Topological properties of four networks in protein structures

Abstract In this paper, we investigate the complex networks of interacting amino acids in protein structures. The cellular networks and their random controls are treated for the four threshold distances between atoms. The numerical simulation and analysis are relevant to the topological properties of the complex networks in the structural classification of proteins, and we mainly estimate the network’s metrics from the resultant network. The cellular network is shown to exhibit a small-world feature regardless of their structural class. The protein structure presents the positive assortative coefficients, when the topological property is described as a tendency for connectivity of high-degree nodes. We particularly show that both the modularity and the small-wordness are significantly followed the increasing function against nodes.