

PFRMAT ABF1
TARGET T0037
AUTHOR 6792-8330-8583 D.Gerloff & F.Cohen, UCSF, gerloff@cgl.ucsf.edu
AUTHOR           and  Marcin Joachimiak, UCSF (graduate student Cohen lab)
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 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
REMARK THE SECONDARY STRUCTURE PREDICTION (1.1) ALONE WAS SUBMITTED 
REMARK (ACCEPTION CODE T0037AB915)
REMARK 40 MINUTES AGO. IF COMPATIBLE WITH THE DEADLINE, WE WOULD LIKE
REMARK THESE TWO SUPERSECONDARY STRUCTURE MODELS. THEY ARE BASED ON
REMARK MOSTLY EMPIRICAL PACKING RULES AND THE ASSEMBLY OF A HYDROPHOBIC
REMARK AND A FUNCTIONAL (CA-BINDING?) SITE IN THE TERTIARY STRUCTURE
REMARK MOST IMPORTANTLY, WE SAW THE NEED TO BURY THE C-TERMINAL HELIX
REMARK IN THE PROTEIN AND TO CONFORM WITH EVOLUTIONARY CONSERVED PACKING
REMARK SITES. WE ARE NOT COMPLETELY SATISFIED EITHER OF THE TWO MODELS
REMARK AND PREDICT THE SUPERSECONDARY STRUCTURE AT VERY LOW RELIABILITY
REMARK AND RESOLUTION (GENERATED IN THE ABSENCE OF A COMPUTER MODEL)
REMARK THE DIFFERENCES BETWEEN MODEL 1 AND 2 ARE CAUSED BY THE UNCERTAINTY  
REMARK AS TO WHETHER THE LONG COIL SEGMENT IN THE MIDDLE CAUSES HELICES
REMARK 3 AND 4 TO BE IN PARALLEL (MODEL 1, A FOLDED LEAF) OR ANTIPARALLEL 
REMARK (MODEL 2) ARRANGEMENT (POSSIBLY A PROBLEM IN THE SEC.STRUCTURE). 
REMARK APOLOGIES FOR THE DELAY !
BEGDAT 1.1  1  1.00
SS 109
K C  0.80
S C  0.80
A C  0.80
K C  0.60
D H  0.80
A H  1.00
L H  1.00
L H  1.00
L H  1.00
W H  1.00
C H  1.00
Q H  1.00
M H  1.00
K H  1.00
T H  0.80
A H  0.80
G C  0.80
Y C  0.80
P C  1.00
N C  0.80
V C  0.50
N H  0.50
I H  0.80
H H  0.80
N H  1.00
F H  1.00
T H  1.00
T H  1.00
S H  1.00
W H  1.00
R H  0.80
D C  0.80
G C  0.80
M H  0.80
A H  0.80
F H  0.80
N H  0.80
A H  0.80
L H  0.80
I H  0.80
H H  0.80
K C  0.50
H C  0.50
R C  0.80
P C  1.00
D C  1.00
L C  0.50
I C  0.50
D C  0.50
F C  0.50
D C  0.50
K C  0.50
L C  0.50
K C  0.50
K C  0.50
S C  0.80
N C  0.80
A H  0.70
H H  0.70
Y H  0.70
N H  0.90
L H  0.90
Q H  1.00
N H  1.00
A H  1.00
F H  1.00
N H  1.00
L H  1.00
A H  1.00
E H  1.00
Q H  1.00
H H  1.00
L H  0.70
G H  0.70
L C  0.80
T C  0.80
K C  0.50
L E  0.60
L E  0.60
D C  1.00
P C  1.00
E C  0.80
D C  0.80
I E  0.50
S E  0.60
V E  0.60
D C  0.50
H C  0.80
P C  1.00
D C  1.00
E C  0.80
K H  0.80
S H  0.80
I H  0.80
I H  0.80
T H  0.80
Y H  0.80
V H  0.80
V H  0.80
T H  0.80
Y H  0.60
Y H  0.50
H H  0.50
Y H  0.50
F H  0.50
S H  0.50
K H  0.50
M C  0.80
K C  0.80
ENDDAT 1.1
BEGDAT 2.1  2  0.2 1
14
  1   2  RT  0.90   0   0  0.00
  1   7  OS  0.90   0   0  0.00
  2   3  OS  0.50   0   0  0.00
  2   7  LS  0.80   0   0  0.00
  3   4  LE  0.80   0   0  0.00
  3   5  RD  0.40   0   0  0.00
  3   6  LE  0.40   0   0  0.00
  3   7  LE  0.60   0   0  0.00
  4   5  --  0.50   0   0  0.00
  4   6  --  0.50   0   0  0.00
  4   7  OS  0.90   0   0  0.00
  5   6  HH  1.00   0   0  0.00
  5   7  --  0.40   0   0  0.00
  6   7  --  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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