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The three dimensional structure of a protein is an outcome of theinteractions of its constituent amino acids in 3D space. Considering the aminoacids as nodes and the interactions among them as edges we have constructed andanalyzed protein contact networks at different length scales, long andshort-range. While long and short-range interactions are determined by thepositions of amino acids in primary chain, the contact networks are constructedbased on the 3D spatial distances of amino acids. We have further divided thesenetworks into sub-networks of hydrophobic, hydrophilic and charged residues.Our analysis reveals that a significantly higher percentage of assortativesub-clusters of long-range hydrophobic networks helps a protein incommunicating the necessary information for protein folding in one hand; on theother hand the higher values of clustering coefficients of hydrophobicsub-clusters play a major role in slowing down the process so that necessarylocal and global stability can be achieved through intra connectivities of theamino acid residues. Further, higher degrees of hydrophobic long-rangeinteractions suggest their greater role in protein folding and stability. Thesmall-range all amino acids networks have signature of hierarchy. The presentanalysis with other evidences suggest that in a protein's 3D conformationalspace, the growth of connectivity is not evolved either through preferentialattachment or through random connections; rather, it follows a specificstructural necessity based guiding principle - where some of the interactionsare primary while the others, generated as a consequence of these primaryinteractions are secondary.

Protein contact networks at different length scales and role of hydrophobic, hydrophilic and charged residues in protein's structural organisation