TABLE 2.

Comparison of the structural analysis performed on the five V82A complexes and their wild-type equivalentsa

StructureSurface area buried by ligand on complexation (Å2)Ratio in shape complementarity V82A/WTNo. of ligand-protease VDWb contactsLigand-protease estimated VDW interaction energy (kcal/mole)
WTV82AWTV82AWTV82A
MA-CAc9288670.83174 (5)159 (3)4.63.5
CA-p2c9779231.00167 (1)164 (1)1.73.1
p1-p6c1,0291,0381.07197 (10)202 (3)0.30.1
SQV6126300.82165 (7)142 (1)18.9d6.7
RTV5265000.72165 (11)130 (2)7.915.2
  • a The structural analysis includes surface area buried by the ligand on complexation, shape complementarity, number of ligand-protease VDW contacts, and ligand protease estimated VDW interaction energy. The numbers shown in parentheses highlight the number of atoms located within VDW radius distance of residue 82 in the corresponding structures.

  • b The distance criterion used for the VDW contacts is 2.4 to 4.2 Å.

  • c In the comparison of the peptide complexes, only equivalent residues were used, since the termini were disordered in some of the crystal structures.

  • d The refinement of SQVWT was carried out using X-PLOR version 2.1 which had slightly different non-bonded energy parameters.