An HCA-segment corresponds to a high density area of hydrophobic clusters
hydrophobic cluster
An hydrophobic cluster is defined as a succession of strong hydrophobic residues separated by less than a given distance in amino acids, called connectivity distance. The strong hydrophobic residues are V, I, L, M, F, Y, W and the connectivity distance is 4 in the standard use of HCA approach, in which the α-helix is used as a two-dimensional support for the 2D HCA transposition of the sequence. These parameters provided the best correspondance between the positions of clusters and regular secondary structures ([SW1992], [IC1997]).


[IC1997]Callebaut I, Labesse G, Durand P, Poupon A, Canard L, Chomilier J, Henrissat B, Mornon JP. Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Cell Mol Life Sci. 1997 Aug;53(8):621-45.
[SW1992]Woodcock S, Mornon JP, Henrissat B. Detection of secondary structure elements in proteins by hydrophobic cluster analysis Protein Eng. 1992 5(7):629-635.