNDARY CONFORMATIONAL PARAMETERS OF THE 3 RE 32 C SIDUES BELONGING TO THE HELIX C-TERMINAL 33 C NHN - SUM OF THE BOUNDARY CONFORMATIONAL PARAMETERS OF THE 3 RE 34 C SIDUES ADJACENT TO THE HELIX N-TERMINAL 35 C NHC - SUM OF THE BOUNDARY CONFORMATIONAL PARAMETERS OF THE 3 RE 36 C SIDUES ADJACENT TO THE HELIX C-TERMINAL 37 C 38 C REMARKS 39 C THE DEFINITIONS OF SN,SC,NSN,SNC ARE SIMILAR TO HN,HC,NHN.HHC 40 C EXCEPT THAT SHEET IS CONSIDERED INSTEAD OF HELIX 41 C 42 HN=0 43 HC=0 44 NHN = 0 45 NHC=0 46 HN=S(H1,8)+S(H1+1.8)+S(H1+2,8) 4 7 HC=S(H2,9)+S(H2-1,9)+S(H2-2,9) 48 IF ((H1-3).LE.0) NHN=0 49 IF ((H1-3).LE.0) GO TO 1 50 NHN=S(H1-1,6)+S(H1-2.6)+S(H1-3,6) 51 1 IF ((H2+3) GT.NN) NHC=0 52 IF ((H2+3).GT.NN) GO TO 2 53 NHC=S(H2+1.7)+S(H2+2,7)+S(H2 + 3 , 7) 54 C 55 2 SN=0 5G SC=0 57 NSN=0 58 NSC=0 59 SN=S(S1,10)+S(51+1,10)+S(S1+2,10) 60 SC = S(S2,11) + S(S2-1. 1 1 ) + S(S2-2,11) 61 IF ((S1-3).LE.0) NSN=0 62 IF ((S1-3).LE.0) GO TO 3 63 NSN=S(S1-1,12)+S(S1-2,12)+S(51-3,12) 64 3 IF ((S2+3).GT.NN) NSC = 0 65 IF ((S2+3).GT.NN) GO TO 4 66 NSC=S(S2+1,13)+S(S2+2,13)+5(S2+3.13) 67 C 68 4 PRINT 10,H1,H2,S1,S2 69 10 FORMAT('0',12X,' BOUNDARY ANALYS. FOR HELIX FROM: ' , 1 5 , ' TO:', 70 1 I5,3X,'AND FOR SHEET FROM: ' , 1 5 , ' T O : ' , 1 5 / ) 71 PRINT 11 M 72 11 FORMAT(' ',12X,'HN',7X,'SN',7X,'HC',7X,'SC',6X,'NHN',6X,'NSN',6X, 00 73 1 'NHC ,6X, 'NSC' ) ** 74 PRINT 12,HN,SN,HC,SC,NHN,NSN,NHC,NSC 75 12 FORMAT(' ',1OX,8(F5.2,4X)//) 76 1 =1+1 77 RETURN 78 END End of F i l e Comparison o f the p r e d i c t i v e a c c u r a c y In T a b l e s 5 and 6 (p. 189 and 198) the r e s u l t s o f Chou and Fasman (1974b) , those o f X-ray a n a l y s i s (Chou and Fasman, 1974b) and those o b t a i n e d b e f o r e and a f t e r r e f i n e m e n t of the program o f t h i s s t u d y are p o o l e d t o g e t h e r . The p r e d i c -t i o n o f the d i f f e r e n t c o n f o r m a t i o n s o f lysozyme (egg w h i t e ) was chosen as an example o f the output y i e l d e d by the p r e s e n t program ( A p p e n d i x ) . The q u a l i t y o f p r e d i c t i o n was a s s e s s e d by the parameters Q a, and the c o e f f i c i e n t s C^, C^ c a l c u l a t e d f o r most o f the p r o t e i n s used i n t h i s s tudy (X-ray d a t a were not a v a i l a b l e f o r some p r o t e i n s ) . For the 8-turn s e a r c h , as r e s u l t s o f the p r e s e n t s t u d y were almost the same as those o f Chou and Fasman (1979) , i t i s r e a s o n a b l e to assume t h a t the a c c u r a c y o b t a i n e d i n t h i s s t u d y i s comparable to t h a t o f Chou and Fasman (1979). A l t h o u g h Chou and Fasman r e p o r t e d t h e i r r e s u l t s and compared them to; X-ray. d a t a (Chou and Fasman, 1979), t h i s e n t i r e p r o c e d u r e w i l l not be r e p e a t e d a g a i n . T a b l e s 7 and 8 (p. 207 and 209) l i s t the v a l u e s o f Q a, C^ and Q^, C^, r e s p e c t i v e l y as o b t a i n e d by Chou and Fasman (1974b) and by the p r e s e n t program. As an e x t r a r e f e r e n c e , v a l u e s r e p o r t e d by Argos et. al_. (1976), who used j o i n t p r e d i c t i o n h i s t o g r a m s r e s u l t i n g from the c o m b i n a t i o n o f f i v e c o m p u t e r i z e d methods ( i n c l u d i n g the method o f Chou and Fasman) were a l s o used 185 The good agreement between X-ray d a t a and the p r e -d i c t i o n from t h i s s tudy (C _> 0.40), except f o r c o n c a n a v a l i n A and a - c h y m o t r y p s i n (C = 0.39), was expected s i n c e t h i s was the aim i n r e f i n i n g the program. In g e n e r a l , the p r e d i c t i v e a c c u r a -cy r e p o r t e d by Chou and Fasman (1974b) was c l e a r l y s u p e r i o r to t h a t o f Argo.s et • a l . (1976), except f o r cytochrome c and myo-gen (Qa» C^). The p a i r e d - s a m p l e t - t e s t r e v e a l e d t h a t the v a l u e s o f C a (P < 0.01) and C g (P < 0.05) c a l c u l a t e d f o r the p r e s e n t p r e d i c t i o n were s i g n i f i c a n t l y improved from the v a l u e s o f Chou and Fasman (1974b). One may argue about the v a l i d i t y o f the pa-rameters Q and C i n t h i s study,and the r e l i a b i l i t y o f the p r e s -e n t , program when a p p l i e d to unknown p r o t e i n s s i n c e the p r e s e n t program was a d j u s t e d to f i t X-ray data : on the b a s i s o f a l i m -ited number o f samples (24 p r o t e i n s ) . Chou and Fasman (1978b) s t u d i e d the i n f l u e n c e o f n e i g h b o u r i n g r e s i d u e s (n-1) and (n+1) i n d i p e p t i d e s and t r i p e p t i d e s on the c o n f o r m a t i o n o f amino a c i d n. They noted t h a t the i n t e r a c t i o n s o f some r e s i d u e s w i t h h i g h a - h e l i x or 3-sheet p o t e n t i a l may r e s u l t i n d i p e p t i d e s or t r i -p e p t i d e s w i t h much lower c o n f o r m a t i o n a l parameters ( e . g . , the c o m b i n a t i o n o f Lys and G l u ) . Hence e f f o r t s to improve the q u a l i t y o f the p r e d i c t i v e methods are s t i l l n e c e s s a r y and one may expect t h a t the e v e n t u a l 'program w i l l become more and more c o m p l i c a t e d s i n c e so many d i f f e r e n t f a c t o r s must be c o n s i d e r e d i n o r d e r to o b t a i n good agreement w i t h X-ray d a t a . Argos e_t a l . 186 (1976) s u g g e s t e d t h a t a p e r f e c t p r e d i c t i v e a l g o r i t h m s h o u l d i n c l u d e a c o n s i d e r a t i o n o f energy m i n i m i z a t i o n , t h e r m a l i z a t i o n , land l o n g - r a n g e i n t e r a c t i o n s . In t h e i r s t u d y , the use o f j o i n t p r e d i c t i o n h i s t o g r a m s , which were shown t o be s u p e r i o r to any i n d i v i d u a l p r e d i c t i o n , d i d not always y i e l d good agreement w i t h X-ray d a t a . Hence, i n the p r e s e n t s t u d y , the m o d i f i c a -t i o n s made to the p r e s e n t program are not c o m p l e t e l y u s e l e s s because i f the models used are a d j u s t e d to f i t e x p e r i m e n t a l d a t a , they can s t i l l p r o v i d e some u s e f u l g u i d e l i n e s f o r un-known systems. In f a c t , i n r e f i n i n g the p r e s e n t program, more c o n s i d e r a t i o n ' t o .' the i n f l u e n c e o f the n e i g h b o u r i n g r e s i -dues, e s p e c i a l l y a t the b o u n d a r i e s , and to the c o n f o r m a t i o -n a l p o t e n t i a l o f the ad j a c e n t . s e g m e n t s , was emphasized. As a r e s u l t , the number o f o v e r l a p p i n g areas between a - h e l i x and B-sheet or between a - h e l i x and B-turn was d e c r e a s e d (Table 5). In g e n e r a l , the p r e d i c t e d r e g i o n s a l s o had boundary r e s i -dues w i t h f a v o r a b l e c o n f o r m a t i o n a l parameters. Hence, at l e a s t one may be c o n f i d e n t t h a t areas w i t h s t r o n g p o t e n t i a l f o r a s p e c i f i c c o n f o r m a t i o n w i l l not be missed when u s i n g the p r e s e n t program. S p e c i a l s i t u a t i o n s may not p e r m i t the a t t a i n -ment o f s a t i s f a c t o r y r e s u l t s . Argos et_ al_. (1976) and Matthews (1975a) agreed t h a t no f a v o r a b l e p r e d i c t i o n can be ex p e c t e d f o r unknown pro-t e i n s u n l e s s they possess some common o r g a n i z a t i o n w i t h the known ones th r o u g h sequence homology. F u r t h e r m o d i f i c a t i o n s 187 of the p r e s e n t program w i l l be made when a d d i t i o n a l d a t a or e x t r a r u l e s f o r the p r e d i c t i v e a l g o r i t h m are r e p o r t e d by Chou and Fasman or o t h e r r e s e a r c h e r s . As i t has been emphasized by Fasman (1980) , the l a c k o f h i g h a c c u r a c y o f the p r e s e n t pre-d i c t i v e methods s h o u l d not sto p r e s e a r c h e r s from u s i n g them to o b t a i n a s u g g e s t i v e model f o r p r o t e i n s . T h i s w i l l p a r t i a l -l y h e l p to get an i n s i g h t on p r o t e i n b e h a v i o r w h i l e X-ray d a t a are not y e t a v a i l a b l e . In summary, i n the p r e s e n t s t u d y , the major frame-work f o r the secondary s t r u c t u r e s e a r c h based on the method of Chou and Fasman (1978a, 1978b) has been c o m p u t e r i z e d . E x t r a m o d i f i c a t i o n s which w i l l be n e c e s s i t a t e d by the advent of improvements i n the p r e d i c t i v e methods are not p e r c e i v e d as b e i n g o f any g r e a t o b s t a c l e to the use o f the b a s i c pro-grams deve l o p e d i n t h i s s t u d y . 188 T a b l e 5. Comparison o f E x p e r i m e n t a l (X-ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman^ and by the P r e s e n t Program B e f o r e and A f t e r i t s Refinement. P r e s e n t Prog ;ram Chou § Fasman X-Ray B e f o r e A f t e r A d e n y l a t e K i n a s e 1-•14 1--9 1-•8 1-•9 (194 aa) 23--31 23--28 c 23-•31 39-•49 41--48 40--48 41-•48 51--67 52--67 55--68 52--64 69--88 69--86 69--86 70-•86 97--109 98--108 97--109 99-•108 123- -132 123- -132 123- -132 124- -133 138- -152 143--156 142- -151 142- -157 157- -167 157- -165 157- -164 159- -162 178- -194 180- -194 186- -194 178- -194 C a r b o x y p e p t i - 19--25 14--29 13--29 14--28 dase A 79--85 72--88 72--88 72--88 (307 aa) 97--110 98--102 98--102 94--103 116- -122 116- -122 112--122 170- -182 173--186 173--184 173--187 215--233 215--233 215--233 215--231 254- -262 286--292 288--305 289--305 288--306 297-302 (cont'd) 189 Table 5. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman^ and by the P r e s e n t -Program B e f o r e and A f t e r i t s Refinement Chou § P r e s e n t Program Fasman X-Ray B e f o r e A f t e r 38-43 81-86 81-85 155-160 180-189 C o n c a n a v a l i n A- 32-40 38-42 J a c k Bean 42-47 d (237 aa) 80-85 155-160 180-188 178-190 a-Chymotrypsin (245 aa) 53- 58 55- 60 55- 60 -76- 90 78- 84 78- 84 -111- 116 111- 116 111- 116 164 -173 238- 244 233- 245 233- 245 234 -245 Cytochrome bg (93 aa) 1-6 -. 7-15 8-31-39 33-42-51 42-53-76 54-9- 15 8- 15 34- 39 33- 38 43- 50 42- 49 54- 61 55- 62 65- 74 64- 74 (cont'd) 190 T a b l e 5. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman and by the Pre s e n t - P r o g r a m B e f o r e . and -After i t s Refinement Present- Program Chou § Fasman X-Ray B e f o r e A f t e r Cytochrome c (104 aa) 2-22 2-20 2-13 14-21 . 9-13 14-18 49-54 55-69 59-69 59-69 62-70 71-75 77-102 89-101 88-101 91-101 a-Hemoglobin 1-8 4-17 4-17 3-18 (141 aa) 8-17 25-34 21-36 20-36 20-35 36-42 45-64 53-73 53-73 52-71 68-76 79-94 79-94 79-84 86-93 80-89 98-103 94-113 96-113 94-112 120-129 120-138 120-138 118-138 (cont'd) 191 Table 5. (cont'd) a Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman and by the P r e s e n t Program:Before"and A f t e r i t s Refinement. Chou § P r e s e n t Program Fasman X-Ray B e f o r e A f t e r B-Hemoglobin 1- 23 6- 23 6- 23 4- 18 (146 aa) 26- 35 26- 34 26- 34 19- 34 37- 45 - - 35- 41 - 51- 56 51- 55 50- 56 59- 71 58- 78 59- 71 57- 76 73- 82 73- 78 82- 99 85- 97 85- 98 85- 94 101- 106 98- 117 101- 118 99- 117 106- 118 122- 129 123- 143 122- 135 123- 143 129- 135 137- 145 137- 144 Lysozyme 3- 15 7- 15 7- 15 5- 15 (129.-i.aa) 27- 36 27- 35 27- 35 25- 35 - 79- 84 79- 84 79- 84 90- 98 89- 99 88- 99 88- 99 105- 112 107- 114 107- 114 108- 115 119- 124 119- 125 119- 124 (cont'd) 192 Table 5. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman and by the P r e s e n t .Program^. B e f o r e - a n d : A f t e r i t s Refinement. Chou § P r e s e n t Program Fasman X-Ray B e f o r e A f t e r Myogen 1-6 1-9 1-6 -(108 aa) 5-24 9-19 8-21 7.-15 24-55 26-33 26-33 26-33 40-50 40-52 40-51 59-79 57-77 57-77 67-71 81-92 81-88 81-88 78-89 96-108 100-108 99-108 102-107 M y o g l o b i n 1-11 4-22 4-22 3-18 (153 aa) 13-22 24-36 22-36 24-36 20-35 38-64 37-43 38-43 36-42 48-77 48-57 51-57 66-87 58-77 58-77 81-96 81-85 -89-99 86-97 86-95 101-119 100-119 101-119 100-118 123-145 123-149 123-128 124-149 130-149 (cont'd) 1?3 Table 5. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman and by the P r e s e n t P r o g r a m . B e f o r e a n d - A f t e r i t s Refinement. Chou § P r e s e n t Program Fasman X-Ray B e f o r e A f t e r P a p a i n 5-10 (212 aa) 24- 30 26- 35 26- 35 24 -41 47- 60 50- 58 50- 57 50 -57 69- 74 68- 77 68- 77 67 -78 - 118- 126 120- 126 117 -126 133- 143 136- 143 136- 143 138 -143 R i b o n u c l e a s e S 1--23 2--13 2--13 3--13 (124 aa) 26--33 28--35 28--35 24--35 45--61 49--59 49--59 50--59 ' S t a p h y l o c o c c a l 3-10 5-10 5-10 Nu c l e a s e - 56-76 56-67 54-67 (149 aa) 57-78 69-76 94-106 98-106 98-110 99-106 120-137 122-137 121-142 122-134 (cont'd) 1 9 4 Table 5. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman and by t h e P r e s e n t Program-Before; and A f t e r i t s Refinement. Chou § P r e s e n t Program Fasman X-Ray B e f o r e A f t e r S u b t i l i s i n BPN' 8-13 _ - 5-10 (275 aa) 15-20 15-19 13-19 14-20 69-75 66-7 5 64-75 64-73 110-120 111-116 111-116 103-117 130-145 132-145 132-145 132-145 195-200 195-200 195-200 -226-238 223-238 222-238 223-238 - - - 242-252 267-275 269-275 267-275 269-275 T h e r m o l y s i n 53-59 55-60 53-58 -(316 aa) 67-74 67-77 67-74 65-88 136-144 137-150 137-150 137-152 163-172 160-180 158-180 159-180 175-180 236-241 234-246 238-246 235-246 261-267 261-273 261-271 259-274 280-295 281-295 281-295 280-296 299-313 302-313 301-313 302-313 (cont'd) 195 Table 5. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman and by the. P r e s e n t . Program Before"• and A f t e r i t s Refinement • P r e s e n t • Program Chou,§ Fasman X-Ray B e f o r e A f t e r P a n c r e a t i c T r y p s i n I n h i b i t o r (58 aa) 44-55 2-7 45-55 2-7 45-54 3-6 45-56 M y o h e m e r i t h r i n 19-29 22-37 19-37 19-38 (118 aa) 33-3-9 44-51 46-63 - 40-62 53-66 58-65 68-85 68-84 70-84 69-87 91-104 92-110 86-96 93-110 106-115 100-108 T h i o r e d o x i n 12-19 10-19 12-19 11-18 (108 aa) 38-48 38-48 38-48 34-49 59-63 84-90 85-91 85-91 -98-108 98-108 98-108 95-107 (cont'd) 196 Table 5. (cont'd) Comparison o f Experiment (X-Ray) and P r e d i c t e d H e l i c a l Regions O b t a i n e d by Chou and Fasman and by the P r e s e n t Program B e f o r e and A f t e r i t s Refinement. Chou § P r e s e n t Program Fasman X-Ray B e f o r e A f t e r Glucagon 14-27 15-27 19-27 (29 aa) Bovine C o l o s t r u m 9-14 5-10 5-10 I n h i b i t o r 6 (67 aa) 17-23 48-59 49-59 48-56 R u s s e l l ' s V i p e r  T o x i n 6 (60 aa) 27-36 47-55 47-55 B l a c k Mgmba 44-53 44-53 T o x i n K e (57 aa) 45-51 a R e f e r e n c e s t o the X-ray d a t a are g i v e n by Chou and Fasman (1974b). b p r e d i c t e d v a l u e s r e p o r t e d by Chou and Fasman (1974b) c R e g i o n o m i t t e d i n p r e d i c t i o n d O v e r p r e d i c t e d r e g i o n ®The r e s u l t s o f Chou and Fasman (1978b) s e r v e as r e f e r e n c e v a l u e s . 197 Table 6.. Comparison. of E x p e r i m e n t a l (X-Ray) and P r e d i c t e d 3-Sheet Regions O b t a i n e d by Chou and Fasman and by the- P r e s e n t Program Bef o r e -and . A f t e r i t s Refinement. Chou § Pre s e n t - P r o g r a m Fasman X-Ray B e f o r e A f t e r A d e n y l a t e K i n a s e (194 aa) 9-14 10-14 27-39 29-39 89-92 90-95 113-118 113-118 169-175 169-174 182-188 10-15 10-15 26-35 34-39 80-85 88-93 89-95 110-118 114-118 151-157 169-175 169-175 182-187 C a r b o x y p e p t i -dase A (307 aa) 33- 42 32- 38 32- 38 32- 36 47- 52 47- 52 47- 52 49- 53 62- 66 61- 66 61- 68 60- 67 105- 107 103- 110 103- 111 104- 109 125- 133 125- 132 - -137- 141 137- 141 137- 141 -189- 195 189- 195 191- 195 190- 196 200- 204 200- 204 200- 204 200- 204 206- 211 206- 211 206- 211 -233- 234 - 234- 238 c 239- 241 243- 248 243- 249 243- 249 -263- 269 263- 269 261- 269 265- 271 277- 281 277- 2 8 1 d 277- 281 -(cont'd) 198 T a b l e 6. (cont'd) Comparison o f E x p e r i m e n t a l 5 1 (X-Ray) and P r e d i c t e d 3-Sheet Regions O b t a i n e d by Chou and Fasman'3 and by the Present. Program B e f o r e and A f t e r i t s Refinement. P r e s e n t Program Chou § Fasman X- Ray B e f o r e A f t e r C o n c a n a v a l i n A 1-7 3-7 3 -12 4- 9 J a c k Bean 9-12 9-12 (237 aa) 25-32 25-29 25-29 25- 29 49-57 47-55 47-55 48- 55 60-65 61-67 60-67 60- 67 79-82 73-79 73-80 73- 78 88-93 88-97 88-96 92- 97 106-109 105-115 106-113 106- 116 125-132 125-133 124-134 124- 132 137-143 140-143 140-144 140- 144 172-177 173-177 173-177 173- 177 193-199 191-199 190-200 190- 199 209-217 210-215 209-215 209- 215 226-230 228-232 229-234 -a-Chymotrypsin 29-33 29-34 29-34 29- 35 (245 aa) 34-42 39-47 39-47 39- 47 51-54 51-54 50-54 50- 54 61-67 61-67 61-68 65- 68 88-91 85-91 85-89 86- 91 (cont'd) 199 T a b l e 6. (cont'd) Comparison o f E x p e r i m e n t a l 3 " (X-Ray) and P r e d i c t e d 3-Sheet Regions O b t a i n e d by Chou and Fasman and by the Present- Program B e f o r e and A f t e r i t s Refinement. P r e s e n t .."Proj gram Chou § Fasman X -Ray B e f o r e A f t e r a-Chymotrypsin 103 -108 103- -108 103- -108 103--108 (245 aa) 117 -122 117- -122 117- -123 119- -122 (cont'd) 134- -143 134- -146 134- 146 134- -140 140- -146 154- -158 155- •163 155- •163 155- -163 180- -182 179- •183 179- 184 179- -184 199- •204 197- •201 199- -203 207- -213 206- 213 206- 214 206- -214 227- -232 227- 232 226- 232 226- -230 Cytochrome ^5 2-•9 4- 7 4- 8 4- 6 (93 aa) 20-•28 21- 29 21- 25 21- 25 30- 33 29- 33 29- 33 28- 32 - - 50- 54 72- 76 73- 79 75- 79 75- 79 Cytochrome C 31- 36 32- 36 (104 aa) 45T 49 - 46- 50 -78- 83 78- 82 80- 85 (cont'd) 200 Table 6. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d 8-Sheet Regions O b t a i n e d by Chou and Fasman and by the : P r e s e n t Program B e f o r e a n d ' A f t e r i t s Refinement • P r e s e n t Program Chou $ Fasman X-Ray B e f o r e A f t e r a-Hemoglobin 36-39 38-43 38-43 _ (141 aa) 40-43 -8-Hemoglobin (146 aa) 37-45 37-42 35-42 Lysozyme 1-6 38-46 2-6 38-46 2-6 38-43 .1-3 38-46 53- 59 51-59 50-58 50-54 56-65 - - 57-60 Myogen (108 aa) M y o g l o b i n (153 aa) (cont'd) 2 0 1 Table 6. (cont'd) cl Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d 3-Sheet Regions O b t a i n e d by Chou and Fasman^ and by the Present: Program B e f o r e and A f t e r i t s Refinement. Chou $ P r e s e n t Program Fasman X- Ray B e f o r e A f t e r P a p a i n - 4-9 4-9 5- 7 (212 aa) 37-45 37-40 37-42 -7.8-82 78-82 - -91-94 91-95 91-95 -110-113 110-113 110-114 111- 112 130-136 130-134 130-135 -161-166 161-166 161-167 162- 167 170-173 170-175 170-174 169- 175 186-188 184-189 185-189 185- 191 197-201 199-208 199-208 206- 208 202-205 R i b o n u c l e a s e S 43-48 43-47 43-48 41- 48 (124 aa) - 61-65 60-65 60- 65 69-82 69-76 69-76 69- 76 - 79-84 79-85 79-•87 94-110 95-110 95-102 96- 110 105-110 _ 116-124 115-124 116- 124 (cont'd) 202 T a b l e 6. (cont'd) Comparison o f E x p e r i m e n t a l 3 " (X-Ray) and P r e d i c t e d g-Sheet Regions O b t a i n e d by Chou and Fasman and by the P r e s e n t Program Before, and A f t e r i t s Refinement. Chou § P r e s e n t Program Fasman. X--Ray B e f o r e A f t e r S t a p h y l o c o c c a l 12-15 13-18 12-18 12 -19 Nuc l e a s e 22-27 22-27 22-27 21 -27 (149 aa) 32-41 30-39 32-41 30 -36 87-94 89-94 88-94 -108-115 111-115 111-115 -S u b t i l i s i n BPN' 8-11 4-11 4-11 (275 aa) 26-31 26-32 28-32 28 -32 - 44-51 44-51 45 -50 81-84 81-84 79-84 -90-96 89-96 89-96 89 -94 103-111 103-108 103-108 -116-124 119;--124 " 119-124 120 -124 147-150 147-152 147-152 148 -152 - 174-180 174-180 -203-207 203-209 205-209 -241-246 241-246 241-24.6 -250-257 250-255 250-255 -(cont'd) 203 Table 6. (cont'd) a. Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d 8-Sheet Regions O b t a i n e d by Chou and Fasman and by t h e P r e s e n t Program .Before and A f t e r i t s Refinement. P r e s e n t Program Chou § Fasman X-•Ray B e f o r e A f t e r T h e r m o l y s i n 1-•4 4--13 4-•17 4-•13 (316 aa) 7--9 14-•20 17--33 21-• 3 3 20--32 15--32 39--42 39-•42 37--50 37--46 41--50 41-•50 52--58 61--66 61-•66 61--66 60-- 6 3 71--84 78-•84 75-•84 98-•106 98--110 97--106 108- •110 110- -116. 112- -116 120- -122 120- •123 120- -124 119- -123 128- -131 128- •131 127- -131 148- -157 151--157 151--157 192- -193 192- -197 221-•225 249--258 249- -258 251--260 266- -274 272-•276 P a n c r e a t i c T r y p s i n 18--24 16--24 16--23 16--24 I n h i b i t o r 29--35 27--35 27--38 27--36 (58 aa) (cont'd) 204 T a b l e 6. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d Sheet Regions O b t a i n e d by Chou and Fasman and by the Present Program B e f o r e and A f t e r i t s Refinement. Chou § P r e s e n t Program Fasman X-Ray B e f o r e A f t e r M y o h e m e r i t h r i n 13- 21 14- 21 14- 18 -; (118 aa) 47- 51 44- 52 T h i o r e d o x i n 4- 7 4- 8 4- 8 2- 8 (108 aa) 22- 25 22- 29 22- 29 22- 29 52- 55 53- 60 53- 60 53- 58 54- 60 77- 81 77- 81 77- 81 77- 81 88-91 G l u c a g o n 6 3-7 6-10 5-10 (29 aa) 20-29 20-26 19-27 Bovine C o l o s t r u m 21-29 21-26 21-26 I n h i b i t o r (67 aa) - 36-38 36-38 R u s s e l l ' s V i p e r - 5-10 5-9 T o x i n 6 20-27 20-27 23-27 (60 aa) 34-37 31-37 32-37 (cont'd) 205 T a b l e 6. (cont'd) Comparison o f E x p e r i m e n t a l (X-Ray) and P r e d i c t e d 3 - S h e e t Regions O b t a i n e d by Chou and Fasman^ and by the- P r e s e n t Program B e f o r e and A f t e r i t s Refinement. Chou § P r e s e n t Program Fasman X-Ray B e f o r e A f t e r B l a c k Mamba - 4-7 4-9 T o x i n K e 18-23 21-25 21-25 (57 aa) 23-31 22-35 29-35 a R e f e r e n c e s t o the X-ray d a t a are g i v e n by Chou and Fasman (1974b) . P r e d i c t e d v a l u e s r e p o r t e d by Chou and Fasman (1974b). c R e g i o n o m i t t e d i n p r e d i c t i o n . ^ O v e r p r e d i c t e d r e g i o n . eThe r e s u l t s o f Chou and Fasman (1978b) s e r v e as r e f e r e n c e v a l u e s . 206 T a b l e 7. Agreement F a c t o r s Q , C o b t a i n e d by Chou and Fasman a, Argos e t a l . , and t h e . P r e s e n t Program Qa C a r b o x y p e p t i d a s e A 8 9 a 8 2 b 9 0 C . 8 1 a .70 b .83° (bovi n e ) C o n c a n a v a l i n A 95 95 95 .40 .37 .39 (Jack bean) a-Chymotrypsin 73 64 73 .39 .21 .39 (bovi n e ) Cytochrome b 5 84 82 89 .69 .67 .79 (bovi n e ) Cytochrome c 73 89 74 .45 .78 .48 (horse) a-Hemoglobin 81 72 79 .59 .38 .58 (horse) 3^Hemoglobin 83 64 84 .52 .25 .65 (horse) Lysozyme 94 79 94 .89 .59 .91 (hen egg w h i t e ) Myogen 66 85 69 .35 .72 .42 (ca r p ) M y o g l o b i n 81 72 79 .67 .43 .71 (sperm whale) (cont'd) -2 07 Table 7. (cont'd) Agreement F a c t o r s Q a, C a o b t a i n e d by Chou and Fasman a, Argos e t a l _ . b , and the Present- Program*" Qa P a p a i n (papaya) 88 89 81 82 R i b o n u c l e a s e S (bovine) 93 92 87 87 S t a p h y l o c o c c a l n u c l e a s e ^ 85 87 60 66 S u b t i l i s i n BPN' (B. a m y l o l i q u e -f a c i e n s ) 80 76 80 64 .55 67 T h e r m o l y s i n (B. thermopro-t e o l y t i c u s ) 85 81 89 74 64 80 P a n c r e a t i c t r y p s i n i n h i b i t o r ( b o v i n e ) 90 71 94 82 51 87 M y o h e m e r i t h r i n (T. p y r o i d e s ) 73 61 87 42 20 .70 T h i o r e d o x i n d (E. c o l i ) 77 77 54 . 54 a R e s u l t s o b t a i n e d by Chou and Fasman (1974b) ^ R e s u l t s o b t a i n e d by Argos e_t aJL. (1976) c R e s u l t s o b t a i n e d by our program. ^ P r o t e i n s not t e s t e d by Argos et. a l . (1976) 208 Table 8. Agreement F a c t o r s Q^ ., o b t a i n e d by Chou and Fasman a, Argos e t a _ l . b , and the' P r e s e n t P r o g r a m 0 QB C B C a r b o x y p e p t i d a s e A 8 3 a 7 0 b 8 4 c .54 a .33 b .70° (bovi n e ) C o n c a n a v a l i n A 90 72 90 .77 .45 .78 (Jack bean) a-Chymotrypsin 92 75 92 .80 .49 .82 (bovine) Cytochrome b 5 85' 82 86 . 73 . 67 . 74 (bovine) Cytochrome c d 8 9 - 9 0 (horse) a-Hemoglobin d 9 6 - 9 6 -(horse) B-Hemoglobin d 95 - 96 --(horse) Lysozyme 83 6 i ; 90 .68 .20 .78 (hen egg w h i t e ) Myogen d 100 - 100 (carp) M y o g l o b i n d 100 - 100 (sperm whale) (cont'd) 209 Table 8. (cont'd) Agreement F a c t o r s Q^, o b t a i n e d by Chou and Fasman , Argos e_t al_. , and the P r e s e n t Program C, Q P a p a i n (papaya) 88 89 81 82 Myohemeri t h r i n (T. p y r o i d e s ) 88 93 R i b o n u c l e a s e S (bovine) 93 93 87 87 S t aph-y.Lo c o'c c a 1 n u c l e a s e e 85 88 57 64 S u b t i l i s i n BPN' (B. a m y l o l i q u e -f a c i e n s ) 91 63 89 54 17 52 T h e r m o l y s i n (B. thermoproteo-l y t i c u s ) 75 75 80 44 47 54 T h i o r e d o x i n P a n c r e a t i c t r y p s i n i n h i b i t o r ( b o v i n e ) 89 85 95 79 97 81 89 61 74 96 a R e s u l t s o b t a i n e d by Chou and Fasman (1974b). ^ R e s u l t s o b t a i n e d by Argos e t a l . (1976). c R e s u l t s o b t a i n e d by our program. ^ P r o t e i n s w i t h l i t t l e o r no sheet c o n f o r m a t i o n s were not t e s t e d by Argos ejt a l . (1976) . e P r o t e i n s not t e s t e d by Argos e t a l . (1976) . 210 C o n f o r m a t i o n s o f some food r e l a t e d p r o t e i n s The second o b j e c t i v e o f t h i s s t u d y was to o b t a i n some i n f o r m a t i o n on the c o n f o r m a t i o n o f food r e l a t e d p r o t e i n s such as b o v i n e serum albumin (BSA) , a s ^ - c a s e i n , . B - c a s e i n , K-c a s e i n , chymosin, a - l a c t a l b u m i n , 8 - l a c t o g l o b u l i n , o v a l b u m i n , p e p s i n , and t r y p s i n o g e n . Table 9 l i s t s the p e r c e n t a g e o f a-h e l i x , B - s h e e t , and B - t u r n found f o r each p r o t e i n u s i n g the m o d i f i e d program. T a b l e 10 shows the p o s s i b l e l o c a t i o n s o f the d i f f e r e n t c o n f o r m a t i o n s . The s c h e m a t i c diagram c o r r e s p o n -d i n g to each o f the t e s t e d p r o t e i n s can be found i n F i g u r e s I to X. Some r e f e r e n c e s were found to c o r r o b o r a t e the r e l i a -b i l i t y o f the p r e d i c t i o n from the p r e s e n t s t u d y . Loucheux-L e f e b v r e . e t a l . (1978), u s i n g the method o f Chou and Fasman (1974b), o b t a i n e d 23% a - h e l i x , 31% B - s h e e t , and 21% B - t u r n f o r K - c a s e i n ( b o v i n e ) . These r e s u l t s are q u i t e comparable to those of the p r e s e n t s t u d y (20, 33, and 29%). The l o c a t i o n s of the d i f f e r e n t c o n f o r m a t i o n s were almost the same, except f o r h e l i x 90-97 which was p r e d i c t e d as B-sheet by the p r e s -ent program, and h e l i x 62-68 which was not p r e d i c t e d by L o ucheux-Lefebvre e t a l . (1978). a - L a c t a l b u m i n was p r e d i c t e d by the method of Lim (1974b) to c o n t a i n 43% h e l i x and'12% B-sheet compared to 38% h e l i x and 15% B-sheet o b t a i n e d i n the p r e s e n t s t u d y . Ovalbumin was r e p o r t e d to be composed of 40% h e l i x by Yang and Doty (1957) u s i n g ORD, w h i l e a v a l u e of 25-30% h e l i x was found by Gorbunoff (1969). E x t r a r e f -i l l erences would be u s e f u l to e v a l u a t e the p r e c i s i o n o f the r e -s u l t s o f Yang and Doty (1957) , o f Gorbunoff (1969) , and o f the p r e s e n t s t u d y (44% h e l i x ) . The b o v i n e g a s t r i c p r o t e a s e s , chymosin and p e p s i n , are v e r y homologous i n t h e i r amino a c i d sequence and t h e i r zymogens may even be a c t i v a t e d by a - s i m i l a r mechanism- (Foltmann et a ] . , 197 3 ) . T h i s i s p a r t i a l l y r e f l e c t e d i n the p r e -d i c t i o n from the p r e s e n t study which y i e l d e d h i g h p e r c e n t a g e s o f g-sheet and v e r y low p e r c e n t a g e s o f a - h e l i x f o r b o t h (40.2 v e r s u s 3.71 f o r chymosin, and 33.4 v e r s u s 1.8% f o r pep-s i n ) . The d i f f e r e n c e i n the v a l u e s between the two enzymes may be e x p l a i n e d by d i f f e r e n c e i n t h e i r s o u r c e , chymosin from b o v i n e source and p e p s i n from p o r c i n e s o u r c e . The p a n c r e a t i c p r o t e a s e s , a - c h y m o t r y p s i n and t r y p s i n , a l s o e x h i b i t homology i n t h e i r p r i m a r y s t r u c t u r e (Huang and Tang, 1970). Hence, i t was not s u r p r i s i n g t o observe a v e r y s i m i l a r c o n f o r m a t i o n a l p a t t e r n between the two enzymes: 33.5% g-sheet v e r s u s 9.0% a - h e l i x f o r a - c h y m o t r y p s i n w i t h X-ray d i f f r a c t i o n (Chou and Fasman, 1974b), and 31.0% g-sheet v e r s u s 13.5% a - h e l i x f o r t r y p s i n w i t h the p r e s e n t program. A l t h o u g h no r e f e r e n c e was found f o r BSA, i t may be r e a s o n a b l e to compare i t to ovalbumin as they b o t h b e l o n g to the albumin group. The h i g h p e r c e n t a g e o f a - h e l i x p r e d i c t e d f o r BSA (52.1%) may be comparable to t h a t o f ovalbumin 212 (44.1%). However, the p e r c e n t a g e o f 8-sheet was much lower f o r BSA (2.2%) compared to 20.5% f o r ovalbumin. a ^ - C a s e i n and 8-c a s e i n were p r e d i c t e d to c o n t a i n v e r y s i m i l a r p e r c e n t a g e s o f the t h r e e types o f c o n f o r m a t i o n (14.6, 26.1, and 30.1% f o r a ^ - c a s e i n v e r s u s 13.9, 23.0, and 33.0% f o r 8 - c a s e i n ) . U n f o r -t u n a t e l y , t h e r e i s no r e f e r e n c e to check the p r e s e n t r e s u l t s . No r e f e r e n c e was found to a s s e s s the p r e c i s i o n o f the p r e d i c -t i o n f o r 8 - l a c t o g l o b u l i n (35.8% a - h e l i x and 30.9% 8-sheet) A l l the r e s u l t s c o n c e r n i n g food r e l a t e d p r o t e i n s s h o u l d be c o n s i d e r e d as s u g g e s t i v e and s h o u l d be c o n f i r m e d by o t h e r t e c h n i q u e s (CD, ORD, X - r a y ) . N e v e r t h e l e s s , one ad-vantage o f the method o f Chou and Fasman (1987a, 1978b) i s t h a t i t a l l o w s the d e t e c t i o n o f areas e x h i b i t i n g p o t e n t i a l f o r b o t h a - h e l i x and 8-sheet c o n f o r m a t i o n s . Hence, conforma^ t i o n a l changes observed w i t h CD may be e x p l a i n e d by the t r a n -s i t i o n s t h a t those s e n s i t i v e areas have undergone. A l l the c o n f o r m a t i o n a l t r a n s i t i o n phenomena may h e l p to u n d e r s t a n d p r o t e i n f u n c t i o n a l i t i e s such as g e l a t i o n , foaming,and e m u l s i -f y i n g a c t i v i t y . I t has been obse r v e d t h a t d e n a t u r a t i o n o f p r o t e i n s must o c c u r to some e x t e n t b e f o r e those p r o p e r t i e s are a c t u a l l y e x h i b i t e d . For i n s t a n c e , f o r g l u c a g o n (29 amino a c i d r e s i d u e s ) , i t has been h y p o t h e s i z e d t h a t the t r a n s i t i o n from a- to 8 - c o n f o r m a t i o n o f the r e g i o n 19-27 i s n e c e s s a r y f o r the r e c e p t o r b i n d i n g because o f the more compact s t r u c t u r e ' 213 r e s u l t i n g from such a t r a n s i t i o n f ( C h o u and Fasman, 1978b). I t was a l s o observed t h a t g l u c agon i n the g e l s t a t e has a . h i g h e r p e r c e n t a g e o f 3-sheet (52%) than glucagon i n s o l u t i o n (21%) ( G r a t z e r et a l . , 1967; Epand, 1971). The p r e d i c t i v e method:can h e l p to l o c a t e the s e n s i t i v e a r e a 19-27 (Chou and Fasman, 1978b). In s i c k l e c e l l hemoglobin, the r e p l a c e -ment o f some a-formers or 8-breakers by s t r o n g 8-formers ( V a l ) r e s u l t s i n the t r a n s i t i o n from a- to 6-conformation o f the s e c t i o n 1-6. T h i s l e a d s to the a g g r e g a t i o n o f hemoglobin c e l l s due to i n t e r c h a i n i n t e r a c t i o n s r e p l a c i n g i n t r a c h a i n ones (Chou-and Fasman, 1978b). In summary, even though a complete p i c t u r e o f -p r o t e i n b e h a v i o r cannot be e x p e c t e d w i t h o u t the c o n s i d e r a -t i o n o f the t h r e e - d i m e n s i o n a l o r g a n i z a t i o n which has a g r e a t impact on the whole problem, the knowledge o f the secondary s t r u c t u r e remains one o f the u s e f u l means to e x p l o r e the complex n a t u r e o f p r o t e i n s . 214 •Table 9. P e r c e n t a g e s o f H e l i x , 3-Sheet and 3-Turn of Some Food R e l a t e d P r o t e i n s O b t a i n e d from the P r e s e n t Program H e l i x (•%) Sheet (%) Turn (%) Bovine serum albumin 52.1 2.2 29.6 (582 aa) a -.-Casein (bovine) 14.6 26.1 30.1 s i (199 aa) 3-Casein ( b o v i n e ) 13.9 23.0 33.0 (209 aa) K - C a s e i n (bovine) 20.1 33.1 29.0 (169 aa) Chymosin ( b o v i n e ) 3.7 40.2 36.2 (323 aa) a - L a c t a l b u m i n (bovine) 38.2 14.6 37.4 (123 aa) 3 - L a c t o g l o b u l i n ( b o v i n e ) 35.8 30.9 17.3 (162 aa) Ovalbumin 44.1 20.5 19.5 (385 aa) P e p s i n ( p o r c i n e ) 1.8 33.4 46.9 (326 aa) T r y p s i n o g e n ( b o v i n e ) 13.5 31.0 35.4 (229 aa) 215 T a b l e 10. H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by. the P r e s e n t Program H e l i x Sheet Bovine serum albumin (582 aa) 6-33 38-58 63-70 72-81 100-106 122-134 140-145 164-170 179-187 192-201 206-221 223-242 289-295 305-313 318-329 341-361 373-381 418-423 450-463 497-512 517-533 535-552 573-581 403-415 (cont'd) 216 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by the-. P r e s e n t Program Bovine serum albumin (cont'd) (582 aa) Turns: 1-4, 34-37, 59-62, 82-85, 88-91, 95-98, 105- 108, 107- 110, 109- 112 , 116- 119, 118- 121, 135- 138, 145- 148, 155- 158, 157- 160, 171- 174, 188- 191, 202- 205 , 243- 246, 245- 248 , 263- 266 , 265- 268 , 270- 273, 276- 279 , 278- 281, 284- 287 , 296- 299 , 301- 304, 314- 317, 332- 335, 336- 339 , 363- 366, 382- 385 , 424- 427 , 431- 434, 435- 438, 437- 440, 443- 446, 446- 449, 464- 467 , 471- 474, 474- 477 , 480- 483, 482- 485 , 489- 492 , 513- 516, 553- 556 , 559- 562 , 569- 572. H e l i x Sheet a ^ - j - C a s e i n (bovine) 13-18 20-26 (209 aa) 34-42 30-32 52-65 91-95 97-101 135-140 142-146 149-158 163-173 (cont'd) 217 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by the P r e s e n t Program H e l i x Sheet a - ^ - c a s e i n (bovine) (cont'd) Turns: 1-4, 8-11, 27-29, 43-46, 45-48, 48-51, 66-69, 72-75, 87-89, 87-90, 112-115, 159-162 174-176, 176-179, 182-185, 184-187, 188-191, 190-193. 8 - c a s e i n (bovine) (209 aa) 1.1-6 11-16 29-37 43-50 23-27 39-41 52-60 92-95 123-130 138-143 160-165 187-193 66-69, 71-74, 112, 111-114, 158-160, 166-169, 203-206. Turns: 8-11, 17-20, 61-63, 62-65, 75-78, 85-88, 104-107, 109-136-317, 146-149, 152-155, 178-181, 180-183, 201-204, (cont'd) 218 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by the P r e s e n t Program H e l i x Sheet K - c a s e i n ( b o v i n e ) (169 aa) Turns: 1- 7 22- 26 9- 16 28- 32 62- 68 38- 43 102- 108 48- 56 137- 147 72- 79 93- 98 121- 126 159- 169 69- 72, 80-82, 85- 88, 99-101, 109-112, 113-116, 127-129, 129-132, 133-136, 149-152, 156-158. Chymosin (bov i n e ) 2-6 8-12 (323 aa) 318-323 20-22 29-33 40-42 45-47 65-69 82-86 91-97 94-103 105-108 113-116 122-126 (cont'd) 219 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by the P r e s e n t Program H e l i x Sheet Chymosin (bov i n e ) (cont'd) 136-143 148-156 165-171 180-183 185-194 198-204 212-215 229-240 253-255 275-277 296-298 301-303 306-310 Turns: 13-16, 24-27, 34-37, 36-39, 47-50, 50-53, 52-55, 59-62, 61-64, 76-79, 78-81, 87-90, 109-112, 127-130, 132-135, 144-147, 158-161, 161-164, 172-175, 176, 179, 207-210, 208-211, 216-219, 218-221, 224-227, 226-228, 241-244, 247-250, 250-252, '. 272-274, 278-280, 279-282, 283-286,--291-294, 293-295, 312-315. Ccont'd) 220 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by the- P r e s e n t Program H e l i x Sheet a - L a c t a l b u m i n ( b o v i n e ) (123 aa) 1-16 89-99 104-123 26-31 52-59 72-75 Turns: 17-20, 32-35, 33-36, 34-37, 43-46, 45-48, 47-50, 48-51, 61-64, 64-67, 66-69, 68-71, 76-79, 82-85, 85-88, 100-103. 8 - L a c t o g l o b u l i n ( b o v i n e ) (162 aa) 22-37 67-78 80-87 129-143 156-162 1-5 12-20 39-43 56-61 92-95 102-107 115-123 145-151 Turns: 6-9, 49-52, 63-66, 88-91, 96-99, 125-128, 152-155. (cont'd) 221 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by the. P r e s e n t . Program H e l i x Sheet Ovalbumin (385 aa) 5- 23 27- 29 31- 41 51- 56 102- 109 77- 79 133- 143 86- 91 169- 189 117- 121 198- 206 145- 149 221- 232 156- 161 239- 245 194- 196 248- 259 208- 219 259- 268 276- 282 284- 290 291- 305 319- 334 364- 371 340- 362 373- 379 Turns: 24-27, 45-48, 47-50, 62-65, 65-68, 71-74, . 73-76, 80-83, 92-95, 95-98, 97-100, 125-128, 152-155, 162-165, 165-168, 190-193, 235-238, 245-48, 269-272, 307-310, 311-314. (cont'd) 222 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by the P r e s e n t . Program H e l i x Sheet P e p s i n (por c i n e ) 6 5-70 (326 aa) 15- 21 26- 31 38- 40 71- 75 83- 91 99- 103 111- 115 140- 146 151- 155 164- 167 179- 182 191- 194 203- 205 211- 214 228- 231 245- 249 259- 267 274- 277 298- 313 Turns: 11-14, 22-25, 32-35, 34-37, 35-38, 45-48, 50-53, 52-55, 54-57, 57-60, 59-62, 76-79, 79-82, 94-97, 96-99, 107-110, 116-119, 125-128, 129-132, 137-140, 147-150, 156-159, 158-161, 160-163, 171-174, 175-178, 187-190, (cont'd) 223 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by the P r e s e n t Program H e l i x Sheet; P e p s i n (porcine) (cont'd) (326 aa) Turns: 198-201, 200-203, 206-209, 207-210, 215-218, 217-220, 221-224, 223-226, 232-235, 238-241, 240-243 , 250-253', 251-254 , 255-258 , 268-270 , 270-273, 278-281, 279-282, 282-285, 288-291, 292-295, 293-296, 315-318. T r y p s i n o g e n (bovine) (229 aa) 92-102 106-111 141-146 223-228 12-18 21-25 28-30 52-58 61-64 68-71 82-87 120-125 161-172 193-199 211-221 (cont'd) 224 Table 10. (cont'd) H e l i x , Sheet, and Turn Regions o f Some Food R e l a t e d P r o t e i n s as P r e d i c t e d by t h e - P r e s e n t Program H e l i x Sheet T r y p s i n o g e n ( b o v i n e ) (cont'd) (229 aa) Turns: 3-6, 7-10, 26-27, 32-35, 46-49, 48-51, 65-67, 78-81, 88-91, 103-105, 112-115, 117-119, 126-129, 129-132, 132-135, 134-137, 149-152, 151-154, 154-157, 158-161, 173-175, 175-178, 177-180, 179-182, 181-184, 182-185, 200-203, 205-208, 208-210. 2 2 5 CONCLUSIONS A computer program has been w r i t t e n i n F o r t r a n language t o p r e d i c t the secondary s t r u c t u r e o f p r o t e i n s based on the method of Chou and Fasman (1978a, 1978b), which m a i n l y r e l i e s on the f r e q u e n c y o f o c c u r r e n c e o f each amino a c i d r e s i d u e i n a c e r t a i n c o n f o r m a t i o n . T h i s l e d to the c l a s s i f i c a t i o n o f the 20 amino a c i d s as e i t h e r f o rmer, i n d i f f e r e n t t o , o r b r e a k e r o f the c o n f o r m a t i o n s . Four programs have been d e s i g n e d to l o c a t e each type o f c o n f o r m a t i o n i n v o l v e d i n the secondary s t r u c t u r e (a-h e l i x , 8-sheet and 8-turn) and to s o l v e the p o s s i b l e over-l a p p i n g a- and 8-areas. Each program c o n s i s t s o f the main program and s e v e r a l s u b r o u t i n e s which c o r r e s p o n d t o the v a r i o u s s t e p s to be f o l l o w e d i n the method ( n u c l e a t i o n , p r o p a g a t i o n and t e r m i n a t i o n ) , or to the v a r i o u s c o n d i t i o n s to be checked (<P a>, <Pg >> c h a r a c t e r assignment, conforma-t i o n a l parameters o f the boundary r e s i d u e s , and p o s s i b l e p r e s e n c e o f a n t i p a r a l l e l 8 - s h e e t s ) . For the 8-turn s e a r c h , because of the c o n s t a n t number of r e s i d u e s i n v o l v e d ( f o u r ) and the l e s s c o m p l i c a t e d p r e d i c t i v e r u l e , the program c o r r e s p o n d i n g t o i t i s much s i m p l e r than the o t h e r ones. On t e s t i n g the p r e s e n t program on 24 d i f f e r e n t p r o t e i n s , some m i s s i n g a r e a s and d i f f e r e n c e s i n the bound-a r y r e s i d u e s i b e t w e e n the r e s u l t s o f the p r e s e n t study and .2.2.6 those o f Chou and Fasman were observed. A f t e r a thorough a n a l -y s i s of the problem, some m o d i f i c a t i o n s were added to the program o f t h i s s t u d y , i n c l u d i n g the f o l l o w i n g . The c o n d i t i o n t h a t a t l e a s t two t h i r d s o f formers f o r h e l i x n u c l e a t i o n may not be s a t i s f i e d i n some c a s e s , a l t h o u g h the e v e n t u a l l y p r e -d i c t e d a r e a met the g e n e r a l r e q u i r e m e n t o f b e i n g comprised o f one h a l f o r more h e l i x f o r m e r s . S i m i l a r l y the r e q u i r e m e n t o f l e s s than one t h i r d o f b r e a k e r s f o r 3-sheet n u c l e a t i o n may l e a d t o the o m i s s i o n o f a p o t e n t i a l 3-sheet a r e a , a l t h o u g h i t c o n t a i n s enough 3-formers. Hence, the type o f r e s i d u e s i n the n u c l e a t i o n a r e a , as w e l l a s , the surround-i n g , r e s i d u e s may s t a b i l i z e the a r e a c o n f o r m a t i o n such t h a t the presence of some b r e a k e r s cannot provoke i t s d i s r u p t i o n . For the boundary r e s i d u e s o f the p r e d i c t e d a- and 3 - a r e a s , the use o f the boundary c o n f o r m a t i o n a l parameters (P a^> ^ aN' J?3C' P g N ) r e s u l t s i n p r e d i c t i v e v a l u e s c l o s e r t o those o f Chou and Fasman (1974b, 1978b) and o f X-ray d a t a (Chou and Fasman, 1974b, 1978b). The.use o f those parameters a l s o h e l p s to a v o i d p r e d i c t i n g too many o v e r l a p p i n g a - and 3~ a r e a s , o r o v e r l a p p i n g a - h e l i x and 3 - t u r n . The method o u t l i n e d by Chou and Fasman (1978a, 1978b) to s o l v e the problem o f o v e r l a p p i n g a - and 3 - r e g i o n s proved to be u s e f u l i n most c a s e s . However, ambiguous s i -t u a t i o n s may o c c u r where the a r e a under c o n s i d e r a t i o n e x h i b -227 i t s . s t r o n g p o t e n t i a l f o r b o t h c o n f o r m a t i o n s . In such cases more emphasis s h o u l d be g i v e n t o the presence o f a n t i p a r a l l e l 6-sheets and to the type o f r e s i d u e s p r e s e n t i n the a r e a a l -though i t may happen t h a t the average < P a > or < P g > does not su p p o r t the same c o n f o r m a t i o n as the r e s i d u e assignment. The r a t i o n o f l e n g t h o f the p r e d i c t e d a - h e l i x and 3-sheet i s another u s e f u l f a c t o r t o e v a l u a t e the importance o f each one I t i s not unexpected t h a t f o r the p r e d i c t i o n o f unknown pro-t e i n s which e x h i b i t some homology w i t h known ones, t h i s p r o -cedure g i v e s l e s s problems than f o r c o m p l e t e l y unknown pro-t e i n s . Comparing the p r e d i c t i v e a c c u r a c y parameters ^a(B) a n d ^a(3) °btained by Chou and Fasman (1974b), Argos et a l . (1976) and the p r e s e n t program, i t appears t h a t p r e -d i c t i o n s from the p r e s e n t study and those o f Chou and Fasman (1974b) are i n g e n e r a l b e t t e r than those o f Argos ejt a l . (1976). The p a i r e d - s a m p l e t - t e s t r e v e a l e d t h a t the v a l u e s of C a (P < 0.01) and C g (P < 0.05) c a l c u l a t e d f o r the p r e s e n t p r e d i c t i o n were s i g n i f i c a n t l y improved from the v a l -ues o f Chou and Fasman (1974b). For most o f the p r o t e i n s used i n t h i s s t u d y , except f o r c o n c a n a v a l i n A and a-chymo-t r y p s i n (C = 0.39), good agreement w i t h X-ray d a t a (C >_ 0.40) was o b s e r v e d as an e x p e c t e d consequence o f the m o d i f i -c a t i o n s g i v e n t o the p r e s e n t program. 228 S t i m u l a t e d by those p o s i t i v e r e s u l t s , the program developed i n t h i s s t u d y was a p p l i e d to food r e l a t e d p r o t e i n s so as to p r o v i d e a p o s s i b l e means o f e x p l a i n i n g and p r e d i c -t i n g food p r o t e i n b e h a v i o r under v a r i o u s c o n d i t i o n s . A l t h o u g h r e f e r e n c e s c o u l d not be f o u n d . f o r a l l o f the p r o t e i n s t e s t e d (bovine serum a l b u m i n , a ^ - c a s e i n , B - c a s e i n , K - c a s e i n , chymosin, a - l a c t a l b u m i n , 8 - l a c t o g l o b u l i n , o v a l b u m i n , p e p s i n , and t r y p s i n o g e n ) , the p r e d i c t e d r e g i o n s f o r K.-casein and a -l a c t a l b u m i n were v e r y s i m i l a r t o those r e p o r t e d by o t h e r r e s e a r c h e r s . They e i t h e r used the method o f Chou and Fasman (Loucheux-Lefebvre e_t al_. , 1978)' , or t h e i r own method (Lim, 1974b). In summary, the main o b j e c t i v e o f t h i s s t u d y to c o m p u t e r i z e the method of. Chou and Fasman (1978a, 1978b) was a t t a i n e d . E x t r a m o d i f i c a t i o n s o f the program w i l l be made when a d d i t i o n a l d a t a or new s e t o f r u l e s ( i n c o r p o r a t i n g l o n g -range i n t e r a c t i o n and energy m i n i m i z a t i o n f a c t o r s ) are pub-l i s h e d by Chou and Fasman or o t h e r r e s e a r c h e r s . So f a r most o f the p r e d i c t i v e methods do not always ensure h i g h p r e d i c t i v e a c c u r a c y and c a u t i o n s h o u l d be g i v e n to the pre-d i c t i o n o f unknown p r o t e i n s . N e v e r t h e l e s s c o n s i d e r i n g the c o s t and the l e n g t h y and complex o p e r a t i o n s i n v o l v e d i n the X-ray t e c h n i q u e , the p r e d i c t i v e a l g o r i t h m s s t i l l remain a v a l u a b l e t o o l f o r access to the c o m p l i c a t e d o r g a n i z a t i o n 229 o f p r o t e i n s w h i l e a w a i t i n g f o r c o n f i r m a t i o n by X-ray a n a l y s i s . F u r t h e r m o r e , the a c c u r a c y o f the p r e d i c t i v e methods may be im-proved by combining them w i t h CD or ORD t e c h n i q u e s which con.-" s t i t u t e a n a d d i t i o n a l means to s o l v e ambiguous cases o f over-l a p p i n g a - and 3-areas. The pe r c e n t a g e o f each c o n f o r m a t i o n i n «proteins can be o b t a i n e d u s i n g t h e s e t e c h n i q u e s . 230 LITERATURE CITED A n g l e m i e r , A. F. and Montgomery, M. N., 1976. In " P r i n c i p l e s o f Food S c i e n c e " , p. 205-284, Ed. Fennema, 01 ' R. , P a r t I , M a r c e l Dekker I n c . Ar g o s , P., Schwarz, J . and Schwarz, J . , 1976. An assessment o f p r o t e i n secondary s t r u c t u r e p r e d i c t i o n methods based on amino a c i d sequence. B i o c h i m . B i o p h y s . A c t a 439: 261-273 A n f i n s e n , C. B., Haber, E., S e l a , M. and White, F. H., J r . , 1961. 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B. and F i n k e l s h t e i n , A. V., 1970. Connexion between the secondary and p r i m a r y s t r u c t u r e s of • g l o b u l a r p r o t e i n s . B i o f i z i k a 15: 757-767 Scanu, A. M., E d e l s t e i n , C. and K e i n , P., 1975. In "The Plasma P r o t e i n s " , 2nd ed., V o l . I , p. 317-391, Academic P r e s s , New York. S c h i f f e r , M. and Edmunson, A. B., 1967. Use o f h e l i c a l wheels to r e p r e s e n t the s t r u c t u r e o f p r o t e i n s and to i d e n t i f y segments w i t h h e l i c a l p o t e n t i a l . B i o p h y s . J . 7: 121-135 Scheraga, H. A., 1960. S t r u c t u r a l s t u d i e s o f r i b o n u c l e a s e . I I I . A model f o r the secondary and t e r t i a r y s t r u c -ture. J . Amer. Chem. Soc. 82:3847-3852 S z e n t - G y o r g y i , A. G. and Cohen, C , 1957. Rol e o f p r o l i n e i n p o l y p e p t i d e c h a i n c o n f i g u r a t i o n o f p r o t e i n s . S c i e n c e 126: 697-698 Takano, T., K a l l a i , 0. B., Swanson, R. and D i c k e r s o n , R. E., 1973. The s t r u c t u r e o f f e r r o c y t o c h r o m e c. a t 2.45$. r e s o l u t i o n . J . B i o l . Chem. 248: 5234-5255 Venkatachalam, C. M., 1968. S t e r e o c h e m i c a l c r i t e r i a f o r p o l y p e p t i d e s and p r o t e i n s . V. C o n f o r m a t i o n o f a system o f t h r e e l i n k e d p e p t i d e u n i t s . B i o p o l y m e r s 6: 1425-2436 W a l l a c e , D. G., 1976. P r e d i c t i o n o f the secondary and -'• t e r t i a r y s t r u c t u r e o f p l a s t o c y a n i n . B i o p h y s . Chem. 4; 123-130 Yang, J . T. and Doty, P., 1957. The o p t i c a l r o t a t o r y d i s p e r -s i o n o f p o l y p e p t i d e s and p r o t e i n s i n r e l a t i o n t o c o n f i g u r a t i o n . J . Amer. Chem. Soc. 79: 761-775 239 Zimm, B. H. and Bragg, J . K., 1959. Theory o f the phase t r a n s i t i o n between h e l i x and random c o i l i n p o l y p e p t i d e c h a i n s . J . Chem. Phys. 31: 526-535 240 APPENDIX How t o Use the Programs A f t e r c o n v e r t i n g the e n t i r e p r o t e i n sequence i n t o a s e r i e s o f c o r r e s p o n d i n g numbers, the f o l l o w i n g s e t o f c a r d s must be p r e p a r e d as i n p u t d a t a f o r the program o f h e l i x , 3-sheet and 3 - t u r n p r e d i c t i o n . The f i r s t card: o f the s e t g i v e s the t o t a l number o f amino a c i d r e s i d u e s o f the p r o t e i n i n q u e s t i o n (NN) and the number o f d a t a c a r d s (N). Each o f those d a t a c a r d s i s composed o f 16 numbers or amino . a c i d r e s i d u e s , except the l a s t d a t a c a r d which may or may not be f i l l e d w i t h 16 numbers. The f o l l o w i n g format has been used f o r NN and N: (6X, 14, 6X, 14). J 1 I ! ! I ! I ! I t t I I t t I I I T j 6 b l a n k s NN 6 b l a n k s N An example o f how the f i r s t c a r d l o o k s l i k e f o r a p r o t e i n o f 164 amino a c i d r e s i d u e s (NN = 164 and N = 1 1 ) : 1 6 4 1 1 I I I t t I I t t I i T t t I I I I t I i Column 1 6 10 16 20 • 241 The p r o t e i n sequence i s r e p o r t e d on the subr sequent c a r d s (16 d a t a per card) whose format has a r b i -t r a r i l y been chosen as 16 15. In o t h e r words, each o f the 16 numbers w i l l occupy f i v e columns on a c u r r e n t IBM c a r d of 80-column w i d t h . To keep a l l the numbers r i g h t j u s t i f i e d , the o n e - d i g i t d a t a s h o u l d be l o c a t e d a t columns 5xn (n = 1, 2, 3, 4, 1 6 ) , and the t w o - d i g i t ones: s h o u l d s t a r t a t ( 5 n - l ) columns. A t y p i c a l d a t a c a r d may l o o k l i k e : 8 1 2 1 4 3 9 1 2 j t t i i t t i i i i i i i t i i i t i t i i i t t t t i i 1 5 10 15 20 25 30 An echo p r i n t o f the i n p u t d a t a i n the p r e d i c t i o n o u t p u t enables the d e t e c t i o n o f any t y p o g r a p h i c a l e r r o r . In summary, i n o r d e r t o use the programs f o r h e l i x , s h e e t , and t u r n p r e d i c t i o n , one has t o e n t e r the p r o t e i n sequence i n the form o f an " i n t r o d u c t o r y " c a r d (which p r o v i d e s the t o t a l number o f amino a c i d s and the t o t a l number o f d a t a c a r d s ) f o l l o w e d by the a c t u a l d a t a c a r d s (16 d a t a per c a r d ) . In a d d i t i o n to the p r o t e i n sequence, e x t r a i n f o r -m a t i o n c o n c e r n i n g the p o s i t i o n s o f the o v e r l a p p i n g h e l i c e s and s h e e t s are n e c e s s a r y f o r the u t i l i z a t i o n o f the 242 o v e r l a p p i n g program. For t h i s r e a s o n , the l a s t d a t a c a r d o f the p r o t e i n sequence w i l l i m m e d i a t e l y be f o l l o w e d by a second s e t of c a r d s which c o n s i s t s o f : an " i n t r o d u c t o r y " c a r d o f the same format s i m i l a r t o the f i r s t one (6X, 14, 6 X , . I 4 ) . The two numbers i n q u e s t i o n are the t o t a l number o f v a l u e s g i v i n g the p o s i t i o n s o f the o v e r l a p p i n g h e l i c e s and 3-sheets ( i t w i l l always be a m u l t i p l e o f f o u r because p a i r s o f h e l i c e s and 3-sheets are i n v o l v e d i n the p r o c e d u r e ) , and the t o t a l number of d a t a c a r d s (16 d a t a per c a r d ) . f o r c o n v e n i e n c e , keep the format o f 16 15 (5 columns f o r each datum) f o r the d a t a c a r d s c a r r y i n g the i n f o r m a t i o n on the p o s i t i o n s o f the d i f f e r e n t p a i r s o f o v e r l a p p i n g h e l i c e s and 3-sheets. On each c a r d , the boundary v a l u e s o f h e l i c e s and 3-sheets were a r r a n g e d a c c o r d i n g t o the f o l l o w i n g ways: HI SI H2 S2 H3 S3 J t t I I t t Column 1 5 10 15 20 25 30 HI : N-boundary o f the h e l i x s t a r t i n g from HI to H2 SI : N-boundary of the 3-sheet s t a r t i n g from SI to S2 H2 : C-boundary of the h e l i x H1-H2 S2 : C-boundary of the 3 - sheet-Sl-S2 H3 : N-boundary of the h e l i x s t a r t i n g from H3 to H4 243 Hence the r e l a t i v e p o s i t i o n s o f h e l i c e s and 8-sheets a l t e r n a t e w i t h each o t h e r . An 80-column c a r d can c o n t a i n up to e i g h t p a i r s o f v a l u e s . In summary, i n o r d e r to use the o v e r l a p p i n g program, two s e t s o f c a r d s must be p r e p a r e d . The f i r s t s e t p r o v i d e s the computer w i t h the i n f o r m a t i o n on the p r o t e i n sequence and the second s e t , which i m m e d i a t e l y f o l l o w s the f i r s t , c o n t a i n s d a t a on the r e l a t i v e p o s i t i o n s o f the o v e r l a p p i n g h e l i c e s and 8-sheets. For c o n v e n i e n c e , the same type of format i s used i n each s e t o f c a r d s . 244 63 70 72 81 88 95 134 106 100 116 L T 122 j u u u u L m i i s m i . 155 140 145 -pi 179 164 170 206 263 270 276 284 289 MASLWL 296 305 313 -JLWIMJUUL 32 9 318 361 381 , 3 7 3 -MSUUUJiSJL-403 i*15 418 423 J v W \ A W A A V W V _ J i m -431 463 443 V 471 480 512 517 533 535 552 559 581 1 Fig. I - Schematic diagram of the predicted secondary structure of bovine serum albumin 1 3 18 20 26 42 34 65 52 72 91 95 97 101 140 135 Wvw^ 49 1 58 1 _ywwwvwv^ 182 112 199 Fig. I I - Schematic diagram of the predicted secondary structure of a s l - c a s e i n (bovine) 2 4 6 mm i 16 1] 23 27 37 39 kl 43 50 52 60 i — i / A / l A / V A , 0O00000OO PflPPPOPQ. A A A A A A A A A , 178 193 187 WvWW \_ 20*9 Fig. I l l - Schematic diagram of the predicted secondary structure of 3-casein (bovine) 247 32 28 26 38 1+3 TsAMAA. "+8 56 vwvwwv\ 68 62 W V V v V V v ^ , 85 126 121 133 1^7 137 108 102 113 Fig. IV - Schematic diagram of the predicted secondary structure of K-casein (bovine) 2 4 8 29 33 Fig. V - Schematic diagram of the predicted secondary structure of chymosin (bovine) 249 16 31 26 43 47 52 59 — ^ A A A / W W . 75 72 ,-JVWV. 82 89 99 MJUUUL19WL-123 104 Fig. VI - Schematic diagram of the predicted secondary structure of a-Lactalbumin (bovine) 250 123 115 129 49 43 39 / V v V v V 61 7VWWV 87 80 78 67 92 107 102 J W V Y V V 95 143 145 151 W v N A A A T 162 154 1 5 A A A A A _ 37 22 20 1 2 Fig. VII - Schematic diagram of the predicted secondary structure of 3-Lactoglobulin (bovine) 251 5 23 t O O O t O O O D 51 56 62 J 71 79 77 91 109 102 - -^^t 133 1«*3 145 149 P g Q O O t l Q O O O O A / y A ^ A g g Q 0 (LO C 194 196 198 i u o 219 221 23 A A / y \ 0 0 0 0 0 0 0 0 0 / y v y V A / y y v / ^ A A A ^ a<L0QQ0O0QQ0 206 208 2 2 V o o Q 0 g r 385 379 373 371 jU£UJL^vyvAAAAA 3 Qfl oo P O P Qoo oo 340 290 334 305 319 • 0 0 D 0 Q Q 0 0 O I Q 0 O 0 O O p _ , F i g . VIII - Schematic diagram of the predicted secondary structure of ovalbumin 252 , 164 167 I A A A A 171 215 267 259 , r - ^ v V W W V V V - l 272 A AAA278 288 313 298 326 Fig. IX - Schematic diagram of the predicted secondary structure of pepsin C^orGineO) 253 25 46 33 53, 59 6"+ '— ' 71 68 A A A A _ • 82 . 87 J - W W V W - , 102 92 Q^0tL0Q.0P0flPJL_ h 0 6 i n UMJUL-117 1 2 5 1 3 2 141 146 _JULOJUL-154 1 7 2 1 6 1 1 7 8 2 0 0 2 0 5 ^ A V A V v V v V v \ 2 2 1 2 2 3 2 2 ! SLWLSUU Fig. X - Schematic diagram of the predicted secondary structure of trypsinogen (bovine) 2 5 4 ********************************* ALPHA-HELIX PREDICTION ********************************* TOTAL NUMBER OF AA: NUMBER OF DATA LINES: 129 9 PROTEIN SEQUENCE to 12 20 14 8 2 5 7 1 1 1 1 1 13 12 2 9 1 1 4 3 19 2 8 19 16 1 1 8 3 18 20 5 1 12 14 7 is 3 14 3 17 6 1 17 3 2 3 17 8 16 '17 4 19 8 10 1 1 6 1 1 3 16 2 18 18 3 •4 8 2 17 15 8 16 2 3 1 1 5 3 10 15 1G 1 1 1 1 1 16 16 4 10 17 1 16 20 3 5 1 12 10 20 16 4 8 4 8 13 3 1 18 20 1 18 3 2 5 12 8 17 4 20 6 1 18 10 2 8 5 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PRELIMINARY SEARCH FOR REGIONS WITH HELIX POTENTIAL RULE 1 3 26 24 80 90 103 1 19 23 33 38 85 98 1 16 124 KM : 16 SEARCH FOR ACTUAL HELICES FROM THE POTENTIAL REGIONS J : 3 OA: 8 T3: 4.0000 L: 1 HELIX NUCLEATION 8 1 4 5 5 12 2 2 O J B 9 J C 12 T3 5 7 1 0 0 H E L I X P R O P A G A T I O N J B 7 J C 12 T4 6 0 0 0 0 H E L I X FORMERS IN 6 O V E R L A P P I N G R E S I D U E S J B 3 JD 12 M5 3 L : 1 T H E O R I T . AND ACTUAL # B R E A K E R S FROM J B TO JD J B 13 J C 16 T3 3 7 3 0 0 H E L I X P R O P A G A T I O N J 1 3 J 2 14 T4 9 5 0 0 0 TT : 6 OOOO ACTUAL AND T H E O R I T . H FORMERS FROM J 1 TO J 2 J 1 3 J 2 15 T4 10 0 0 0 0 . TT : 6 5 0 0 0 ACTUAL AND T H E O R I T . H FORMERS FROM J 1 TO J 2 P S E U D O - H E L I X FROM J 1 TO J 2 : 15 BOUNDARY A N A L Y S I S OF THE N - T E R M I N A L , T 1 , T 2 , T 5 4 . 0 8 0 3 . 2 4 0 4 . 4 4 0 STEP 5 . M 0 J 1 C L O S E TO O ( J l L E , T 1 , T 2 , T 5 , T T , I LE , T 1 , T 2 , T 5 , T T , I L E . T . 1 , T 2 , T 5 , T T , I L E , T 1 . T 2 , T 5 , T T , I L E , T 1 , T 2 , T 5 , T T , I L E , T 1 , T 2 , T 5 , T T , I L E , T 1 , T 2 . T 5 , T T , I BOUNDARY T1 , T 2 T 1 , T 2 , T 5 T 1 , T 2 , T 5 11 5 . 0 3 0 0 A N A L Y S I S OF THE C - T E R M I N A L 12 13 14 15 16 17 T 1 6 1 0 0 7 3 0 0 7 8 0 0 7 9 0 0 4 6 0 0 ' 5 8 0 0 T2 , T 5 T1 , T 2 T 1 , T 2 , T 5 T 1 , T 2 , T 5 T 1 , T 2 . T 5 T 1 , T2 T 1 , T 2 , T 5 T 1 , T 2 , T 5 T 1 , T 2 , T 5 T 1 , T 2 , T 5 . TT 3 . 7 9 0 3 . TT 3 . 7 8 0 3 . 7 9 0 5 5 0 0 5 9 0 0 2 9 0 0 8 5 0 0 4 6 0 0 4 8 0 0 2 0 0 0 4 6 0 3 . 4 6 0 7 9 0 5 8 0 7 8 0 7 9 0 7 3 0 0 3 0 6 1 0 3 3 3 4 3 4 3 3 3 . 4 6 0 4 6 0 STEP 3 . J 2 C L O S E TO 0 ' 3 . 8 5 0 4 . 0 5 0 0 . 0 0 0 0 4 3 7 5 7 S T E P 6 , 4 . 5 6 0 0 . 0 0 0 0 3 4 7 0 0 0 . 0 0 0 0 3 0 1 1 0 0 3 3 3 4 4 4 5 4 4 8 0 4 8 0 4 6 0 2 0 0 8 5 0 3 9 0 2 9 0 5 5 0 5 9 0 3 4 6 0 2 2 0 0 5 1 0 0 4 7 0 0 0 5 0 0 5 6 0 0 1 7 0 0 7 5 0 0 5 . 4 4 4 O . O . 0 . 0 . O . . 1 7 0 . 5 6 0 7 5 0 0 5 0 0 0 0 0 4 1 8 0 6 0 0 0 0 8 2 4 1 3 0 0 0 0 4 3 7 5 7 0 0 0 0 3 4 7 0 0 0 0 0 0 4 1 5 3 7 0 . 0 0 0 1 6 0 2 0 1 STEP 1 0 , STEP STEP STEP 2 4 . STEP 2 5 . STEP 2 8 . STEP 41 , STEP 5 4 , STEP 5 5 , 16 19 S T E P 7 , B - T U R N B - T U R N B - T U R N B - T U R N B - T U R N B - T U R N B - T U R N J 2 C L O S E 0 J 2 - 1 0 , M 0 J 2 S E A R C H AT C -S E A R C H AT C S E A R C H A T ' C -S E A R C H AT S E A R C H AT C -S E A R C H AT C -S E A R C H AT T E R M I N A L T E R M I N A L T E R M I N A L T E R M I N A L T E R M I N A L T E R M I N A L T E R M I N A L J 2 = J 2 . M 0 J 2 J 2 = J 2 4 . 4 7 0 3 . 2 2 0 3 . 5 1 0 4 8 0 5 . 1 7 0 0 . 0 0 0 0 4 1 5 3 7 J 2 - 1 J 2 + 1 J 2 - 2 J 2 - 2 , J 2 - 3 J 2 - 4 J 2 - 4 , M 0 J 2 , M 0 J 2 , RMJ2 RMJ2 , RMJ2 , RMJ2 , RMJ2 S T E P 6 0 , J 2 + 4 , R M J 2 EVENTUAL H E L I X FROM J 1 : 7 TO J 2 : 15 J •16 J A 21 T 3 2 OOOO L 3 H E L I X N U C L E A T I O N J 17 JA 22 T 3 2 OOOO L 3 H E L I X N U C L E A T I O N J 18 JA 2 3 T3 1 OOOO L 4 H E L I X N U C L E A T I O N J 19 JA 24 T3 0 5 0 0 0 L 4 H E L I X N U C L E A T I O N J 2 0 JA 2 5 T3 1 5 0 0 0 L 3 H E L I X N U C L E A T I O N J 2 1 J A 26 T3 1 5 0 0 0 L 3 H E L I X N U C L E A T I O N J 22 J A 27 T3 1 OOOO L 4 H E L I X N U C L E A T I O N J 2 3 J A 28 T3 2 OOOO L 3 H E L I X N U C L E A T I O N J 24 JA 29 T 3 3 OOOO L 2 H E L I X N U C L E A T I O N J 2 5 J A 3 0 T3 3 5 0 0 0 L 2 H E L I X N U C L E A T I O N J 26 JA 31 . T 3 3 5 0 0 0 L 2 H E L I X N U C L E A T I O N J 27 J A 32 T 3 4 5 0 0 0 L 1 H E L I X N U C L E A T I O N J 1 27 J 2 3 3 T4 5 5 0 0 0 TT : 3 5 0 0 0 ACTUAL AND Tr *** V 2 . V 3 : 1 1 o * * * PSEUDO-HELIX FROM J1: 27 TO J2: 33 BOUNDARY ANALYSIS OF THE N-TERMINAL T1,T2,T5 4.560 5 090 3.310 STEP 5,M0J1 CLOSE TO 0 LE , T 1 T2 T5.TT I 24 3.2200 3.6900 5.1400 0 00005 1870 0 B-TURN SEARCH AT N-TERMINAL LE ,T1 T2 T5.TT I 25 3.5300 4.3100 4.6700 0 000165386 1 B-TURN SEARCH AT N-TERMINAL LE ,T1 T2 T5.TT I 26 3.3800 4.7100 4.5800 0 0000287 17 2 B-TURN SEARCH AT N-TERMINAL LE ,T1 T2 T5 , TT I 27 3.8100 5.1500 4.2 100 0 000007501 3 B-TURN SEARCH AT N-TERMINAL LE ,T1 T2 T5 , TT I 28 4.5600 5.0900 3.3100 0 0OO02508 1 4 B-TURN SEARCH AT N-TERMINAL LE .T1 T2.T5.TT i 29 4.9000 4.5500 3.0100 0 0O0OO6671 5 B-TURN SEARCH AT N-TERMINAL LE . T 1 T2 T5 , TT I 30 5.0000 3.5900 3.5200 0 000037652 6 B-TURN SEARCH AT N-TERMINAL T1 .T2,T5 4.560 5 090 3.3 10 LC: 1 STEP 12 ,M0J1, B-TURN PR.OBLEM T1 .T2.T5 3.530 4 310 4.670 STEP 14, M0J1 B -T PROBL. T1.T2.T5 3.240 4 270 4.720 STEP 22.M0J1 B -T PROBL. T1 .T2.T5 3.380 4 710 4.580 STEP 26. M0J1 B -T PROBL. T1 ,T2,T5 3.530 4 310 4.670 STEP 29, J1 + 5 , RMJ 1 T1,T2.T5 3.220 3 690 5.140 STEP 57. J1 + 2 , RMJ 1 BOUNDARY ANALYSIS OF THE C-TERMINAL T1,T2 4.570 3.240 STEP 3, J2 CLOSE TO O T1 .T2.T5 TT 5.220 3.320 3. 010 0.000028704 STEP 6. J2 CLOSE 0 T 1 .T2.T5 TT 4.570 3.240 3. 780 0.000018405 STEP7 , J2- 10 M0J2 LE , T 1 T2 T5.TT,I 29 4.9000 4.5500 3.0100 0 000006671 0 B-TURN SEARCH AT C-TERMINAL LE . T 1 T2 T5 , TT I 30 5.0000 3.5900 3.5200 0 000037652 1 B-TURN SEARCH AT C-TERMINAL LE ,T 1 ,T2,T5.TT,I 31 5.1300 3.7800 2.9300 0 000021341 2 B-TURN SEARCH AT C-TERMINAL LE .T1 T2 T5.TT I 32 5.2200 3.3200 3.0100 0 000028704 3 B-TURN SEARCH AT C-TERMINAL LE ,T1 T2 T5.TT I 33 4.5700 3.2400 3.7800 0 000018405 4 B-TURN SEARCH AT C-TERMINAL LE , T 1 T2 T5.TT I 34 4.0800 3.3900 4.3300 0 000040267 5 B-TURN SEARCH AT C-TERMINAL LE , T 1 T2 T5 , TT I 35 4.0800 3.3900 4.3300 0 000096638 6 B-TURN SEARCH AT C-TERMINAL T1 ,T2,T5 4.080 3 390 4.330 STEP 10, J2 = J2 , M0J2 T1 , T2 4.080 3 390 STEP 16 J2 = J2 T 1 ,T2,T5 4.570 3 240 3.780 STEP 19 J2- 1 ,M0J2 T1 .T2.T5 4.080 3 390 4.330 STEP 24, J2+1 ,M0J2 T1 ,T2,T5 5.220 3 320 3.010 STEP 25. J2-2 . RMJ2 T1 .T2 5.990 4 070 STEP 28, J2-2, RMJ2 EVENTUAL HELIX FROM J1: 27 TO J2 : 35 *** V2.V3: O 35 J 24 JA 29 T3 3 0000 L : 2 HELIX NUCLEATION J 25 JA 30 T3 3 5000 L : 2 HELIX NUCLEATION J 26 JA 31 T3 3 5000 L : 2 HELIX NUCLEATION J 27 JA 32 T3 4 5000 L : 1 HELIX NUCLEATION JB 33 JC 36 T3 4 5700 HELIX PROPAGATION JB 31 JC 36 T4 5 0000 HELIX FORMERS IN 6 OVERLAPPING RESIDUES JB 27 JD 36 M5 3 L : 1 THEORIT. AND ACTUAL H BREAKERS FROM JB TO JD J1 27 J2 36 T4 7 5000 TT : 5 0000 ACTUAL AND THEORIT. # FORMERS FROM J1 TO PSEUDO-HELIX FROM J1: 27 TO J2: 36 BOUNDARY ANALYSIS OF THE N-TERMINAL T1 ,T2,T5 4.560 5 090 3.310 STEP 5.M0J1 CLOSE TO 0 LE T 1 T2.T5.TT, I 24 3.2200 3.6900 5.1400 0 000051870 0 B-TURN SEARCH AT N-TERMINAL LE T1 T2 T5.TT,I 25 3.5300 4.3100 4.6700 0 000165386 1 B-TURN SEARCH AT N-TERMINAL LE T1 T2 T5.TT,I 26 3.3800 4.7100 4.5800 0 000028717 2 B-TURN SEARCH AT N-TERMINAL LE T1 T2 T5 , TT , I 27 3.8100 5.1500 4.2100 0 000007501 3 B-TURN SEARCH AT N-TERMINAL LE T 1 T2 T5.TT,I 28 4.5600 5.0900 3.3100 0 000025081 4 B-TURN SEARCH AT N-TERMINAL LE T1 T2 T5 , TT , I 29 4.9000 4.5500 3.0100 0 000006671 5 B-TURN SEARCH AT N-TERMINAL LE T1 T2 T5.TT,I 30 5.0000 3.5900 3.5200 0 000037652 6 B-TURN SEARCH AT N-TERMINAL T1 .T2.T5 4.560 5 090 3.310 LC: 1 STEP 12 .M0J1. B-TURN PROBLEM T1 ,T2,T5 3.530 4 310 4.670 STEP 14, M0J1 B -T PROBL. T1 ,T2,T5 3.240 4 270 4.720 STEP 22. M0J1 B -T PROBL. T1 ,T2,T5 3.380 4 7 10 4.580 STEP 26, M0J1 B -T PROBL. T1,T2,T5 3.530 4 310 4.670 STEP 29, J1+5 , RMJ 1 T1,T2,T5 3.220 3 690 5.140 STEP 57, J1+2 , RMJ 1 BOUNDARY ANALYSIS OF THE C-TERMINAL T1.T2 3.240 3.910 STEP 3, J2 CLOSE TO 0 T1 ,T2,T5, TT 4 .080 3. 390 4 . 330 0.000096638 STEP 6, J2 CLOSE 0 T1.T2.T5, TT 3 . 240 3 . 910 5 . 150 O.000058913 STEP7, J2- 10 M0J2 LE T1 T2,T5,TT,I 32 5.2200 3 . 3200 3 . 0100 0 000028704 0 B-TURN SEARCH AT C-TERMINAL LE T 1 T2,T5,TT,I 33 4.5700 3 . 2400 3 . 7800 O OOOO18405 1 B-TURN SEARCH AT C-TERMINAL LE T1 T2,T5,TT. I 34 4.0800 3 . 3900 4 . 3300 0 000040267 2 B-TURN SEARCH AT C-TERMINAL LE T1,T2,T5,TT,I 35 4.0800 3 . 3900 4 . 3300 0 000096638 3 B-TURN SEARCH AT C-TERMINAL LE T1 T2,T5,TT,I 36 3.2400 3 .9100 5 . 1500 0 000058913 4 B-TURN SEARCH AT C-TERMINAL LE T1 T2,T5,TT. I 37 3.3000 4 . 3500 4 . 6800 0 000099602 5 B-TURN SEARCH AT C-TERMINAL LE T 1 T2,T5,TT,I 38 3.7400 4 .5600 4 . 1000 0 000031194 6 B-TURN SEARCH AT C-TERMINAL T1 ,T2,T5 3 . 300 4 35C 4 .680 STEP 10, J2 = J2 , M0J2 T1 ,T2 3 . 300 4 350 STEP 16 J2 = J2 EVENTUAL HELIX FROM J1 : 27 TO J2: 35 *** V2.V3: 0 ) 8 * * * J 80 JA 85 T3 3.5000 L : 0 HELIX NUCLEATION PSEUDO-HELIX FROM J1 : 79 TO J2 : 84 SPECIAL CASE J 90 JA 95 T3 3.5000 L : 1 HELIX NUCLEATION J 91 JA 96 T3 3.5000 L : 1 HELIX NUCLEATION J 92 JA 97 T3 4.5000 L : 1 HELIX NUCLEATION J1 .91 J2 98 T4 5.5000 TT 4 OOOO ACTUAL AND THEORIT. H FORMERS FROM J1 TO J2 J1 90 J2 98 T4 6.5000 TT 4 5000 ACTUAL AND THEORIT. H FORMERS FROM J1 TO J2 PSEUDO-HELIX FROM J1: 90 TO J2: 98 BOUNDARY ANALYSIS OF THE N-TERMINAL T1.T2.T5 3.500 4.530 4.680 STEP 5.M0J1 CLOSE TO 0 LE,T1 ,T2,T5,TT, I 87 4.3400 4.1600 3.5500 0.000018842 0 B-TURN SEARCH AT N-TERMINAL LE,T1,T2,T5.TT , I 88 4.1000 4.3700 3.5200 0.000017229 1 B-TURN SEARCH AT N-TERMINAL LE.T1, T 2 , T 5 , T T , I 89 4.0800 4.4700 3.5500 0.000043301 2 B-TURN SEARCH AT N-TERMINAL LE,T 1 , T2 ,T5,TT,I LE.T1 ,T2,T5,TT,I LE,T1,T2,T5.TT,I LE.T1 ,T2,T5,TT.I 90 3.9200 91 3.5000 92 4.1500 93 4.2500 T 1 ,T2,T5 ,T2,T5 ,T2,T5 ,T2,T5 •T2.T5 ,T2,T5 T1 . T1 . T 1 . T1 . T 1 4 . 1700 4 . 5300 4 . 6 100 3 . 6500 3 . 500 4 4 . 100 3.690 4 .080 4 . 100 4 . 340 4.1500 0.000021250 3 B-TURN SEARCH AT N-TERMINAL 4.6800 0.000140820 4 B-TURN SEARCH AT N-TERMINAL 3.9 100 0.000034921 5 B-TURN SEARCH AT N-TERMINAL 4.4200 0.000028372 6 B-TURN SEARCH AT N-TERMINAL 530 4.680 LC: 2 STEP 12 ,M0J1, B-TURN PROBLEM 3.520 STEP 14.M0J1 B-T PROBL. 4.320 STEP 22.M0J1 B-T PROBL. 3.550 STEP 26.M0J1 B-T PROBL. 3.520 STEP 29, J1 + 5 ,RMJ1 3.550 STEP 57, J1+2 ,RMJ1 370 080 470 370 160 LE.T1,T2 LE.T1 ,T2 LE.T1 ,T2 LE,T1,T2 LE.T1,T2 LE.T1 ,T2 LE,T1,T2 , T5,TT, , T5.TT, , T5.TT, •T5.TT, •T5.TT, , T5,TT, .T5.TT. BOUNDARY T 1 , T2 T1,T2,T5, T1 ,T2,T5, 94 4.7400 ANALYSIS OF THE C-TERMINAL 95 96 97 98 99 100 8200 4600 0700 9200 4100 3600 T1,T2,T5 T 1 , T2 T1 ,T2,T5 TT 3.920 4. TT 4.070 3 .920 5000 9100 7800 7900 5900 7400 5800 3.410 3. 3.410 3. 3.920 4. 590 4 . 790 4 3 3 2 3 3 4 5 740' 740 590 3 . 3 . 590 8700 1500 9900 4100 8600 9500 9100 4 . 950 3.860 STEP 3, J2 CLOSE TO O 410 0.000005550 STEP 6, 860 0.000020898 STEP7, 0.000077456 0 B-TURN 0.000027821 1 B-TURN 0.000004358 2 8-TURN 0.OOO0O5550 3 B-TURN 0.OO002O898 4 B-TURN 0.000234478 5 B-TURN 0.000203148 6 B-TURN STEP 10 STEP 16 STEP 19 J2 CLOSE 0 J2-10 , M0J2 SEARCH AT C-SEARCH AT C-SEARCH AT C-SEARCH AT C-SEARCH AT C-SEARCH AT SEARCH AT C-TERMINAL TERMINAL TERMINAL TERMINAL TERMINAL TERMINAL TERMINAL J2 = J2 , M0J2 J2 = J2 J2-1 ,M0«J2 EVENTUAL HELIX FROM J1: 90 TO J2: 99 *** V2.V3: 23' J 103 JA 108 T3 3 5000 L : 2 HELIX NUCLEATION J 104 JA 109 T3 4 OOOO L : 2 HELIX NUCLEATION J 105 JA 1 10 T3 5 OOOO L : 1 HELIX NUCLEATION JB 1 1 1 JC 114 T3 3 7500 HELIX PROPAGATION J1 105 J2 112 T4 6 5000 TT : 4 OOOO ACTUAL AND THEORIT M FORMERS FROM J1 TO J2 PSEUDO-HELIX FROM J1: 105 TO J2 : 1 12 BOUNDARY ANALYSIS OF THE N-TERMINAL T1 .T2.T5 4.230 4 790 3.680 STEP 5.M0J1 CLOSE TO 0 LE,T1,T2 T5 . TT I 102 3.6000 3.0900 5.1800 0 000117 249 0 B-TURN SEARCH AT N-TERMINAL LE,T 1 ,T2 T5.TT I 103 3.7000 3.2300 5.1800 0 000015919 1 B-TURN SEARCH AT N-TERMINAL LE,T1,T2,T5,TT I 104 4.1100 3.5200 4.3800 0 000092656 2 B-TURN SEARCH AT N-TERMINAL LE,T1 ,T2 T5, TT I 105 4.6200 4.1400 3.7800 0 000032989 . 3 B-TURN SEARCH AT N-TERMINAL LE,T1,T2 T5, TT I 106 4.2300 4.7900 3.6800 0 000041504 4 B-TURN SEARCH AT N-TERMINAL LE,T1,T2 T5.TT I 107 4.9800 . 4.7300 2.7800 0 000001267 5 B-TURN SEARCH AT N-TERMINAL LE,T 1 ,T2 T5.TT I 108 4.6400 5.2700 3.0800 0 000021603 6 B-TURN SEARCH AT N-TERMINAL T 1 ,T2,T5 4.230 4 790 3.680 LC: 0 STEP 12 ,M0J1, B-TURN PROBLEM T1 .T2.T5 3.700 3 230 5.180 STEP 14.M0J1 B -T PROBL. T1 ,T2,T5 3.160 2 580 6.040 STEP 22.M0J1 B -T PROBL. BOUNDARY ANALYSIS OF THE C-TERMINAL T1.T2 3.670 3.940 STEP 3, 02 CLOSE TO 0 T1 ,T2,T5, TT 3.750 4.120 4. 420 0.000132510 STEP 6, 02 CLOSE 0 T1 ,T2,T5, TT 3.670 3.940 4. 650 0.000073624 STEP7, 02-10 , , M002 LE , T 1 ,T2, .T5, , TT , , I 108 4.6400 5.2700 3.0800 0. 00002 1603 0 B-TURN SEARCH AT C-TERMINAL LE , T 1 .T2, . T5, TT , , I 109 4.5600 4.8300 3.0700 0. 000025633 1 B-TURN SEARCH AT C-TERMINAL LE . T 1 .T2, ,T5, , TT, I 1 10 4.1700 4.0200 4.1300 O. 000007027 2 B-TURN SEARCH AT C-TERMINAL LE ,T1 .T2, ,T5. , TT , , I 1 1 1 3.7500 4.1200 4.4200 0. 000132510 3 B-TURN SEARCH AT C-TERMINAL LE,T1,T2, ,T5, . TT, I 1 12 3.6700 3.9400 4.6500 0. 000073624 4 B-TURN SEARCH AT C-TERMINAL LE ,T1 .T2,T5, , TT , I 1 13 3.8300 3.7500 4.7100 0. 000189688 5 B-TURN SEARCH AT C-TERMINAL LE ,T1 .T2, ,T5, .TT, I 1 14 3.7300 3.6100 4.7100 0. 000040602 6 B-TURN SEARCH AT C-TERMINAL T1 , T2.T5 3.830 3. 750 4.710 STEP 10, 02 = 02 . M002 T 1 ,T2 3.830 3. . 750 STEP 16 , , 02 = 02 T1 ,T2,T5 3.670 3. .940 4.650 STEP 19 , , 02-1 ,M002 T 1 , T2,T5 3.730 3. 610 4.710 STEP 24, 02+1 , M0J2 T1 ,T2,T5 3.750 4. 120 4.420 STEP 25, J2-2 , RM02 T 1 ,T2 4.750 5. 310 STEP 28, J2-2, RM02 EVENTUAL HELIX FROM 01: 107 TO 02: 114 *** V2.V3: 24 37 *** 0 : 119 OA: 124 T3: 5.5000 L: 0 HELIX NUCLEATION °J 01: 119 02: 124 T4: 5.5000 TT: 3.0000 ACTUAL AND THEORIT. H FORMERS FROM 01 TO 02 PSEUDO-HELIX FROM 01: 119 TO 02: 124 LE.T1 ,T2,T5,TT, I LE.T1 ,T2,T5,TT, I LE,T 1 ,T2,T5,TT,I LE.T1,T2,T5,TT,I LE,T1,T2,T5,TT,I LE.T1 ,T2.T5,TT,I LE,T1,T2,T5,TT,I BOUNDARY T1,T2,T5 116 3.5700 117 3 118 4 4 700 0100 119 4.6000 120 4.6700 .6900 . 5600 ,T2,T5 121 4 122 4 T1 T1,T2,T5 T1 ,T2,T5 T1.T2.T5 T1,T2,T5 T1 .T2.T5 ANALYSIS 4.670 5 3.2200 1800 5300 1700 OOOO 9000 7300 670 5 470 4 560 3 010 4 470 4 570 3 OF THE N-TERMINAL 000 3.100 4.9900 4800 9000 6000 1000 0700 0400 3 . 100 4 . 3. 3 . 3 . 3 . 3 . 000 180 870 530 180 220 STEP 5.M001 CLOSE TO 0 0O0024614 0 B-TURN 480 720 900 480 4 .990 SEARCH AT N-TERMINAL 1 B-TURN SEARCH AT N-TERMINAL 2 B-TURN SEARCH AT N-TERMINAL 3 B-TURN SEARCH AT N-TERMINAL 4 B-TURN SEARCH AT N-TERMINAL 5 B-TURN SEARCH AT N-TERMINAL 6 B-TURN SEARCH AT N-TERMINAL STEP 12 ,M0U1, B-TURN PROBLEM STEP 14.M001 B-T PROBL. STEP 22.M001 B-T PROBL. STEP 26.M001 B-T PROBL. STEP 29. 01+5 .RM01 STEP 57. 01+2 .RM01 O O.OOO1045O9 0.000025958 0.000015142 O.0OOO35514 0.000020156 0.000000862 LC: 1 LE,T1,T2,T5.TT,I LE , T 1 ,T2,T5 , TT,I LE ,T 1 ,T2.T5,TT,I LE.T1 ,T2.T5,TT, I BOUNDARY ANALYSIS OF THE C-TERMINAL T1 ,T2 3.330 4.470 STEP 3, 02 CLOSE TO 0 T1,T2,T5,TT 3.710 4.650 3.940 0.000039396 STEP 6, 02 CLOSE 0 T1,T2,T5,TT 3.330 4.470 4 120 4.6700 5.0000 3.1000 121 4.6900 4.9000 3.0700 122 4.5600 4.7300 3.0400 123 3.7100 4.6500 3.9400 170 0.000110850 O.000035514 O 0.000020156 1 0.000000862 2 0.000039396 3 STEP7, 02-10 . M002 B-TURN SEARCH AT C-TERMINAL B-TURN SEARCH AT C-TERMINAL B-TURN SEARCH AT C-TERMINAL B-TURN SEARCH AT C-TERMINAL LE,T 1 ,T2,T5, TT , I 124 3.3300 4.4700 4 . 1700 0 .000110850 4 B-TURN SEARCH AT C -TERMINAL LE.T1 ,T2,T5, , TT , I 125 3.2500 3.8000 4 . i 6500 0 .000059173 5 B-TURN SEARCH AT C -TERMINAL LE,T 1 .T2,T5, TT , I 126 3.4800 4.1700 4 . 2900 0 .000037464 6 B-TURN SEARCH AT C -TERMINAL T1 ,T2,T5 3 . 250 3 . 800 4.650 STEP 10, J2=J2 , M0U2 T1 ,T2 3 . 250 3 . 800 STEP 16 , , J2=J2 T1 ,T2,T5 3 . 330 4 . 470 4 . 170 STEP 19 , , J2-1 ,M0d2 T 1 ,T2,T5 3 . 480 4 . 170 4 . 290 STEP 24 , J2+1 , M0J2 T1 ,T2,T5 3 . 710 4 . 650 3 . 940 STEP 25 , J2-2 , RMd2 T1 • T2 4.410 5 . 840 STEP 28, J2-2, RMJ2 T1 ,T2,T5 4 . 560 4 . 730 3.040 STEP 4 1 , 02-3 , RMd2 T1 ,T2,T5 4.670 5 .000 3 . 100 STEP 54, J2-4 ,RMd2 T 1 .T2,T5 4 . 690 4 . 900 3 .070 STEP 55, J2-4 ,RMJ2 EVENTUAL HELIX FROM J1: 119 TO J2 : 124 *** V2,V3: 0 0 *** END OF PROGRAM CTN ******************************** * BETA-SHEET PREDICTION ********************************* TOTAL NUMBER OF AA : NUMBER OF DATA LINES: 129 9 PROTEIN SEQUENCE 12 20 14 8 2 5 7 1 1 1 1 1 13 12 2 9 1 1 4 3 19 2 8 19 16 1 1 8 3 18 20 5 1 12 14 7 16 3 14 3 17 6 1 17 3 2 3 17 8 16 17 4 19 8 10 1 1 6 1 1 3 16 2 18 18 3 4 8 2 17 15 8 16 2 3 1 1 5 3 10 15 16 1 1 1 1 1 16 16 4 10 17 1 16 20 3 5 1 12 10 20 16 4 8 4 8 13 3 1. 18 20 1 18 3 2 5 12 8 17 4 20 6 1 18 10 2 8 5 1 1 0 0 0 O 0 0 0 0 0 0 0 0 0 0 PRELIMINARY SEARCH FOR REGIONS WITH SHEET POTENTIAL - RULE 2 1 19 21 25 37 51 53 73 76 83 87 6 21 25 34 41 53 69 76 80 85 89 8 1 4 5 5 12 2 2 O 89 95 104 1 1 1 1 18 121 IM = 36 95 99 109 1 13 121 129 SEARCH FOR ACTUAL SHEETS FROM THE POTENTIAL REGIO G : 1 MA: 5 T3 : 2 OOOO N: 2 K> G : 2 MA: 6 T3 : 3 OOOO N: 1 cn J1: 1 J2: 6 T4 : 4 OOOO TT 3.OOOO CO PSEUDO-SHEET FROM d1 : 1 TO d2: 6 EVENTUAL SHEET FROM d1 TO G 19 MA 22 T3 1 OOOO N: 1 G 21 MA 25 T3 2 OOOO N: 2 G 22 MA 25 T3 2 OOOO N: 2 G 25 MA 29 T3 3 OOOO N: 1 MB 30 MC 33 T1 4 7000 T2 3 5900 J1 25 d2 31 T4 4 OOOO TT 3 5000 d1 25 d2 32 T4 4 OOOO TT 4 OOOO PSEUDO-SHEET FROM d1: 25 TO d2: 32 EVENTUAL SHEET FROM d1 : 25 TO G 37 MA 41 T3 3 OOOO N: 0 d1 37 d2 42 T4 3 OOOO TT 3 OOOO d1 37 d2 45 T4 5 OOOO TT 4 5000 d1 37 d2 45 T4 5 OOOO TT 4 5000 PSEUDO-SHEET FROM d1: 37 TO d2: 45 SHEET NUCLEATION SHEET NUCLEATION ACTUAL AND THEORIT tt .FORMERS FROM d1 TO d2 d2 : V2, V3 25 SHEET NUCLEATION SHEET NUCLEATION SHEET NUCLEATION SHEET NUCLEATION SHEET PROPAGATION ACTUAL AND THEORIT'. ACTUAL AND THEORIT. tt FORMERS FROM d1 TO d2 tt FORMERS FROM d1 TO d2 d2: 32 *** V2,V3 36 SHEET NUCLEATION ACTUAL AND THEORIT. ACTUAL AND THEORIT. ACTUAL AND THEORIT. tt FORMERS FROM d1 TO d2 tt FORMERS FROM d1 TO d2 tt FORMERS FROM d1 TO d2 EVENTUAL SHEET FROM 01 : 38 TC G 51 MA 54 T3 : 2 .0000 N : 2 G 53 MA 57 T3 . 4 .0000 N 1 MB 58 MC 61 T1 3 . 6300 T2 : 3 8700 01 53 02 59 T4 6 OOOO TT : 3 5000 PSEUDO-SHEET FROM J1 : 53 TO 02 : 59 EVENTUAL SHEET FROM 01 : 51 TC G 60 MA 64 T3 3 OOOO N 1 MB 56 MC 59 T 1 4 2000 T2 : 4 7500 MB 56 MD 64 V6 3 V8 : 1 PSEUDO-SHEET FROM <J 1 : 56 TO 02 : 64 EVENTUAL SHEET FROM 01 : 56 TC G 66 MA 69 T3 1 OOOO N 2 G 73 MA 76 T3 2 OOOO N 0 G 76 MA 80 T3 3 OOOO N 1 G 83 MA 86 T3 2 OOOO N 2 G 87 MA 90 T3 2 OOOO N 1 G 89 MA 93 T3 3 OOOO N 1 J1 88 J2 95 T4 5 OOOO TT : 4 OOOO PSEUDO-SHEET FROM J1: 88 TO 02: 95 EVENTUAL SHEET FROM 01 : 88 TC G 95 MA 99 T3 2 OOOO N 2 G 96 MA 99 T3 2 OOOO N 2 G 104 MA 108 T3 2 OOOO N 1 G 105 MA 109 T3 3 OOOO N 0 J1 105 02 1 10 T4 3 OOOO TT : 3 OOOO 01 105 02 112 T4 4 OOOO TT : 4 OOOO 01 105 02 1 13 T4 5 OOOO TT : 4 5000 PSEUDO-SHEET FROM J1: 105 TO 02 : 1 13 EVENTUAL SHEET FROM 01 105 TO 02: 46 * * * V2,V3 8 -| 4 * * * SHEET NUCLEATION SHEET NUCLEATION SHEET PROPAGATION ACTUAL AND THEORIT. H FORMERS FROM 01 TO 02 02 : 59 *** V2,V3 : 17 SHEET NUCLEATION SHEET PROPAGATION THEORITIC. AND ACTUAL H BREAKERS FROM MB TO MD 02 : 65 *+* V2 V3 19 SHEET NUCLEATION SHEET NUCLEATION SHEET NUCLEATION SHEET NUCLEATION SHEET NUCLEATION SHEET NUCLEATION ACTUAL AND THEORIT. H FORMERS FROM 01 TO 02 02 : 94 *** V2.V3 35 21 SHEET NUCLEATION SHEET NUCLEATION SHEET NUCLEATION SHEET NUCLEATION ACTUAL AND THEORIT. ACTUAL AND THEORIT. ACTUAL AND THEORIT. # FORMERS FROM 01 TO 02 H FORMERS FROM 01 TO 02 H FORMERS FROM 01 TO 02 02: 113 *** V2.V3 : 36 32 *** G : 1 1 1 MA : 1 14 T3 : 2 OOOO N: 0 G : 1 18 MA : 121 T3 : 3 OOOO N : 1 01 : 1 18 02 : 122 T4 : 3 OOOO TT : 2 5000 01 : 1 18 02 : 125 T4 : 5 OOOO TT : 4 OOOO PSEUDO-SHEET FROM 01: 118 TO 02: 125 EVENTUAL SHEET FROM 01: 120 TO G : 121 MA : 125 T3 : 3 OOOO N: 0 MB : 12G MC : 129 T 1 : 3 4600 T2 : 4.1700 MB: 121 MD : 129 V6 : 3 V8 : 1 PSEUDO-SHEET FROM 01: 12 1 TO 02 : 129 EVENTUAL SHEET FROM 01: 121 TO DO O U l END OF PROGRAM SHEET NUCLEATION SHEET NUCLEATION ACTUAL AND THEORIT. If FORMERS FROM 01 TO 02 ACTUAL AND THEORIT. # FORMERS FROM 01 TO 02 02: 127 *** V2.V3 : 23 20 ** SHEET NUCLEATION SHEET PROPAGATION THEORITIC. AND ACTUAL ff BREAKERS FROM MB TO MD 02: 129 *** V2.V3 39 32 * * * OVERLAPPING RESOLUTION TOTAL NUMBER OF AA : NUMBER OF DATA LINES: 129 9 (7\ PROTEIN SEQUENCE 12 20 14 8 2 5 7 1 1 1 1 1 13 12 2 9 8 1 1 4 3 19 2 8 19 16 1 1 8 3 18 20 5 1 1 12 14 7 16 3 14 3 17 6 1 17 3 2 3 17 4 8 16 17 4 19 8 10 1 1 6 1 1 3 16 2 18 18 5 3 4 8 2 17 15 8 16 2 3 1 1 5 3 10 15 5 16 1 1 1 1 1 16 . 16 4 10 17 1 16 20 3 5 1 12 12 10 20 16 4 8 4 8 13 3 1 18 20 1 18 2 3 2 5 12 8 17 4 20 6 1 18 10 2 8 5 2 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 O 0 PAIRS OF OVERLAPPING HELICES AND SHEETS 27 27 35 32 89 88 99 94 107 107 114 113 119 120 124 124 *** COMPARISON OF THEIR LENGTH *** L-HELIX: L-SHEET: ***** COMPARISON OF P-HELIX AND P-SHEET ***** RATI0=LH/LS: 1.0 H1 S1 27 27 H2 S2 35 32 A1: 1.128 A1: 1.058 A2 : A2 : 1 .033 1 . 135 A1 •> A2 A1 < A2 FROM H1 TO H2 FROM S1 TO S2 *** COMPARISON OF ASSIGNMENTS TYPES *** HHF 6 .00 H1 HF 4 .00 27 IIH 0.0 H2 IH 0. 25 BH -0.50 35 TTH: 9.750 BBH 0.0 SSF 2 .00 TTS: 4.250 SF 3 .00 IS O. 75 TTH BS -0.50 BBS -1 .00 TTS FROM H1 TO H2 HHF 4 .00 HF 2 .00 I I H 0.0 IH 0. 25 BH -O. 50 BBH 0.0 SSF 2 .00 SF 2 .00 IS O. 75 BS 0.0 BBS 0.0 S1 27 S2 32 TTH: 5.750 TTS: 4.750 TTH > TTS FROM S1 TO S2 BOUNDARY ANALYS. FOR HELIX FROM: 27 TO: 35 AND FOR SHEET FROM: 27 TO: 32 HN SN HC SC NHN NSN NHC NSC 2.89 3.84 4.17 2.61 3.81 3.33 3.61 2.11 H1 S1 OL1 *** COMPARISON OF THEIR LENGTH *** L-HELIX: 11 L-SHEET: 7 ***** COMPARISON OF P-HELIX AND P-SHEET ***** 89 H2 : 99 A1: 1.030 A2: 1.105 A1 < A2 FROM H1 TO H2 88 S2 : 94 Al: 0.933 A2: 1.164 A1 < A2 FROM S1 TO S2 *** p-HELIX AND P-SHEET OF INTERS. AREA : H1 TO S2 *** 89 0L2: 94 A1: 0.908 A2: 1.092 A1 < A2 FROM H1 TO S2 RATIO=LH/LS: 1.0 to <3 HHF 4 .OO H1 HF 5 .00 89 IIH 0.0 • H2 *** COMPARISON OF ASSIGNMENTS TYPES *** IH O. 75 99 BH -O. 50 TTH: 9.250 BBH 0.0 SSF 6.00 TTS: 7.250 SF 2 .00 IS O. 75 BS 1 . 50 BBS 0.0 TTH > TTS FROM H1 TO H2 HHF HF IIH IH BH 2.00 2.00 0.0 0.75 -0.50 S1 : 88 S2 : 94 TTH: 4.250 BBH 0.0 SSF 4 .00 TTS: 6.000 SF 2 .00 IS O. 50 BS -O. 50 BBS 0.0 TTH < TTS FROM S1 TO S2 HHF 2 .OO HF 1 .00 IIH 0.0 IH 0. 75 BH -0.50 BBH O.O SSF 2 .00 SF 2 .00 IS O. 50 BS -0.50 BBS O.O OL 1 89 *** ASSIGNM. TYPES IN OVERL. AREAS 0L2: 94 TTH: 3.250 TTS: 4.OOO H1 TO 52 *** . TTH < TTS FROM H1 TO S2 BOUNDARY ANALYS. FOR HELIX FROM: 89 TO : 99 AND FOR SHEET FROM: 88 TO: 94 HN SN 3.11 3.97 HC 4 .06 SC 4.11 NHN 3.31 NSN 4.21 NHC 3 . 63 NSC 2 . 38 *** COMPARISON OF THEIR LENGTH *** L-HELIX: 8 L-SHEET: 7 ***** COMPARISON OF P-HELIX AND P-SHEET ***** H1 : 107 H2 : 114 A1: 1.086 A2: 1.106 A1 < A2 FROM H1 RATIO=LH/LS: 1.0 TO H2 S1 HHF 4 .00 H1 107 HF 3 .00 : 107 S2 IIH 0.0 113 A1: 1 . 101 A2: 1. 131 A1 < A2 *+* COMPARISON OF ASSIGNMENTS TYPES *** FROM S1 TO S2 IH O. 50 H2 1 14 BH -0. 50 TTH: 7.000 BBH 0.0 SSF 2.00 TTS: 5.250 SF 2 .00 IS 1 . 25 BS 0.0 BBS 0.0 TTH > TTS FROM H1 TO H2 HHF 4 .00 S1 HF 3 .OO 107 IIH 0.0 S2 IH 0. 25 1 13 BH -0.50 TTH: 6.750 BBH 0.0 SSF 2 .00 TTS: 5.000 SF 2 .OO IS 1 .00 BS 0.0 BBS 0.0 TTH > TTS FROM S1 TO S2 BOUNDARY ANALYS. FOR HELIX FROM: 107 TO: 1 14 AND FOR SHEET FROM: 107 TO: 1 13 HN 3 . 37 SN 4 .04 HC 3 .09 SC 3 . 30 NHN 3 .66 NSN 4.84 NHC 4 . 07 NSC 2.40 00 *** COMPARISON OF THEIR LENGTH *** L-HELIX: 6 L-SHEET: 5 ***** COMPARISON OF P-HELIX AND P-SHEET ***** H1 : 119 H2 : 124 A1: 1.127 A2: 1.190 A1 < A2 FROM H1 TO H2 S1 : 120 S2 : 124 A1: 1.150 A2: 1.320 A1 < A2 FROM S1 TO S2 *** COMPARISON OF ASSIGNMENTS TYPES *** RATIO=LH/LS: 1.0 HHF 2 .00 HF 4 .00 IIH O. 50 IH 0.0 BH 0.0 BBH 0.0 SSF 4 .00 SF 2 .00 IS 0. 25 BS 0.0 BBS - 1 .00 H1 1 19 H2 124 TTH: 6.500 TTS: 5.250 TTH > TTS FROM H1 TO H2 HHF 2 .00 S 1 HF 4 .OO 120 IIH 0.0 S2 IH 0.0 124 BH 0.0 TTH: 6.000 BBH 0.0 SSF 4 .00 TTS: 6.250 SF 2 .00 IS O. 25 BS 0.0 BBS 0.0 TTH < TTS FROM S1 TO S2 BOUNDARY ANALYS. FOR HELIX FROM: 119 TO: 124 AND FOR SHEET FROM: 120 TO: 124 HN SN 3.85 4.20 HC 2 . 58 SC 3 . 29 NHN 3.51 NSN 3 . 94 NHC 3 . 82 NSC 3 . 26 END OF PROGRAM ********************************* * * * BETA-TURN PREDICTION * * * ********************************* TOTAL NUMBER OF AA: 129 NUMBER OF DATA LINES: 9 PROTEIN SEQUENCE 12 20 14 8 2 5 7 1 1 1 1 1 13 12 2 1 1 4 3 19 2 8 19 16 1 1 8 3 18 20 5 12 14 7 16 3 14 3 17 6 1 17 3 2 3 8 16 17 4 19 8 10 1 1 6 1 1 3 16 2 18 3 4 8 2 17 15 8 16 2 3 1 1 5 3 10 16 1 1 1 1 1 16 16 4 10 17 1 16 20 3 5 12 10 20 16 4 8 4 8 13 3 1 18 20 1 3 2 5 12 8 17 4 20 6 1 18 10 2 8 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 DEFINITION OF PARAMETERS PRB : PROBABILITY OF OCCURRENCE OF THE B-TURN STARTING FROM I PRBO : PROBABILITY OF OCCURRENCE OF THE B-TURN STARTING FROM ( A 1 : 0 980 A2 : 1 142 A3 : 0 917 PRB : 0 0000260832 A 1 : 0 935 A2 : 1 190 A3 : 0 902 PRB: 0 0000410533 A 1 : O 845 A2 : 1 062 A3 : 1 075 PRB : 0 0000635500 A1 : 0 940 A2 : 0 810 A3 : 1 1 10 PRB : 0 0000809601 POTENTIAL BETA-TURN 4 7 A 1 1 100 A2 0 947 A3 0 867 PRB 0 0000199969 A1 1 210 A2 0 922 A3 0 795 PRB 0 0000186667 A 1 1 390 A2 0 832 A3 0 662 PRB 0 00000284 20 A1 1 367 A2 0 947 A3 0 642 PRB 0 00000941 1 1 A 1 1 427 A2 0 885 A3 0 645 PRB 0 0000087780 A 1 1 362 A2 0 862 A3 0 732 PRB 0 0000060648 A1 1 252 A2 0 887 A3 0 805 PRB 0 0000301103 A 1 1 147 A2 0 897 A3 0 877 PRB 0 00004 18056 A 1 0 927 A2 0 822 A3 1 1 17 PRB 0 0000824127 POTENTIAL BETA-TURN 13 16 A 1 : 0 940 A2 : 0 962 A3 : 1 .012 PRB : 0 0000437570 A 1 : 0 947 A2: 0 865 A3: 1 . 140 PRB : 0 0000347003 A 1 : 0 865 A2 : 0 870 A3 : 1 . 292 PRB : 0 0000415369 9 8 1 • 1 17 4 18 5 15 5 1 12 18 2 5 2 0 0 -1) 1 2 3 4 5 6 7 8' 9 10 1 1 12 13 14 15 16 to o A 1 : 0.895 A2 : 1.050 A3 : 1 . 187 PRB : 0 0001602011 17 POTENTIAL BETA-TURN 17 20 A 1 : 0.837 A2 : 0.957 A3 : 1 . 277 PRB : 0 0001182275 18 POTENTIAL BETA-TURN 18 2 1 PRBO: 0.00016020 PRB : 0.00011823 B-TURN NOT AT A 1 • 0.727 A2 : 1.010 A3 1 302 PRB : 0 0001574771 19 POTENTIAL BETA-TURN 19 22 PRBO: 0.00011823 PRB O.00015748 B-TURN NOT AT A1 0. 732 A2 1 . 155 A3 1 197 PRB 0 0002064347 20 POTENTIAL BETA-TURN 20 23 PRBO: 0.00015748 PRB 0.00020643 B-TURN NOT AT A1 0. 752 A2 0-. 975 A3 1 270 PRB 0 00007 18997 2 1 A 1 0.810 A2 1 .067 A3 1 180 PRB 0 0000580124 22 A1 0.810 A2 1 .067 A3 1 180 PRB 0 0000623697 23 A 1 0.805 A2 0.922 A3 1 285 PRB 0 0000518699 24 A 1 0.882 A2 1 . 077 A3 1 167 PRB 0 0001653858 25 POTENTIAL BETA-TURN 25 28 A 1 0.845 A2 1 . 177 A3 1 145 PRB 0 0000287166 26 A 1 0 . 877 A2 1 . 287 A3 1 052 PRB 0 0000075013 27 A 1 1 .065 A2 1 . 272 A3 0 827 PRB 0 0000250810 28 A 1 1 . 150 A2 1 . 137 A3 0 752 PRB 0 0000066706 29 A 1 1 . 175 A2 0.897 A3 0 880 PRB 0 0000376522 30 A 1 1 . 282 A2 0.945 A3 0 732 PRB 0 0000213408 3 1 A 1 1 . 305 A2 0. 830 A3 0 752 PRB 0 0000287039 32 A 1 1.142 • A2 0.810 A3 0 945 PRB 0 0000184053 33 A 1 1 .020 A2 0. 847 A3 1 082 PRB 0 0000402674 34 A 1 1 .020 A2 0.847 A3 1 082 PRB 0 0000966383 35 POTENTIAL BETA-TURN 35 38 A1 0.810 A2 0.977 A3 1 287 PRB 0 0000589133 36 A 1 0.825 A2 1 .087 A3 1 170 PRB 0 0000996024 37 POTENTIAL BETA-TURN 37 40 A1 0.935 A2 1 . 140 A3 1 025 PRB 0 0000311938 38 A 1 1 .007 A2 1 .002 A3 1 040 PRB 0 0000373146 39 A 1 1 .047 A2 1 .077 A3 0 890 PRB 0 0000233034 40 A 1 1 .007 A2 1 .002 A3 1 040 PRB 0 0000332659 41 A 1 0.975 A2 0.960 A3 1 032 PRB 0 0001052027 42 POTENTIAL BETA-TURN 42 45 BUT AT 17 BUT AT 19 BUT AT 20 A1 A1 O. 787 0. 787 A2: 0.975 A2: 0.975 A3: 1.257 A3: 1.257 POTENTIAL BETA-TURN A1 : 0.872 A2: 0.887 A1: 0.770 A2: 0.842 POTENTIAL BETA-TURN A1: 0.795 A2: 0.807 POTENTIAL BETA-TURN 44 A3 : A3 : 46 47 1 . 232 1 . 385 49 A3: 1.352 PRB: 0.0000643061 PRB: 0.0002575084 PRB: 0.0000305896 PRB: 0.0004730921 PRB: 0.000190524 1 47 50 PRBO: 0.00047309 PRB: 0.00019052 A1: 0.795 A2: 0.807 A3: 1.352 POTENTIAL BETA-TURN 48 51 PRB: O.0001233840 A 1 A 1 PRBO: 0.00019052 0.795 A2: 0.807 0.825 A2: 0.987 PRB: 0.00012339 A3: 1.352 A3: 1.247 POTENTIAL BETA-TURN 50 A1: 0.775 A2: 0.987 A3: POTENTIAL BETA-TURN 51 53 1 . 280 54 PRB: 0.000074647 1 PRB: 0.0002899796 PRB: 0.0001639226 PRB: 0.00016392 PRBO: 0.00028998 A1: 0.837 A2: 1.090 A3: 1.157 POTENTIAL BETA-TURN 52 55 PRB: 0.0001016651 43 44 45 46 47 B-TURN NOT AT 47 48 B-TURN NOT AT 48 49 50 51 B-TURN NOT AT 51 52 BUT AT BUT AT 46 47 PRBO: 0.00016392 PRB: 0.00010167 B-TURN NOT AT 52 BUT AT BUT AT 50 5 1 A 1 0 887 A2 1 280 A3 0 940 PRB 0 0000063427 53 A1 0 992 A2 1 187 A3 0 900 PRB 0 0000122351 54 A 1 1 152 A2 1 325 A3 O 657 PRB 0 0000027842 55 A 1 1 050 A2 1 147 A3 0 930 PRB 0 0000195839 56 A1 0 940 A2 1 010 A3 1 140 PRB 0 0000374550 57 A 1 0 907 A2 0 967 A3 1 132 PRB 0 0000537943 58 A 1 0 875 A2 0 985 A3 1 225 PRB 0 0003699916 59 POTENTIAL BETA-TURN 59 62 A 1 0 977 A2 1 105 A3 1 075 PRB 0 OO0135951 1 • 60 A1 0 960 A2 1 215 A3 1 015 PRB 0 0000074547 61 A 1 0 882 A2 1 205 A3 1 167 PRB 0 0000106576 62 A1 0 865 A2 0 997 A3 1 292 PRB O 0000631370 63 A 1 0 737 A2 0. 842 A3 1 442 PRB 0 0003364808 64 POTENTIAL A1: 0.807 BETA-TURN A2: 0.777 64 67 A3: 1.382 PRB: 0.0002860161 65 POTENTIAL BETA-TURN 65 68 PRBO: 0.00033648 PRB: 0.00028602 B-TURN NOT AT 65 BUT AT 64 A1: 0.847 A2: 0.852 A3: 1.232 PRB: 0.0000977233 66 POTENTIAL BETA-TURN 66 69 PRBO: 0.00028602 PRB: 0.00009772 B-TURN NOT AT 66 BUT AT 65 A1: 0.737 A2: 0.855 A3 : 1 247 PRB : 0 0000477890 67 A1: 0.737 A2: 0.855 A3 : 1 247 PRB : 0 0000390700 68 A1: 0.685 A2: 0.810 A3 : 1 367 PRB : 0 0005213434 69 POTENTIAL BETA-TURN 69 72 A 1 : 0.722 A2: 0.745 A3 : 1 365 PRB : 0 0000921187 70 POTENTIAL BETA-TURN 70 73 ^ PRBO: 0.00052134 PRB: 0.00009212 B-TURN NOT AT 70 BUT AT 69 A1: 0.747 A2: 0.830 A3: 1.375 PRB: 0.0001277295 71 POTENTIAL BETA-TURN 71 74 PRBO: 0.000092 12 PRB: 0.00012773 B-TURN NOT AT 70 BUT AT 7 1 A1: 0.907 A2: 0.967 A3: 1.132 PRB: 0.0001700662 72 POTENTIAL BETA-TURN 72 75 PRBO: 0.00012773 PRB: 0.00017007 B-TURN NOT AT 7 1 BUT AT 72 A1 0 890 A2 1 077 A3 1 072 PRB 0 0000267724 73 A1 " 0 812 A2 1 067 ' A3 1 225 PRB 0 00004 2854 1 74 A1 0 9 15 A2 1 245 A3 0 952 PRB 0 0000345801 75 A 1 0 755 A2 1 057 A3 1 185 PRB 0 0000109324 76 A 1 0 755 A2 1 057 A3 1 185 PRB 0 0000238228 77 A1 0 780 A2 1 022 A3 1 152 PRB 0 0001605189 78 POTENTIAL BETA-TURN 78 81 A1 0 865 A2 0 830 A3 1 200 PRB 0 0000391935 79 A 1 1 025 A2 1 017 A3 0 967 PRB 0 0000507419 80 A 1 1 152 A2 1 045 A3 0 817 PRB 0 0000229824 8 1 A 1 1 152 A2 1 04 5 A3 0 817 PRB 0 0000057240 82 A1 0 990 A2 1 025 A3 1 010 PRB 0 0000202062 83 A1 0 940 A2 0 835 A3 1 227 PRB 0 0000858498 84 POTENTIAL BETA-TURN 84 87 A1: 0.907 A2: 0.910 A3: 1.197 PRB: 0.0001672002 85 POTENTIAL BETA-TURN 85 88 PRBO: 0.0OOO8585 PRB: 0.00016720 B-TURN NOT AT 84 A 1 0.922 A2 1 .020 A3 1 080 PRB 0 0000135564 86 A 1 1 .085 A2 1 .040 A3 0 887 PRB 0 0000188424 87 A1 1 .025 A2 1 .092 A3 0 880 PRB 0 0000172292 88 A1 1 .020 A2 .1.117 A3 0 887 PRB 0 0000433009 89 A 1 0 . 980 A2 1 .042 A3 1 037 PRB 0 0000212503 90 A 1 O. 800 A2 1 . 132 A3 1 170 PRB 0 0001408203 9 1 POTENTIAL BETA-TURN 9 1 94 A1 0.962 A2 1 . 152 A3 0 977 PRB 0 0000349207 92 A 1 0.987 A2 0.912 A3 1 105 PRB 0 0000283722 93 A 1 1 . 1 10 A2 0.875 A3 0 967 PRB 0 0000774560 94 A 1 1 . 205 A2 0.977 A3 0 787 PRB 0 0000278207 95 A1 1.115 A2 1 . 195 A3 0 747 PRB 0 0000043579 96 A1 1 .017 A2 1 . 197 A3 0 852 PRB 0 0000055502 97 A 1 0.980 A2 1 . 147 A3 0 965 PRB 0 0000208980 98 A1 0.852 A2 0.935 A3 1 237 PRB 0 0002344783 99 POTENTIAL BETA-TURN 99 102 A 1 0.840 A2 0.645 A3 1 477 PRB 0 00020314 77 100 POTENTIAL BETA-TURN 100 103 PRBO: 0.00023448 PRB: 0.00020315 B-TURN NOT AT 100 A1: 0.790 A2: 0.645 A3: 1.510 PRB: 0.0003399635 101 POTENTIAL BETA-TURN 101 104 PRBO: 0.00020315 PRB: 0.00033996 B-TURN NOT AT 100 A1: 0.900 A2: 0.772 A3: 1.295 PRB: 0.0001172489 102 POTENTIAL BETA-TURN 102 105 PRBO: 0.00033996 PRB: 0.00011725 B-TURN NOT AT 102 A1: 0.925 A2: 0.807 A3 : 1 295 PRB : 0 0000159186 103 A 1 : 1 .027 A2: 0.880 A3: 1 095 PRB : 0 0000926563 104 POTENTIAL BETA-TURN 104 107 A 1 : 1 . 155 A2: 1.035 A3 : 0 945 PRB : 0 0000329891 105 A1: 1.057 A2: 1.197 A3 : 0 920 PRB : 0 0000415044 106 A1 : 1 .245 A2: 1.182 A3 : 0 695 PRB : 0 0000012667 107 A1 1 160 A2 1.317 A3 0 770 PRB O 0000216031 A 1 1 1 35 A2 1 . 207 A3 0 767 PRB 0 0000256332 A1 1 037 A2 1 .005 A3 1 032 PRB 0 0000070270 A1 0 927 A2 1 .030 A3 1 105 PRB O 0001325099 POTENTIAL BETA-TURN 1 1 1 114 A1 O 832 A2 0.985 A3 1 162 PRB 0 0000736242 A1 0 877 A2 0.937 A3 1 177 PRB 0 0001896883 POTENTIAL BETA-TURN 1 13 1 16 A1 0 852 A2 0.902 A3 1 177 PRB 0 0000406022 A 1 0 8 15 A2 0. 967 A3 1 180 PRB 0 0002571961 POTENTIAL BETA-TURN 1 15 1 18 A1 0 892 A2 0.805 A3 1 247 PRB 0 0000246138 A 1 0 867 A2 1 .045 A3 1 120 PRB 0 0001045087 POTENTIAL BETA-TURN 1 17 120 A1 1 002 A2 1 . 132 A3 0 975 PRB 0 0000259582 A 1 1 150 A2 1 .042 A3 0 900 PRB 0 0000151422 A1 1 167 A2 1 . 250 A3 0 775 PRB 0 0000355142 A1 1 172 A2 1 . 225 A3 0 767 PRB 0 0000201564 A1 1 140 A2 1.182 A3 0 760 PRB 0 0000008619 A 1 0 927 A2 1 . 162 A3 0 985 PRB 0 0000393956 A 1 0 832 A2 1.117 A3 1 042 PRB 0 0001108504 A 1 0 807 A2 0.95O A3 1 162 PRB 0 0000591727 A1 0 865 A2 1 .04 2 A3 1 072 PRB 0 0000374636 END OF PROGRAM 77 108 109 1 10 1 1 1 1 12 1 13 1 14 1 15 1 16 1 17 1 18 1 19 120 121 122 123 124 125 1 26 

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