Contact capacity potentials reflect mainly hydrophobicity of the amino acids.
Hydrophobicity is the major driving force for protein folding.
Without pairwise contact potentials we can use a simple and fast dynamic programming algorithm to align a sequence with a structure. N.N. Alexandrov, R. Nussinov and R.M. Zimmer Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. World Scientific Publishing Co., Singapore, pp.