Distribution of dipeptides in different protein structural classes: an effort to find new similarities.

Finding any regularity in the sequences of proteins and determining their correlation with structural features are of great interest for an understanding of molecular biology. We statistically analyzed the relative frequencies of all 400 possible dipeptides in a data set containing randomly selected proteins of different defined structural classes including all-alpha, all-beta, alpha + beta and alpha/beta families. We found that the distribution of dipeptides is not the same for different structural classes, and some of them are significantly far from a random distribution. A tendency of a given amino acid to localize in the first or second position of a dipeptide depending on the structural class of protein was also found. Interestingly, some amino acids may be substituted for each other in the first or second positions of specific dipeptides in each structural class. This finding apparently contrasts with the routine expectation from the viewpoint of amino acid properties, as classically understood.