title: A comparative analysis of protein interfaces.
abstract: Proteins perform various functions through interacting with other molecules. Analyzing the characteristics of residues on the interaction interfaces provides insights into the mechanisms of these interactions. In this study, we analyze the characteristics of five different interfaces: protein-protein interfaces, protein-DNA interfaces, protein-RNA interfaces, protein-carbohydrate interfaces, and protein-ligand interfaces. The analysis reveals that these interfaces are different in residue composition. These differences in residue composition reflect the differences in the mechanisms that facility different types of interactions. Regardless of the differences in residue composition, all of the five types of interfaces are more conservative than the non-interface protein surfaces. Additionally, our results also show that it is important to consider the effect of solvent accessibility when investigating residues' propensities for different parts of the proteins.
authors.affiliation: Department of Mathematics and Computer Science, Franklin & Marshall College, Lancaster, PA 17604, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Hu
authors.forename: Changhui
authors.initials: C
authors.lastname: Yan
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D019277:Entropy; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties
chemical_list: D000596:Amino Acids; D011506:Proteins