Quaternion contact ribbons: a new tool for visualizing intra- and intermolecular interactions in proteins.

Protein side chain interactions between residues separated by at least one loop or turn or break in the amino acid sequence are called 'nonlocal contacts' in this manuscript, and contiguous sets of such interactions located between segments of secondary structure are called 'contact zones.' A new interactive program, the quaternion contact ribbon tool, has been developed to help protein chemists identify, straighten if twisted, and display contact zones between two neighboring segments of helix.