A protein conformational search space defined by secondary structure contacts.

A conformational search space describing the relative position and orientation of protein secondary structure elements in three-dimensions was defined. These spatial relations were encoded by homogeneous transformation matrices between pairs of residues "in contact" in two different secondary structure elements. A database of all occurrences of spatial relations for five hydrophobic residues was built. The use of one residue contact per pair of secondary structure elements, which were approximated by standard (phi, psi) assignments, was sufficient to reproduce accurately the core structure of proteins with known three-dimensional structures.