Hydrophobic clusters in protein structures.
Globular proteins fold such that the hydrophobic groups are packed inside forming hydrophobic clusters, and the hydrophilic groups are present on the surface. In this article we analyze clusters of hydrophobic groups of atoms in 781 protein structures selected from the PDB. Our analysis showed that every structure consists of two types of clusters: at least one large cluster that forms the hydrophobic core and probably dictates the protein fold; and numerous smaller clusters, which might be involved in the stabilization of the fold. We also analyzed the preference of the hydrophobic groups in each of the amino acids toward forming hydrophobic clusters. We find that hydrophobic groups from the hydrophilic amino acids also contribute toward cluster formation.
Arunachalam
J
J
Centre of Advanced Studies in Crystallography and Biophysics, University of Madras, Chennai 600025, India.
Gautham
N
N
D000595:Amino Acid Sequence; D016000:Cluster Analysis; D018360:Crystallography, X-Ray; D016208:Databases, Factual; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012995:Solubility; D013499:Surface Properties; D014867:Water / Q000737:chemistry
D011506:Proteins; D014867:Water