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Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

Figure 9

Neighbor-dependent effects.

A. ILE (left) – ALA (center conformation A, coil, PDB entry 1N55, residue 69 of chain A). Ile likely prevents H-bond acceptor to Ni+1. B. VAL (right) – ARG (cent, A, coil, 2FWH_527A). Val likely prevents H-bond donor to Oi−1. C. ASN (left) – SER (cent, A, coil, 3C8W_9A). Asn forms hydrogen bond to Ni+1. D. PRO (right) – ARG (cent, A, coil, 2RKV_296A). Very close steric bump of Pro CD with Ni. E. PHE (left) – SER (cent, B, coil, 2GS8_248A). Favorable hydrophobic interaction with Tyri+1. F. TYR (right) – PRO (cent, P, turn, 3CA8_34A). Tyr unfavorable electro. interaction with Oi−1.

Figure 9

doi: https://doi.org/10.1371/journal.pcbi.1000763.g009