Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Chapter 10

Protein Contact Order Prediction: Update

YI SHI, JIANJUN ZHOU, DAVID S. WISHART and GUOHUI LIN

10.1 Introduction

Contact order (CO) is the most widely adopted property used to measure the topological complexity of a protein structure. More specifically, contact order quantitatively measures the nonadjacent amino acid proximity within a folded protein. A contact between two distinct amino acid residues in a protein is formed when there is a pair of heavy atoms (C, O, S, or N), one from each residue, whose physical (Euclidean) distance is within a defined threshold [22, 36]. The absolute contact order (denoted as Abs_CO in this chapter) of a protein is defined as the average number of residues separating the contacts inside the protein (where two sequentially adjacent residues are separated by one residue). The relative contact order, or simply the contact order (denoted as CO), is the Abs_CO normalized over the protein length.

Mathematically, given a protein with a primary sequence of length , we use to denote its th amino acid residue. For two distinct residues and , if there ...