The SOCKET program finds the Knobs-into-Holes mode of packing between alpha-helices (Crick, 1953) which is characteristic of coiled coils. It unambiguously defines the beginning and end of coiled-coil motifs in protein structures and assigns a heptad register to the sequence, highlighting the core-residues with a RasMol script (Sayle & Milner-White, 1995) if required.

This type of packing is arguably the simplest and most regular kind of tertiary and quaternary interaction which occurs in proteins; yet the sequences and architectures of coiled coils are reasonably diverse, despite sharing the same packing characteristics . A better understanding of the relationship between the sequence and structure of this motif has implications not just for the design of new coiled coils and their recognition in protein sequences, but also for the prediction of quaternary-interactions between proteins.

Specifically, the purposes of SOCKET are:

• To objectively and unambiguously define the location of a coiled-coil motif in a protein structure, so that its sequence can be used to test new coiled-coil prediction algorithms and benchmark existing ones.

• To automatically collect statistics on frequencies of amino acids at each of the heptad positions (a, b, c, d, e, f, g) of the sequence/structure motif. Such data are useful for training computer programs which predict coiled coils from primary structure, and for providing insights into new design rules.

• To highlight unusual assemblies of alpha-helices which go beyond the traditional coiled coil; again it is hoped that design principles, founded on knobs-into-holes packing between alpha-helices, will enable us to create novel and useful protein assemblies.

References

• Crick, F.H.C. (1953) Acta Cryst. 6 689-697
• Sayle, R. & Milner-White E.J. Trends in Biochemical Sciences 20 (9) 374
• Walshaw, J. & Woolfson, D.N. (2001) J. Mol. Biol., 307 (5), 1427-1450

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