Hydrophobicity and structural classes in proteins

The bulk hydrophobic character for the 20 natural amino acid residues, has been obtained from a database of 60 protein structures, grouped in the four structural classes alpha alpha, beta beta, alpha + beta and alpha/beta. The hydrophobicity coefficients thus obtained are compared with Ponnuswamy's original values using scales normalized to average = 0.0 and standard deviation = 1.0. Even though most of the amino acid residues do not change their hydropathic character in the different structural classes, their behaviour suggests the convenience that averaging methods should only consider proteins of the same structural class and that this information should be included in the secondary structure methods.