Protein Engineering vol. 5 no. 7 pp. 629-635, 1992
© 1992 Oxford University Press
RESEARCH-ARTICLE |
Detection of secondary structure elements in proteins by hydrophobic cluster analysis
Centre de Recherches sur les Macromolécules Végétales CNRS, BP 53X, F-38041 Grenoble, France 1Laboratoire de Minéralogie-Cristallographie, Départment des Macromolécules Biologiques. Universités Paris 6 et Paris 7, CNRS URA 09. Tour 16. 4 place Jussieu, F-75252 Paris cedex 05, France
2To whom correspondence should be addressed
Hydrophobic cluster analysis (HCA) is a protein sequence comparison method based on 
-helical representations of the sequences where the size, shape and orientation of the clusters of hydrophobic residues are primarily compared. The effectiveness of HCA has been suggested to originate from its potential ability to focus on the residues forming the hydrophobic core of globular proteins. We have addressed the robustness of the bidimensional representation used for HCA in its ability to detect the regular secondary structure elements of proteins. Various parameters have been studied such as those governing cluster size and limits, the hydrophobic residues constituting the clusters as well as the potential shift of the cluster positions with respect to the position of the regular secondary structure elements. The following results have been found to support the -helical bidimensional representation used in HCA: (i) there is a positive correlation (clearly above background noise) between the hydrophobic clusters and the regular secondary structure elements in proteins; (ii) the hydrophobic clusters are centred on the regular secondary structure elements; (iii) the pitch of the helical representation which gives the best correspondence is that of an -helix. The correspondence between hydrophobic clusters and regular secondary structure elements suggests a way to implement variable gap penalties during the automatic alignment of protein sequences.
Keywords: computer analysis/helical nets/hydrophobic cluster analysis/secondary structure assignments
Received March 2, 1992; revised May 6, 1992; accepted July 16, 1992.
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