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Open Access Research article

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization

Dhriti Sengupta and Sudip Kundu*

Author Affiliations

Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92 APC Road, Kolkata-700009, India

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BMC Bioinformatics 2012, 13:142  doi:10.1186/1471-2105-13-142

Published: 21 June 2012

Additional files

Additional file 1 :

PDB codes of the 495 proteins used in the study.

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Additional file 2 :

Transition profiles of largest cluster in different subnetworks are compared for 495 proteins. The size of largest connected component is plotted as a function of Imin in different subnetworks for 495 proteins. The cluster sizes are normalized by the number of amino acid in the protein. The different subnetworks are A) Long-range all residue network (LRN-AN). B) Short-range all residue network (SRN-AN). C) All-range all residue network (ARN-AN). D) All-range hydrophobic residue network (ARN-BN). E) All-range hydrophilic residue network (ARN-IN). F) All-range charged residue network (ARN-CN). G) Long-range hydrophobic residue network (LRN-BN). H) Short-range hydrophobic residue network (SRN-BN).

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Additional file 3 :

Different nature of cluster in ARN-AN, LRN-AN and SRN-AN. The nature of cluster in SRN-AN is chain like while the cluster is much more well connected and non-chain like in LRN-AN and ARN-AN.

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Additional file 4 :

Relative highest frequency distribution in ARN, LRN and SRN. A. The number of occurrences of possible combination of cliques are normalized against the number of hydrophobic/hydrophilic/charged residues present in the protein. The frequency distribution (in %) of the clique types with highest normalized clique occurrence value is plotted for ARN, LRN and SRN at 0% Imin cutoff. The sum of all relative values of different clique types for each sub-network type is 100. B. The percentage of charged residues cliques increase with the increase in Imincutoff. This trend is followed at all length-scales. The sum of all relative values of different clique types at each Imincutoff is 100. Some sub-network types are not shown in the figure since they have a very less or no relative occurrence value.

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Additional file 5 :

Illustrative figure explaining perimeters of cliques. Higher perimeter of cliques means amino acids placed more distantly in primary structure come close in 3D space. So these residues must be of high importance in protein structure formation.

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