Figure 2.

The UNRES model of polypeptide chains. The interaction sites are peptide-bond centers (p), and side-chain ellipsoids of different sizes (SC) attached to the corresponding α-carbons with different “bond lengths”, b_SC. The α-carbon atoms are represented by small open circles. The equilibrium distance of the C^α…C^α virtual bonds is taken as 3.8 Å, which corresponds to planar trans peptide groups. The geometry of the chain can be described either by the virtual-bond vectors dC_i (C^α_i…C^α_i+1), i = 1, 2,…, N - 1 and dX_i (C^α_i…SC_i), i = 2, 3,…, N - 1 (represented by thick dashed arrows), where N is the number of residues, or in terms of virtual-bond lengths, backbone virtual-bond angles θ_i, i = 2, 3,…, N - 1, backbone virtual-bond-dihedral angles γ_i, i = 2, 3,…, N - 2, and the angles α_i and β_i, i = 2, 3,…, N - 1 that describe the location of a side chain with respect to the coordinate frame defined by C^α_i-1, C^α_i and C^α_i+1. The angles κ_i used here are complements of the θ_i angles, i.e., π − θ_i.