A homology measure for protein fold classes has been constructed by locally projecting consecutive secondary structures onto a lattice. Taking into account hydrophobic forces we have found a mechanism for formation of domains containing magic numbers of secondary structures and multipla of these domains. We have performed a statistical analysis of available protein structures and found agreement with the predicted preferred abundances. Furthermore, a connection between sequence information and fold classes is established in terms of hinge forces between the structural elements.
Physical Review Letters, 1996, Vol 77, Issue 4, p. 779-782