  Lattice-model simulations and experiments of some small proteins suggest that
folding is essentially controlled by a few conserved contacts. Residues of
these conserved contacts form the minimum set of native contacts needed to
ensure foldability. Keeping such conserved specific contacts in mind, we
examine contacts made by two secondary structure elements of different helices
or sheets and look for possible 'packing units' of the protein structure. Two
short backbone fragments of width five centred at the C? atoms in contact is
called an H-form, which serves as a candidate for the packing units. The
structural alignment of protein family members or even across families
indicates that there are conservative H-forms which are similar both in their
sequences and local geometry, and consistent with the structural alignment.
Carrying strong sequence signals, such packing units would provide 3D
constraints as a complement of the potential functions for the structure
prediction.
