RINALYZER uses the RINERATOR module that can predict non-covalent interactions between residues and can represent a protein as a two dimensional interaction graph. I have two queries:

a). How's the 'interatomic contact' different from Vander waals overlaps? Do the contacts include all possible overlaps between the atoms (that include all the electrostatic interactions, salt bridges, and Vander waals overlaps).

b) Is there any option to provide any "contact criteria" while computing RIN- say I am interested to look at non-covalent interactions within 5.0 Å. (if at least one atom corresponding to residue 'i' and any atom from residue 'j' were closer than 5.0 Å.) From the PROBE paper, it seems that all the interactions are roughly within 5.0 Å (upper limit of London dispersion forces). I have always used this distance criteria while computing networks from Normal mode analysis and MD trajectory data. From the atomic parameters used by REDUCE and PROBE to predict interactions, it seems that the distances are roughly within 5.0 Å.

I am attaching two papers on REDUCE and PROBE algorithm that RINALYZER considers.