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).
Shown at the right is the structure of serine.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. These amino acids are usually found at the surface of proteins, as discussed in the Proteins 2 module. These are serine (Ser), threonine (Thr), cysteine (Cys), asparagine (Asn), glutamine (Gln), and tyrosine (Tyr). Six amino acids have side chains that are polarīut not charged. This fact has important implications for proteins' tertiary structure (see the Proteins 2 module for a discussion of tertiary structure). These side chains are composed mostly of carbon and hydrogen, have very small dipole moments, and tend to be repelled from water. Shown at the right is the structure of valine. Side chains are glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), proline (Pro), phenylalanine (Phe), methionine (Met), and tryptophan (Trp). The nine amino acids that have hydrophobic Amino acids are grouped according to what their side chains are like.
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