CORRELATIONS IN PROTEIN SEQUENCES AND PROPERTY CODES

Correlation functions in large sets of non-homologous protein sequence s are analysed. Finite size corrections are applied and fluctuations a re estimated. As symbol sequences have to be mapped to sequences of nu mbers to calculate correlation functions, several property codes are t ested as such mappings. We found hydrophobicity autocorrelation functi ons to be strongly oscillating. Another strong signal is the monotonou sly decaying alpha-helix propensity autocorrelation function. Furtherm ore, we detected signals corresponding to an alternation of positively and negatively charged residues at a distance of 3-4 amino acids. To look beyond the property codes gained by the methods of physical chemi stry, mappings yielding a strong correlation signal are sought for usi ng a Monte Carlo simulation. The mappings leading to strong signals ar e found to be related to hydrophobicity or alpha-helix propensity. A c luster analysis of the top scoring mappings leads to two novel propert y codes. These two property codes are gained from sequence data only. They turn out to be similar to known property codes for hydrophobicity or polarity. (C) 1998 Academic Press Limited.