Figure 9.

Example dihedral probability distributions for individual amino acids (alanine, panel I; threonine, panel II): (A) probability of finding a given combination of ϕ and ψ angles in the experimentally obtained starting conformations; (B) probability of finding a given combination of ϕ and ψ angles simulated with the 54A8 parameter set; (C) probability distributions of the ϕ dihedral angle; (D) probability distributions of the ψ dihedral angle. The plots were constructed from conformations sampled during the last 5 ns of the simulations as described in Figures 7 and 8. The total numbers of alanine and threonine residues included in this analysis are 357 and 351, respectively.