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Analysis of accessible surface of residues in proteins

Centre de Biophysique Moléculaire Numérique (CBMN), Faculté des Sciences Agronomiques de Gembloux (FSAGx), 5030 Gembloux, Belgium

Reprint requests to: Robert Brasseur, CBMN, Passage des Déportés, 2, FSAGx, B-5030 Gembloux, Belgium; e-mail: brasseur.r{at}fsagx.ac.be; fax: 32-8162-2522.

We analyzed the total, hydrophobic, and hydrophilic accessible surfaces (ASAs) of residues from a nonredundant bank of 587 3D structure proteins. In an extended fold, residues are classified into three families with respect to their hydrophobicity balance. As expected, residues lose part of their solvent-accessible surface with folding but the three groups remain. The decrease of accessibility is more pronounced for hydrophobic than hydrophilic residues. Amazingly, Lysine is the residue with the largest hydrophobic accessible surface in folded structures. Our analysis points out a clear difference between the mean (other studies) and median (this study) ASA values of hydrophobic residues, which should be taken into consideration for future investigations on a protein-accessible surface, in order to improve predictions requiring ASA values. The different secondary structures correspond to different accessibility of residues. Random coils, turns, and ß-structures (outside ß-sheets) are the most accessible folds, with an average of 30% accessibility. The helical residues are about 20% accessible, and the difference between the hydrophobic and the hydrophilic residues illustrates the amphipathy of many helices. Residues from ß-sheets are the most inaccessible to solvent (10% accessible). Hence, ß-sheets are the most appropriate structures to shield the hydrophobic parts of residues from water. We also show that there is an equal balance between the hydrophobic and the hydrophilic accessible surfaces of the 3D protein surfaces irrespective of the protein size. This results in a patchwork surface of hydrophobic and hydrophilic areas, which could be important for protein interactions and/or activity.

Keywords: Solvent accessibility; Pex files; hydrophobicity; secondary structure; amphipathy

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