Average geometrical properties (standard deviations are shown in parentheses) calculated from the equilibrium MD trajectories of the unbound and bound gp120 models.

aNumber of hydrogen bonds. A hydrogen bond is considered to exist when the donor-hydrogen-acceptor angle is larger than 120° and the donor-acceptor distance is less than 3.5 Å.
bTotal solvent accessible surface area.
cNumber of native contacts. A native contact is considered to exist if the distance between two atoms is less than 6 Å.
dRadius of gyration.
eNumber of residues in the corresponding secondary structure elements.
fPotential energy calculated with GROMOS96 43a1 force field using PME method.