

PFRMAT ABF1
TARGET T0021
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 s 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  64
G  C  1.0
A  C  1.0
K  C  1.0
E  C  1.0
P  C  1.0
D  C  1.0
P  C  1.0
D  C  0.0
K  C  0.0
L  H  1.0
K  H  1.0
K  H  1.0
A  H  1.0
I  H  1.0
V  H  1.0
Q  H  1.0
V  H  1.0
E  H  1.0
H  H  1.0
D  H  1.0
E  H  1.0
R  H  1.0
P  H  1.0
A  H  1.0
R  H  1.0
L  H  1.0
I  H  1.0
L  H  1.0
N  H  1.0
R  H  1.0
R  C  1.0
P  C  1.0
P  C  1.0
A  C  1.0
E  C  1.0
G  C  1.0
Y  E  1.0
A  E  1.0
W  E  1.0
L  C  0.0
K  C  0.0
Y  C  0.0
E  C  1.0
D  C  1.0
D  C  1.0
G  C  1.0
Q  C  0.0
E  C  0.0
F  H  1.0
E  H  1.0
A  H  1.0
N  H  1.0
L  H  1.0
A  C  0.0
D  C  0.0
V  E  1.0
K  E  1.0
L  E  1.0
V  E  1.0
A  E  1.0
L  E  1.0
I  C  1.0
E  C  1.0
G  C  1.0
ENDDAT 1.1
END
