
PFRMAT ABF1
TARGET T0004
AUTHOR 7972-9465-6839 FINKELSTEIN Alexei V.  Institute of Protein Research,
AUTHOR                142292 Pushchino, Moscow Regoin, Russia
AUTHOR                E-MAIL:   afinkel@sun.ipr.serpukhov.su
REMARK Initial secondary structure prediction is done by the program "ALB" 
REMARK (Finkelstein, 1983; deposited at PDB and EMBL), mode "GLOBULE".
REMARK Guidelines of the program is described in:
REMARK O.B.Ptitsyn, A.V.Finkelstein (1983) Biopolymers 22:15-25.
REMARK
REMARK For protein fold prediction, we used "predicted", as well as 
REMARK "also possible" beta-strands suggested by ALB program.
REMARK
REMARK Prediction of secondary structure contacts follows from the
REMARK the analisis of various 6-stranded beta-sandviches.
REMARK Guidelines of the analysis are given in:
REMARK A.V.Finkelstein, O.B.Ptitsyn (1987) Progr.Biophys.Mol.Biol.50:171-190.
REMARK
REMARK  ??  Badly explained how to present a prediction of hydrophobic
REMARK  ??  (NOT H-bonded) contacts between strands, and now (31.7) no
REMARK  ??  time to ask.
REMARK  ??  I had submitted the following predictions of contacts,  
REMARK  ??                  SEE BELOW
REMARK  ??  where                
REMARK  ??  "PE" ment a parralel, non_H-bonded contact of strands (-40 deg.)
REMARK  ??  "OT" ment antiparralel, non_H-bonded contact of strands (140 deg.)
REMARK  ??     (note that both "PE" and "OT" are allowed, according to the
REMARK  ??     Example in the "Formats for ab initio predictions")
REMARK  ??  - and the testing program had rejected this prediction....
REMARK  ??  
REMARK  ??  Now I use "KK 0.45" and "HH 0.45" to show the contacts between
REMARK  ??  the edge strands of beta-sheets, and have no possibility to
REMARK  ??  show other non-H-bonded contacts of the strands...
REMARK
REMARK   BEGDAT 2.1  1   .5  2
REMARK   11
REMARK   1 2 HH 1.00 0 0 0.00            
REMARK   1 3 PE 0.90 0 0 0.00
REMARK   1 6 OT 0.50 0 0 0.00 
REMARK   2 3 OT 0.50 0 0 0.00
REMARK   2 4 PE 0.50 0 0 0.00
REMARK   2 5 HH 1.00 0 0 0.00
REMARK   2 6 PE 0.90 0 0 0.00
REMARK   3 6 HH 1.00 0 0 0.00
REMARK   4 5 OT 0.90 0 0 0.00
REMARK   4 6 KK 1.00 0 0 0.00
REMARK   5 6 OT 0.50 0 0 0.00
REMARK   ENDDAT 2.1
REMARK   BEGDAT 2.1  2   .2  2
REMARK   11
REMARK   1 2 HH 1.00 0 0 0.00            
REMARK   1 4 OT 0.90 0 0 0.00
REMARK   1 6 OT 0.50 0 0 0.00 
REMARK   2 3 HH 1.00 0 0 0.00
REMARK   2 4 PE 0.50 0 0 0.00
REMARK   2 5 OT 0.50 0 0 0.00
REMARK   2 6 PE 0.90 0 0 0.00
REMARK   3 5 PE 0.90 0 0 0.00
REMARK   3 6 OT 0.50 0 0 0.00
REMARK   4 6 KK 1.00 0 0 0.00
REMARK   5 6 HH 1.00 0 0 0.00
REMARK   ENDDAT 2.1
REMARK   BEGDAT 2.1  3   .2  2
REMARK   11
REMARK   1 2 HH 1.00 0 0 0.00            
REMARK   1 5 PE 0.90 0 0 0.00
REMARK   1 6 OT 0.50 0 0 0.00 
REMARK   2 3 HH 1.00 0 0 0.00
REMARK   2 4 PE 0.50 0 0 0.00
REMARK   2 5 OT 0.50 0 0 0.00
REMARK   2 6 PE 0.90 0 0 0.00
REMARK   3 4 OT 0.90 0 0 0.00
REMARK   3 6 OT 0.50 0 0 0.00
REMARK   4 6 KK 1.00 0 0 0.00
REMARK   5 6 HH 1.00 0 0 0.00
REMARK   ENDDAT 2.1
REMARK
BEGDAT 1.1  2  1.0
SS 84
A C 0.95
E C 0.75
I E 0.50
E E 0.50
V E 0.50
G C 0.65
R C 0.65
V C 0.65
Y C 0.65
T C 0.65
G C 0.75
K C 0.75
V C 0.75
T C 0.75
R C 0.75
I E 0.65
V E 0.90
D E 0.65
F E 0.50
G E 0.50
A E 0.65
F E 0.90
V E 0.90
A E 0.90
I E 0.90
G C 0.75
G C 0.75
G C 0.95
K C 0.95
E C 0.75
G E 0.50
L E 0.65
V E 0.65
H E 0.65
I E 0.65
S C 0.65
Q C 0.65
I C 0.65
A C 0.75
D C 0.75
K C 0.75
R C 0.65
V C 0.65
E C 0.65
K C 0.75
V C 0.65
T C 0.65
D C 0.65
Y E 0.50
L E 0.50
Q E 0.50
M E 0.50
G C 0.95
Q C 0.95
E C 0.65
V E 0.65
P E 0.65
V E 0.65
K E 0.90
V E 0.90
L E 0.65
E E 0.65
V E 0.65
D C 0.50
R C 0.95
Q C 0.95
G C 0.75
R C 0.50
I E 0.65
R E 0.65
L E 0.65
S E 0.65
I E 0.65
K C 0.75
E C 0.95
A C 0.95
T C 0.95
E C 0.95
Q C 0.95
S C 0.95
Q C 0.95
P C 0.95
A C 0.95
A C 0.95
ENDDAT 1.1
BEGDAT 2.1  1   .2  2
6
1 2 HH 1.00 0 0 0.00            
1 3 KK 0.45 0 0 0.00
2 5 HH 1.00 0 0 0.00
3 6 HH 1.00 0 0 0.00
4 5 HH 0.45 0 0 0.00
4 6 KK 1.00 0 0 0.00
ENDDAT 2.1
END

