Residue interaction networks (RIN)

Given a protein structure, its corresponding RIN is generated by inspecting its atoms and looking for non-covalent bonds between them. We used RING 2.0⁸ to perform this task. Given the PDB representation of a protein, the RING-2.0 algorithm generates the graph in two steps. The first identifies a list of residue-residue pairs eligible to undergo an interaction based merely on distance measurements. The second characterizes every contact by identifying the specific type of interaction, which can be Hydrogen bond, Van der Waals, Ionic bridges, π-π-Stacking,π-cation and Disulfide bridges.

RING 2.0 allows the RIN generation according to various parameters that the user can select. All RINs produced in this study have been generated using the default options. In particular, for the Network policy parameter we used the Closest option, where all atoms of a residue-residue pair are considered to measure the distance; for the Interaction type we used the Multiple option, where RING reports multiple interactions per residue pair but only one interaction per interaction type; for the Distance threshold we used the Strict option, where each type of interaction has a specific threshold depending on its strength, as reported in Table 2.

Threshold distance values for the Strict option of RING 2.0.