Understanding contact patterns of protein structures from protein contact map and investigation of unique patterns in the globin‐like folded domains

Abstract

Proteins are biochemical compounds made up of one or more polypeptides in a specific order, typically folded into a functionally active form. Proteins are categorized into four different structural classes according to the topology of α-helices and β-strands. In this study, we modeled these four structural classes as an undirected network depicting amino acids as nodes and interaction between them as edges. Results infer that basic protein classes can be easily recognized as well as distinguished by utilizing protein contact maps (PCM). Toward studying the globin-like fold, the helix-loop-helix region contacts were seen to be of a unique pattern, and these remained in all the folds. Further, the averaged diagonal contacts were analyzed and identified those contacts in α/β proteins were higher in comparison with the other class. Interesting, we noticed that anti-parallel beta sheets were dominant in all-β and α + β classes that lead to similar diagonal patterns. Network properties of all four basic classes were analyzed and found to possess small-world property. Findings infer that PCM may assist classify protein structure classes and it also helps in evaluating the predicted protein structures.