
PFRMAT ABF1
TARGET T0004
AUTHOR 6792-8330-8583 D.Gerloff & F.Cohen, UCSF, gerloff@cgl.ucsf.edu
AUTHOR 9774-5781-2699 S.Benner, UF and ETH, benner@chem.ethz.ch
REMARK THIS PREDICTION ENTRY REPLACES THE PREVIOUS 1.1 and 2.1. ENTRY (T0004AB171)
REMARK BY THE SAME AUTHORS. The 2.1. code for MODEL 2 (represented by the low-
REMARK resolution backbone coordinates in 3.1. entry T0004AB172) was corrected
REMARK in this entry.
REMARK (This prediction results from collaboration between the two groups Benner&Cohen.)
REMARK Secondary structure was predicted according to Benner & Gerloff and
REMARK later refined based on preferred low-resolution tertiary structure models
REMARK for the central part of the target protein (res. 21-74).
REMARK Probabilities for the three-state secondary structure prediction reflect
REMARK (a) center or ending positions in a predicted sec.str. element,
REMARK (b) possible sec.str. alternatives, and (c) correlation or contradiction
REMARK of the prediction with the preferred 3D-models.
REMARK Tertiary structure modelling involved manual combinatorial assembly 
REMARK and application of largely knowledge-based and empirical rules described
REMARK elsewhere (manuscript Pred.Report). In particular, the high number of
REMARK residues predicted INTERIOR in the 2nd predicted helix suggested contacts
REMARK with several of the strands, and possibly packing of this helix in the
REMARK typical "groove" across the sheet. However, the protein is likely to undergo
REMARK quaternary structural interactions; these have not been modeled and could
REMARK severely affect the accuracy of the models.
REMARK Backbone atom traces (coordinates) for the 2 preferred models (1 and 2) are
REMARK submitted in a separate file (for verification of the 2.1. topology codes).
REMARK The resolution of the models, however, too low to enter the 3.1. contest.
BEGDAT 1.1  1  1.00
SS 84
A C  0.00
E E  0.40
I E  0.40
E E  0.40
V C  0.70
G C  0.90
R C  0.70
V H  0.50
Y H  0.50
T H  0.50
G H  0.50
K H  1.00
V H  1.00
T H  1.00
R H  1.00
I H  1.00
V H  1.00
D C  0.70
F C  0.90
G C  0.70
A E  1.00
F E  1.00
V E  1.00
A E  1.00
I E  1.00
G C  1.00
G C  1.00
G C  1.00
K H  0.80
E H  0.80
G H  0.80
L H  0.80
V H  0.80
H H  0.80
I H  0.80
S H  0.80
Q H  0.80
I H  0.80
A H  0.70
D C  0.90
K C  0.90
R C  0.80
V C  0.80
E C  0.80
K C  1.00
V C  1.00
T C  1.00
D C  0.90
Y E  0.70
L E  0.70
Q E  0.70
M E  0.60
G C  1.00
Q C  1.00
E C  1.00
V E  0.50
P E  0.50
V E  0.80
K E  0.90
V E  0.90
L E  0.90
E E  0.90
V E  0.80
D C  0.80
R C  1.00
Q C  1.00
G C  1.00
R E  0.50
I E  1.00
R E  1.00
L E  1.00
S E  1.00
I E  0.80
K E  0.50
E C  0.80
A C  1.00
T C  1.00
E C  1.00
Q C  1.00
S C  1.00
Q C  1.00
P C  0.00
A C  0.00
A C  0.00
ENDDAT 1.1
BEGDAT 2.1  1  0.45 1
21
  1   2  --  0.00   0   0  0.00
  1   3  --  0.00   0   0  0.00
  1   4  --  0.00   0   0  0.00
  1   5  --  0.00   0   0  0.00
  1   6  --  0.00   0   0  0.00
  1   7  --  0.00   0   0  0.00
  2   3  --  0.00   0   0  0.00
  2   4  --  0.00   0   0  0.00
  2   5  --  0.00   0   0  0.00
  2   6  --  0.00   0   0  0.00
  2   7  --  0.00   0   0  0.00
  3   4  PE  0.80   0   0  0.00
  3   5  --  1.00   0   0  0.00
  3   6  --  1.00   0   0  0.00
  3   7  HH  1.00   0   0  0.00
  4   5  --  0.40   0   0  0.00
  4   6  PE  0.90   0   0  0.00
  4   7  OT  0.90   0   0  0.00
  5   6  HH  1.00   0   0  0.00
  5   7  --  1.00   0   0  0.00
  6   7  HH  1.00   0   0  0.00
ENDDAT 2.1
END

