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Weighted and unweighted network of amino acids within protein

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  • Aftabuddin, Md.
  • Kundu, Sudip

Abstract

The information regarding the structure of a single protein is encoded in the network of interacting amino acids considered as nodes. If any two atoms from two different amino acids (nodes) are within higher cut-off distance of London-van der Waals forces, the amino acids are considered to be linked or connected. Several atoms of any amino acids in a protein may be within the above prescribed distance of several atoms of another amino acid resulting in possible multiple links between them. These multiple links are the basis of the weight of the connectivity in a protein network. Each protein has been considered as a weighted and an unweighted network of amino acids. A total of forty nine protein structures that covers the three branches of life on earth has been analyzed and several network properties have been studied. The probability degree and strength distributions of network connectivity have been obtained. It has been observed that the average strength of amino acid node depends on its degree. The results show that the average clustering coefficient of weighted network is less than that of unweighted network. It implies that the topological clustering is generated by edges with low weights. The power-law behavior of clustering coefficients of weighted and unweighted networks as a function of degree indicates that they have signatures of hierarchy. It has also been observed that the network is of assortative type.

Suggested Citation

  • Aftabuddin, Md. & Kundu, Sudip, 2006. "Weighted and unweighted network of amino acids within protein," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 369(2), pages 895-904.
    • Handle: RePEc:eee:phsmap:v:369:y:2006:i:2:p:895-904
    DOI: 10.1016/j.physa.2006.03.056
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    Citations

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    Cited by:

    1. Emerson, Isaac Arnold & Amala, Arumugam, 2017. "Protein contact maps: A binary depiction of protein 3D structures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 465(C), pages 782-791.
    2. Sengupta, Dhriti & Kundu, Sudip, 2012. "Do topological parameters of amino acids within protein contact networks depend on their physico-chemical properties?," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 391(17), pages 4266-4278.

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