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 4.5Å 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.
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.