Depth Analysis of Protein Spatial Structure

Abstract

The issue of amino acid depth in proteins gives important insights to our understanding of protein’s three-dimensional structure. There has already been much research done about the residue depth and atom depth. In this chapter, we construct a method of calculating amino acid depths at the statistical and mathematical overview and apply it to a set of 527 protein structures. We propose the introduction of amino acid depth tendency factors for three-dimensional structures of proteins. The depth tendency factors relate not only to the hydrophobicity indices but also to the electrostatic charge. We find a relationship between the protein size and the number of residues, using the distance between the deepest residue and surface residues. We make predictions regarding the number of residues on the surface of a protein, the deepest amino acid, and the average depth, all of which fit well to a linear functional relationship with the length of a protein. Finally, we predict the depths of multiple peptides in the protein’s three-dimensional structure.