  It is not merely the position of residues that are of utmost importance in
protein function and stability, but the interactions between them. We
illustrate, by using a network construction on a set of 595 non-homologous
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.
