An Analysis of Protein Conservation Residues Network

Identifying protein interface is crucial for the prediction of protein-protein interactions and for protein functional classification. In this work, the protein structure is modeled as an undirected graph with the conservation amino- acid residues the vertices and all atom contacts between them the edges. We find that the conservation residue networks are characterized by intermediate values of clustering coefficient and characteristic path length, which are the typical property of small-world networks. The residues on the protein interfaces typically have higher degree and lower clustering coefficient values than that of the surface residues. Additionally, it is detected that the spatial clustering of the conservation residues is a general phenomenon, consistent with the cooperative nature of residues in determining the structure and function. These results indicate that the conservation residue network propensities can give us some new parameters in protein-protein interface prediction.