While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs and LRNs we do not find the assortative mixing behaviour of any the subclusters in SRNs. All the subnetworks at different length scales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at higher interaction strength between amino acids, give extra stability to the tertiary structure of the thermophiles.
While the nature of transitions of LCC’s sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don’t. While short-range networks having chain like structures exhibit highly cooperative transition long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure.
Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations.
These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges.
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