2.3 Network construction and analysis
The protein structural network (PSN) is a weighted graph representation of residues interconnected to depict a network of interactions. Each residue in the PSN is a node and they are connected to other nodes using edges based on their 3D coordinates. Spatial distance, chemical non-covalent bonds, charge, energy, or many other features are several means of defining network edges. In the current analysis, inter-atomic distance between atoms of non-adjacent residues are used to define interactions. A distance proximity cut-off of 4.5Å is used to define atom contacts. The weight of an edge is defined as the ratio of the total number of atom contacts made between a pair of residues and the maximum number of atom contacts found in the entire dataset between the corresponding amino acids.
The degree parameter and node strength obtained from the sum of all edge weights connected to a node describes the connectivity around the corresponding residues in the PSN. A higher degree would suggest that the well-connected node is a hub in the network. Upon binding, any significant change in the node strength or degree of sites, especially hubs, corresponding to loss or gain of crucial connectivity in the PSN are analysed.