[Analysis of the spatial structure of proteins in terms of residue-residue contacts. II. Contact affinity]

The possibility of detecting the mutual amino acid residue affinity when protein three-dimensional structures are described in terms of residue-residue contact matrices is discussed. The hypothesis of the lack of affinity between amino acid residues is examined; the values of the pertinent elements of the overall residue-residue contact matrices prove not to be statistically different from random estimates in 91%; the chance hypothesis is rejected in 9% of cases, represented as a rule by residues with charged side groups, especially oppositely charged ones.