A new method for finding hydrophobic nuclei and microclusters in protein structure is proposed. The method uses simple and clear-cut criteria based on an analysis of distances between the hydrocarbon groups of all residues. A detailed analysis of the composition and properties of hydrophobic nucleic and microclusters for proteins of different types has been carried out. This approach reveals that a hydrophobic nucleus can be composed not merely of classical hydrophobic amino acids, but also of dicarboxylic acids, their amides, arginine, lysine, histidine and tyrosine. The hydrophobic nucleus defined by this method should be considered as an individual structural unit along with such elements of the secondary structure as alpha-helices, beta-turns and beta-sheets.
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