Multi-Body Interactions within the Graph of Protein Structure

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Contents

We construct a graphical representation of protein structure based on the 3D C-alpha carbon point set, using the Delaunay tessellation to define interacting quadruples of amino acid residues. The tessellation is filtered by two criteria: interaction distance less than 9.5 angstroms and circumsphere radius less than 8.0 angstroms using dataset of 608 protein structures of low mutual sequence identity and a likelihood ratio test, we show that 3-body and 4-body interactions are indeed significant. We identify particular significant three-body interactions by first reducing the dataset to interacting triples, and classifying amino acid residues in a reduced alphabet. Although cystein was previously shown to be a dominant source of 3-body interactions, we now identity additional significant 3-body interactions of charged, hydrophobic and small residues.