Figure 4.
(a) Fractional native contacts, Q, as a function of time. The native contacts were measured as the number of neighboring residues presented in the native structure. Residues are taken to be in contact if any of the atom pairs (including both sidechain and mainchain atoms) are closer than 2.8 Å, excluding residues i and i+1, which always have the contacts through mainchain atoms. Fractional native contact is the number of total native contacts presented in the simulated structure divided by the number of native contacts in the native structure. (b) SFE of the protein as a function of time. The upper dashed line represents the SFE of the starting structure, and the lower dotted line represents that of the native structure. The parameters are those by Eisenberg and McLachlan (43), (i.e., 0.0163, −0.00637, 0.02114, −0.02376, −0.05041, in kcal/mole/Å2, for the surface areas of nonpolar, polar, sulfur, charged oxygen, and charged nitrogen, respectively).