Title: Helix-helix interaction viewed in an angle frame indicates a role of the size of sidechains in packing

Authors: Xiubei Liao

Addresses: Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60045, USA

Abstract: Three-dimensional packing is essential for protein folding. Homology alignment and de nova methods have been used to develop algorithms that would predict protein packing in proteins. Even though hydrophobic cores of proteins are formed through the packing of side chains of hydrophobic residues, the stereological arrangement of individual amino acids and in three dimensional hydrophobic cores is rather difficult to determine. In order to simplify the description of a protein core packing, in this manuscript, we have determined the relationship between angles, distances, and residue usage between two helices. Data from this analysis demonstrate that the contact residues determine the angle and the distance between two helical elements. This approach provides a means to predict the three-dimensional packing of helices in proteins and allows for an understanding of the biological interaction within proteins and among proteins based on surface contact residue parameters.

Keywords: protein structure; helix-helix interaction.

DOI: 10.1504/IJBRA.2020.113019

International Journal of Bioinformatics Research and Applications, 2020 Vol.16 No.4, pp.336 - 354

Accepted: 03 Feb 2018
Published online: 03 Feb 2021 *

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