Chou-Fasman

The Chou-Fasman method of secondary structure prediction depends on assigning a set of prediction values to a residue and then applying a simple algorithm to those numbers.

Chou-Fasman table

Chou-Fasman
Name	P(a)	P(b)	P(turn)	f(i)	f(i+1)	f(i+2)	f(i+3)
Alanine	142	83	66	0.06	0.076	0.035	0.058
Arginine	98	93	95	0.070	0.106	0.099	0.085
Aspartic Acid	101	54	146	0.147	0.110	0.179	0.081
Asparagine	67	89	156	0.161	0.083	0.191	0.091
Cysteine	70	119	119	0.149	0.050	0.117	0.128
Glutamic Acid	151	037	74	0.056	0.060	0.077	0.064
Glutamine	111	110	98	0.074	0.098	0.037	0.098
Glycine	57	75	156	0.102	0.085	0.190	0.152
Histidine	100	87	95	0.140	0.047	0.093	0.054
Isoleucine	108	160	47	0.043	0.034	0.013	0.056
Leucine	121	130	59	0.061	0.025	0.036	0.070
Lysine	114	74	101	0.055	0.115	0.072	0.095
Methionine	145	105	60	0.068	0.082	0.014	0.055
Phenylalanine	113	138	60	0.059	0.041	0.065	0.065
Proline	57	55	152	0.102	0.301	0.034	0.068
Serine	77	75	143	0.120	0.139	0.125	0.106
Threonine	83	119	96	0.086	0.108	0.065	0.079
Tryptophan	108	137	96	0.077	0.013	0.064	0.167
Tyrosine	69	147	114	0.082	0.065	0.114	0.125
Valine	106	170	50	0.062	0.048	0.028	0.053

Algorithm

Contains the following steps:

1. Assign all of the residues in the peptide the appropriate set of parameters.
2. Scan through the peptide and identify regions where 4 out of 6 contiguous residues have P(a-helix) > 100. That region is declared an alpha-helix. Extend the helix in both directions until a set of four contiguous residues that have an average P(a-helix) < 100 is reached. That is declared the end of the helix. If the segment defined by this procedure is longer than 5 residues and the average P(a-helix) > P(b-sheet) for that segment, the segment can be assigned as a helix.
3. Repeat this procedure to locate all of the helical regions in the sequence.
4. Scan through the peptide and identify a region where 3 out of 5 of the residues have a value of P(b-sheet) > 100. That region is declared as a beta-sheet. Extend the sheet in both directions until a set of four contiguous residues that have an average P(b-sheet) < 100 is reached. That is declared the end of the beta-sheet. Any segment of the region located by this procedure is assigned as a beta-sheet if the average P(b-sheet) > 105 and the average P(b-sheet) > P(a-helix) for that region.
5. Any region containing overlapping alpha-helical and beta-sheet assignments are taken to be helical if the average P(a-helix) > P(b-sheet) for that region. It is a beta sheet if the average P(b-sheet) > P(a-helix) for that region.
6. To identify a bend at residue number j, calculate the following value:

p(t) = f(j)f(j+1)f(j+2)f(j+3)

where the f(j+1) value for the j+1 residue is used, the f(j+2) value for the j+2 residue is used and the f(j+3) value for the j+3 residue is used. If:

(1) p(t) > 0.000075;

(2) the average value for P(turn) > 1.00 in the tetrapeptide; and

(3) the averages for the tetrapeptide obey the inequality P(a-helix) < P(turn) > P(b-sheet), then a beta-turn is predicted at that location.

References

External links

• Amino Acid Information