Abstract
The properties of 1172 protein complexes (downloaded from the Protein Data Bank (PDB)) have been studied based on the concept of circular variance as a buriedness indicator and the concept of mutual proximity as a parameter-free definition of contact. The propensities of residues to be in the protein, on the surface or form contact, as well as residue pairs to form contact were calculated. In addition, the concept of circular variance has been used to compare the ruggedness and shape of the contact surface with the overall surface.
Highlights
Formation of protein complexes is a ubiquitous biological process
Knowledge of the structure of individual proteins is rarely sufficient to unequivocally predict the interaction surface of two proteins. This problem manifests itself in the performance of various computational tools designed to predict such complex formation: a large number of predicted structures usually look “reasonable”
A recent study examined the relationship between binding affinity and interfacial buried surface area [16]
Summary
Knowledge of the structure of individual proteins is rarely sufficient to unequivocally predict the interaction surface of two proteins. This problem manifests itself in the performance of various computational tools designed to predict such complex formation: a large number of predicted structures usually look “reasonable”. Given this conundrum, tools that can help improve the ranking of such set of models for a complex can be of significant help. A recent study examined the relationship between binding affinity and interfacial buried surface area [16]. The present paper applies the concept of mutual proximity to delineate contact pairs on the interaction surface and uses the concept of the circular variance to examine some geometric properties of the interaction surface
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