Quantifying Side Chain Interactions

High and low contact criteria. A pair of phenylalanine rings interacting with each other are shown. The lines between the phenylalanines indicate the atoms that are within a distance of 4.5 1

The Interaction strength=

Where nij = the number of atom atom contact between the residues i & j

Ni & Nj are the normalisation factors for the residues i & j.

Imin is user defined interaction cutoff. An (ij) residue pair with Iij > Imin is connected by an edge.

References:

1. Kannan N and Vishveshwara S. Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol.1999 Sep 17;292(2):441-64.