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.