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. The table of numbers is as follows:
Name P(α) P(β) P(β-turn) f(i) f(i+1) f(i+2) f(i+3)
Alanine 1.42 0.83 0.66 0.06 0.076 0.035 0.058 Arginine 0.98 0.93 0.95 0.070 0.106 0.099 0.085 Aspartic Acid 1.01 0.54 1.46 0.147 0.110 0.179 0.081 Asparagine 0.67 0.89 1.56 0.161 0.083 0.191 0.091 Cysteine 0.70 1.19 1.19 0.149 0.050 0.117 0.128 Glutamic Acid 1.39 1.07 0.74 0.056 0.060 0.077 0.064 Glutamine 1.11 1.05 0.98 0.074 0.098 0.037 0.098 Glycine 0.57 0.75 1.56 0.102 0.085 0.190 0.152 Histidine 1.00 0.87 0.95 0.140 0.047 0.093 0.054 Isoleucine 1.08 1.60 0.47 0.043 0.034 0.013 0.056 Leucine 1.41 1.20 0.59 0.061 0.025 0.036 0.070 Lysine 1.14 0.74 1.01 0.055 0.115 0.072 0.095 Methionine 1.45 1.05 0.60 0.068 0.082 0.014 0.055 Phenylalanine 1.13 1.38 0.60 0.059 0.041 0.065 0.065 Proline 0.57 0.55 1.52 0.102 0.301 0.034 0.068 Serine 0.77 0.75 1.43 0.120 0.139 0.125 0.106 Threonine 0.83 1.19 0.96 0.086 0.108 0.065 0.079 Tryptophan 1.08 1.37 0.96 0.077 0.013 0.064 0.167 Tyrosine 0.89 1.47 1.04 0.082 0.065 0.114 0.125 Valine 1.06 1.70 0.50 0.062 0.048 0.028 0.053
The numbers in the first three columns, P(α) P(β) P(turn), are about equivalent to preference parameters for the 20 amino acids for α-helix, β-strand and β-turn respectively, though 1.0 was added to each preference parameter. A preference parameter is the logarithm of the observed counts divided by the expected counts. A preference parameter of 0.0 (which corresponds to 1.0 in this column) indicates that something happens just as often as one expects. Unfortunately Chou and Fasman's mathematicss wasn't up to today's standards so these parameters aren't calculated correctly, but the correct numbers aren't too different from these ones....