A method for comparison of amino acid sequences of proteins to detect regions of conformational similarity. Groups of neighbouring hydrophobic amino acid residues are identified in a HCA plot that is constructed by conceptually folding the entire backbone into an α-helix, rolling the helix two complete revolutions across a two-dimensional surface and noting the positions where α-carbons have contacted the surface. Each contact point is indicated according to the residues attached to it. The two-dimensional visual pattern of neighbouring hydrophobic residues, whether adjacent in the primary sequence or brought together by folding of the helix, is characteristic of the actual conformation, and serves as a basis for comparison of proteins.