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* School of Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey; and Laboratory of Computational Biology, Faculty of Engineering and Natural Sciences, Sabanci University, Orhanli 34956, Tuzla, Istanbul, Turkey
Correspondence: Address reprint requests to Canan Baysal, Tel.: +90-216-483-9523; Fax: +90-216-483-9550; E-mail: canan{at}sabanciuniv.edu.
It is not merely the position of residues that is critically important for a protein's function and stability, but also their interactions. We illustrate, by using a network construction on a set of 595 nonhomologous proteins, that regular packing is preserved in short-range interactions, but short average path lengths are achieved through some long-range contacts. Thus, lying between the two extremes of regularity and randomness, residues in folded proteins are distributed according to a "small-world" topology. Using this topology, we show that the core residues have the same local packing arrangements irrespective of protein size. Furthermore, we find that the average shortest path lengths are highly correlated with residue fluctuations, providing a link between the spatial arrangement of the residues and protein dynamics.
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