MEASURING CORRELATIONS IN PROTEIN SEQUENCES

The paper is devoted to the detection of pair correlations in amino ac id sequences using mutual information and correlation functions. Since statistical dependences are relatively weak, finite sample correction s turn out to be essential for a correct interpretation of the correla tion measures. Statistical fluctuations are reduced by analyzing two l arge sets of protein sequences. The calculation of correlation functio ns requires the assignment of numbers to the 20 amino acids. This is d one by using well-known property codes. Moreover, we look by extensive random sampling for optimized codes which maximize the strength of co rrelations. It turns out that the strongest correlations are related t o hydrophobicity scales and a-helix propensities.