

PFRMAT ABF1
TARGET T0042
AUTHOR 6792-8330-8583 D.Gerloff, M. Joachimiak & F.Cohen, UCSF, gerloff@cgl.ucsf.edu
AUTHOR 9774-5781-2699 S.Benner, UF and ETH, benner@chem.ethz.ch
REMARK (This prediction results from collaboration between the two groups Benner&Cohen.)
REMARK Secondary structure was predicted according to Benner & Gerloff
REMARK both automatically (the automated output has been submitted by
REMARK the Benner group in a secondary structure only submission) and
REMARK manually and later refined based on our preferred tertiary 
REMARK structure models. The model fragment includes res. 2-76 in the target sequence.
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 (helix ends).
REMARK Tertiary structure modelling involved manual combinatorial assembly 
REMARK and application of preferences in helix-helix packing rules
REMARK based on work in the Cohen laboratory.
REMARK Backbone + Cbeta atom traces (coordinates) for the 3 models (1-3) 
REMARK we could build under consideration of the 3 disulfide bridge
REMARK constraints are submitted in a separate file (mostly for 
REMARK verification of the 2.1. topology codes and to show that models
REMARK 1-3 have quite similar topologies overall).
REMARK For this particular tertiary structure modeling, the resolution
REMARK may even be good enough to enter the 3.1. contest (backbone and Cbeta)?
REMARK Our moderate preference for supersecondary structure model 1 is
REMARK based on observed and favorable helix-helix packing angles in 
REMARK known protein structures (work by Harris et al., Cohen group)
BEGDAT 1.1 1 1.0
SS 78
G C 0.80
Y C 0.80
F H 0.80
C H 1.00
E H 1.00
S H 1.00
C H 1.00
R H 1.00
K H 1.00
I H 1.00
I H 1.00
Q H 1.00
K H 1.00
L H 1.00
E H 1.00
D H 1.00
M H 1.00
V H 1.00
G C 0.50
P C 1.00
Q C 1.00
P C 1.00
N C 1.00
E C 1.00
D C 0.50
T H 0.70
V H 1.00
T H 1.00
Q H 1.00
A H 1.00
A H 1.00
S H 1.00
Q H 1.00
V H 1.00
C H 1.00
D H 0.60
K H 0.50
L C 1.00
K C 1.00
I C 1.00
L C 1.00
R C 1.00
G C 1.00
L H 0.50
C H 1.00
K H 1.00
K H 1.00
I H 1.00
M H 1.00
R H 1.00
S H 1.00
F H 1.00
L H 0.60
R H 0.60
R H 0.60
I H 1.00
S H 1.00
W H 1.00
D H 0.70
I H 0.50
L H 0.50
T H 0.50
G C 1.00
K C 1.00
K C 1.00
P C 1.00
Q C 1.00
A C 1.00
I H 0.50
C H 1.00
V H 1.00
D H 1.00
I H 1.00
K H 1.00
I C 0.50
C C 0.50
K C 0.50
E C 0.50
ENDDAT 1.1
BEGDAT 2.1  2  0.20 1
6
  1   2  --  0.40   0   0  0.00
  1   3  RT  0.90   0   0  0.00
  1   4  OS  1.00   0   0  0.00
  2   3  OT  1.00   0   0  0.00
  2   4  --  1.00   0   0  0.00
  3   4  OT  0.40   0   0  0.00
ENDDAT 2.1
END


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Dietlind L. Gerloff                              * * *    Tel. (415) 502-5650
University of California San Francisco         * _   _ *  FAX  (415) 476-6515
Dept. of Cellular and Molecular Pharmacology  *  o   o  *
513 Parnassus ave                             *    .    *
SAN FRANCISCO, CA 94143-0450                   * \___/ *  email:
U.S.A.                                           * * *    gerloff@cgl.ucsf.edu
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