

PFRMAT ABF1
TARGET T0023
AUTHOR   7659-4006-3725   Shestopalov B.V., Institute
REMARK   of Cytology RAS, shest@dcc.cyt.ras.spb.ru
REMARK   The prediction method used is the simplest one.
REMARK   Regions of coil, strand, and helix consist of
REMARK   elementary regions overlaps. Elementary regions
REMARK   of coil, strand, and helix consist of 2, 3, and 5
REMARK   amino acid residues, respectively. In an amino
REMARK   acid sequence these elementary regions are encoded
REMARK   by amino acid residue pairs /i, i+1/, /i, i+2/,
REMARK   and /i, i+4/ for coil, strand, and helix, respec-
REMARK   tively. Among 400 possible different amino acid
REMARK   residue pairs for each structural type only part
REMARK   encodes elementary regions. These pairs are named
REMARK   codons. The distribution of codons for coil,
REMARK   strand, and helix in an amino acid sequence is
REMARK   given in three lines under the sequence. Usually
REMARK   codons of different structural types overlap in
REMARK   a sequence. Choice of codons in such situations
REMARK   is necessary. The choice rule is to exclude the
REMARK   least number of codons until the overlap dis-
REMARK   appear. If an application of this rule gives
REMARK   several variants with the same number of the
REMARK   excluded codons we have an ambiguous case and the
REMARK   respective region of secondary structure can not
REMARK   be predicted.
REMARK       The method has been published /Mol. Biol.,
REMARK   Moscow, Engl. transl., 24/4, p.900-907, 1990,
REMARK   Shestopalov B.V./. The database for codon deter-
REMARK   mination consisted of 62 proteins from Kabsch-
REMARK   -Sander database /Biopolymers, v.22, p.2577-2637,
REMARK   1983/. The codons used here have been determined
REMARK   from the database extended to 257 protein chains
REMARK   with secondary structures determined according
REMARK   Kabsch-Sander method.
BEGDAT   1.1  1  1.0
SS  284
M  C  1.0
K  C  1.0
Q  C  1.0
K  E  1.0
V  E  1.0
V  E  1.0
S  E  1.0
I  E  1.0
G  C  1.0
D  C  1.0
I  E  1.0
N  E  1.0
V  E  1.0
A  C  1.0
N  C  1.0
D  C  1.0
L  C  0.0
P  C  0.0
F  C  0.0
V  E  1.0
L  E  1.0
L  E  1.0
G  C  1.0
G  C  1.0
M  C  1.0
N  C  1.0
V  C  1.0
L  C  1.0
E  C  1.0
S  C  1.0
R  C  1.0
D  H  1.0
L  H  1.0
A  H  1.0
M  H  1.0
R  H  1.0
I  H  1.0
C  H  1.0
E  H  1.0
H  E  1.0
Y  E  1.0
V  E  1.0
T  E  1.0
V  E  1.0
T  E  1.0
Q  C  1.0
K  C  1.0
L  E  1.0
G  E  1.0
I  E  1.0
P  E  1.0
Y  E  1.0
V  E  1.0
F  E  1.0
K  H  1.0
A  H  1.0
S  H  1.0
F  H  1.0
D  H  1.0
K  H  1.0
A  H  1.0
N  H  1.0
R  H  1.0
S  C  1.0
S  C  1.0
I  C  0.0
H  C  0.0
S  C  0.0
Y  C  1.0
R  C  1.0
G  C  1.0
P  C  1.0
G  C  1.0
L  C  1.0
E  C  1.0
E  C  1.0
G  C  1.0
M  C  1.0
K  H  1.0
I  H  1.0
F  H  1.0
Q  H  1.0
E  H  1.0
L  H  1.0
K  H  1.0
Q  H  1.0
T  H  1.0
F  C  0.0
G  C  0.0
V  E  1.0
K  E  1.0
I  E  1.0
I  E  1.0
T  E  1.0
D  E  1.0
V  E  1.0
H  C  1.0
E  C  1.0
P  C  1.0
S  C  1.0
Q  C  1.0
A  C  0.0
Q  C  0.0
P  C  0.0
V  C  0.0
A  C  0.0
D  C  0.0
V  C  1.0
V  E  1.0
D  E  1.0
V  E  1.0
I  C  0.0
Q  C  0.0
L  C  0.0
P  C  0.0
A  C  0.0
F  C  0.0
L  C  0.0
A  C  0.0
R  C  0.0
Q  C  1.0
T  C  1.0
D  C  1.0
L  H  1.0
V  H  1.0
E  H  1.0
A  H  1.0
M  H  1.0
A  H  1.0
K  H  1.0
T  C  1.0
G  C  1.0
A  C  1.0
V  C  1.0
I  E  1.0
N  E  1.0
V  E  1.0
K  C  1.0
K  C  1.0
P  C  1.0
Q  C  1.0
F  C  0.0
V  C  0.0
S  C  0.0
P  C  1.0
G  C  1.0
Q  C  1.0
M  C  1.0
G  C  1.0
N  C  1.0
I  C  1.0
V  C  1.0
D  C  1.0
K  C  1.0
F  C  1.0
K  C  1.0
E  C  1.0
G  C  1.0
G  C  1.0
N  C  1.0
E  C  1.0
K  C  1.0
V  E  1.0
I  E  1.0
L  E  1.0
C  E  1.0
D  C  1.0
R  C  1.0
G  C  1.0
A  C  1.0
N  C  1.0
F  E  1.0
G  E  1.0
Y  E  1.0
D  C  1.0
N  C  1.0
L  E  1.0
V  E  1.0
V  E  1.0
D  E  1.0
M  E  1.0
L  E  1.0
G  E  1.0
F  E  1.0
S  E  1.0
I  E  1.0
M  C  1.0
K  E  1.0
K  E  1.0
V  E  1.0
S  C  1.0
G  C  1.0
N  C  1.0
S  C  1.0
P  C  1.0
V  E  1.0
I  E  1.0
F  E  1.0
D  H  1.0
V  H  1.0
T  H  1.0
H  H  1.0
A  H  1.0
L  H  1.0
Q  H  1.0
C  H  1.0
R  H  1.0
D  C  1.0
P  C  1.0
F  C  1.0
G  C  1.0
A  C  1.0
A  C  1.0
S  C  1.0
G  C  1.0
G  C  1.0
R  C  1.0
R  H  1.0
A  H  1.0
Q  H  1.0
V  H  1.0
A  H  1.0
E  H  1.0
L  H  1.0
A  H  1.0
R  H  1.0
A  H  1.0
G  H  1.0
M  H  1.0
A  H  1.0
V  H  1.0
G  H  1.0
L  H  1.0
A  H  1.0
G  H  1.0
L  H  1.0
F  H  1.0
I  H  1.0
E  H  1.0
A  H  1.0
H  C  1.0
P  C  1.0
D  C  1.0
P  C  1.0
E  C  1.0
H  C  1.0
A  C  1.0
K  C  1.0
C  C  1.0
D  C  1.0
G  C  1.0
P  C  1.0
S  C  1.0
A  C  1.0
L  C  1.0
P  C  1.0
L  C  1.0
A  C  1.0
K  C  1.0
L  H  1.0
E  H  1.0
P  H  1.0
F  H  1.0
L  H  1.0
K  H  1.0
Q  H  1.0
M  H  1.0
K  H  1.0
A  H  1.0
I  H  1.0
D  H  1.0
D  H  1.0
L  H  1.0
V  H  1.0
K  H  1.0
G  H  1.0
F  H  1.0
E  H  1.0
E  H  1.0
L  C  1.0
D  C  1.0
T  C  1.0
S  C  1.0
K  C  1.0
ENDDAT   1.1
END
