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Hydrophobic patches on the surfaces of protein structures
Author(s) -
Lijnzaad Philip,
Berendsen Herman J. C.,
Argos Patrick
Publication year - 1996
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199607)25:3<389::aid-prot10>3.0.co;2-e
Subject(s) - chemistry , lattice protein , monomer , amino acid residue , amino acid , hydrophobic effect , residue (chemistry) , protein structure , organic chemistry , peptide sequence , polymer , biochemistry , gene
A survey of hydrophobic patches on the surface of 112 soluble, monomeric proteins is presented. The largest patch on each individual protein averages around 400 Å 2 but can range from 200 to 1,200 Å 2 . These areas are not correlated to the sizes of the proteins and only weakly to their apolar surface fraction. Ala, Lys, and Pro have dominating contributions to the apolar surface for smaller patches, while those of the hydrophobic amino acids become more important as the patch size Increases. The hydrophilic amino acids expose an approximately constant fraction of their apolar area independent of patch size; the hydrophobic residue types reach similar exposure only in the larger patches. Though the mobility of residues on the surface is generally higher, it decreases for hydrophilic residues with Increasing patch size. Several characteristics of hydrophobic patches catalogued here should prove useful in the design and engineering of proteins. © 1996 Wiley‐Liss, Inc.