How many packing contacts are observed in protein crystals?

Abstract

Most of the protein three-dimensional structures were determined with crystallographic methods in the solid state, where each molecule (therein after referred to as the "reference molecule") is surrounded by several other molecules that can influence its structure. The number of molecules that surround the reference molecule in protein crystal structures is examined on the basis of data extracted from the protein data bank. It is observed that there are as few as three and as many as 18 molecules in contact with the reference molecule, with an average number of about 10. The number of molecules around the reference molecule is smaller at higher symmetries than at lower symmetries and does not depend on the protein shape and dimension. The results reported here are a benchmark that may be useful the detection of potential anomalies and for the analyses of structural information both stored in databases or novel.