The Chou-Fasman Method for Secondary Structure Prediction:
The basic idea is that each amino acid residue is assigned three numbers that describe its propensity to be part of α-helices, β-sheets and tight β-turns. A large number (above 100) for a particular structure means the amino acid has a high preference for that structure, e.g. α-helix, which is typically coupled to low propensity for the other structures. These Chou-Fasman parameters may be determined from the occurrence of different amino acids in different types of secondary structure in known protein structures. The prediction algorithm then contains the following steps:
1. Assign propensities to all residues in the sequence.
2. Scan the peptide and identify regions where 4 out of 6 contiguous residues exhibit P(α)>100, i.e. large probability for α-helix. Extend these nucleation regions in both directions until the average propensity for a set of four contiguous residues is P(α) < 100.
3. Scan the peptide and identify regions where 3 out of 5 contiguous residues have P(β)>100. These regions nucleate β-strands. Extend these in both directions until a set of four contiguous residues have an average P(β) < 100. This ends the β-strand - almost exactly the same as for the helices, but there might now be overlapping segments.
4. Any region containing overlapping α and β assignments are taken to be helical or β depending on if the average P(α) and P(β) for that region is largest. If this reduces an α- or β-region so that it becomes less than 5 residues, the α- or β-assignment for that region is removed.
5. To identify a tight β-turn at residue number i, the product f(turn) = f(i)f(i+1)f(i+2)f(i+3) is calculated. Remember that a tight turn uses two amino acids, and then there is one before and another after the turn too. These numbers are simply proportional to the frequency of each amino acids occurring in each such position of a β-turn.
6. To predict a β-turn, the following three conditions have to be simultaneously fulfilled:
(a) f(turn) > 0.000075, (b) the average value for the turn propensity p(turn) > 100 for the four amino acids and (c) the average p(turn) is larger than the average p(α) as well as p(β), i.e. it is more probable that we have a turn than any other structure.
7. The remaining parts of the sequence are considered coils.
Your task for this activity is to write a script in awk to implement the Chou-Fasman algorithm. You can find values for the Chou-Fasman parameters on the last page.
|
3-letter code
|
1-letter
code
|
p(a)
|
p(13)
|
p(t)
|
f(i)
|
f(i+1)
|
f(i+2)
|
f(i+3)
|
|
ALA
|
A
|
142
|
83
|
66
|
0.06
|
0.076
|
0.035
|
0.058
|
|
ARG
|
R
|
98
|
93
|
95
|
0.070
|
0.106
|
0.099
|
0.085
|
|
ASP
|
D
|
101
|
54
|
146
|
0.147
|
0.110
|
0.179
|
0.081
|
|
ASN
|
N
|
67
|
89
|
156
|
0.161
|
0.083
|
0.191
|
0.091
|
|
CYS
|
C
|
70
|
119
|
119
|
0.149
|
0.050
|
0.117
|
0.128
|
|
GLU
|
E
|
151
|
37
|
74
|
0.056
|
0.060
|
0.077
|
0.064
|
|
GLN
|
Q
|
111
|
110
|
98
|
0.074
|
0.098
|
0.037
|
0.098
|
|
GLY
|
G
|
57
|
75
|
156
|
0.102
|
0.085
|
0.190
|
0.152
|
|
HIS
|
H
|
100
|
87
|
95
|
0.140
|
0.047
|
0.093
|
0.054
|
|
ILE
|
I
|
108
|
160
|
47
|
0.043
|
0.034
|
0.013
|
0.056
|
|
LEU
|
L
|
121
|
130
|
59
|
0.061
|
0.025
|
0.036
|
0.070
|
|
LYS
|
K
|
114
|
74
|
101
|
0.055
|
0.115
|
0.072
|
0.095
|
|
MET
|
M
|
145
|
105
|
60
|
0.068
|
0.082
|
0.014
|
0.055
|
|
PHE
|
F
|
113
|
138
|
60
|
0.059
|
0.041
|
0.065
|
0.065
|
|
PRO
|
P
|
57
|
55
|
152
|
0.102
|
0.301
|
0.034
|
0.068
|
|
SER
|
S
|
77
|
75
|
143
|
0.120
|
0.139
|
0.125
|
0.106
|
|
THR
|
T
|
83
|
119
|
96
|
0.086
|
0.108
|
0.065
|
0.079
|
|
TRP
|
W
|
108
|
137
|
96
|
0.077
|
0.013
|
0.064
|
0.167
|
|
TYR
|
Y
|
69
|
147
|
114
|
0.082
|
0.065
|
0.114
|
0.125
|
|
VAL
|
V
|
106
|
170
|
50
|
0.062
|
0.048
|
0.028
|
0.053
|