Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures

Abstract

Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried position. In this paper we shown that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side‐chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large database of protein structures.