BINARY ASSIGNMENTS OF AMINO-ACIDS FROM PATTERN CONSERVATION

We have developed a simple optimization procedure for assigning binary values to amino acids. The binary values are determined by a maximiza tion of the degree of pattern conservation in groups of closely relate d protein sequences. The maximization is carried out at fixed composit ion. For compositions approximately corresponding to an equipartition of the residues, the optimal encoding is found to be strongly correlat ed with hydrophobicity. The stability of the procedure is demonstrated . Our calculations are based upon sequences in the SWISS-PROT database .