Hydrophobic, hydrophilic and charged amino acids' networks within Protein
Md Aftabuddin 1 and Sudip Kundu 1*
1 University of Calcutta
* To whom correspondence should be addressed. E-mail: skbmbg{at}caluniv.ac.in.
Submitted on September 25, 2006
Revised on November 1, 2006
Accepted on 1 December 2006
 |
Abstract |
|---|
The native three dimensional structure of a single protein is determined by the physico chemical nature of its constituent amino acids. The twenty different types of amino acids, depending on their physico chemical properties, can be grouped into three major classes - hydrophobic, hydrophilic and charged. We have studied the anatomy of the weighted and unweighted networks of hydrophobic, hydrophilic and charged residues separately for a large number of proteins. Our results show that the average degree of the hydrophobic networks has significantly larger value than that of hydrophilic and charged networks. The average degree of the hydrophilic networks is slightly higher than that of charged networks. The average strength of the nodes of hydrophobic networks is nearly equal to that of the charged network; whereas that of hydrophilic networks has smaller value than that of hydrophobic and charged networks. The average strength for each of the three types of networks varies with its degree. The average strength of a node in charged networks increases more sharply than that of the hydrophobic and hydrophilic networks. Each of the three types of networks exhibits the 'small-world' property. Our results further indicate that the all amino acids' networks and hydrophobic networks are of assortative type. While most of the hydrophilic and charged networks are of assortative type, few others have the characteristics of disassortative mixing of the nodes. We have further observed that all amino acids' networks and hydrophobic networks bear the signature of hierarchy; whereas the hydrophilic and charged networks do not have any hierarchical signature.
Key Words:
assortative mixing, hierarchical signature, small-world, weighted and unweighted network
