Hydrophobic amino acids (V, I, L, F, M, Y, W) are encircled and their contours are joined. This one is cut along the horizontal axis and unrolled, in order to get the full environment of each amino acid, as it exists on the 1D sequence. The protein sequence (1D), in which hydrophobic amino acids are represented as white letters, is written on a alpha-helix, displayed on a cylinder.
Statistical studies performed on experimental 3D structures have shown that hydrophobic clusters mainly correspond to regular secondary structures, and have supported the relevance of the chosen hydrophobic alphabet, as well as the alpha-helix as 2D support for revealing this structural information (Woodcock, et al., 1992).įigure 1: Principle of the HCA plot, illustrated on a sequence segment of the alpha1-antitrypsin (adapted from (Callebaut, et al., 1997)).
Hydrophobic Cluster Analysis (HCA) is based on a two-dimensional representation of the protein sequence, in which hydrophobic amino acids congregate into clusters (Callebaut, et al., 1997 Gaboriaud, et al., 1987 Figure 1). Hydrophobic Cluster Analysis GUIDLINES TO HYDROPHOBIC CLUSTER ANALYSIS (HCA) This guideline has been adapted from the supplementary data of the article by Faure and Callebaut, Bioinformatics (2013) in press.
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