The Ramachandran plots of glycine and pre-proline

BACKGROUND: The Ramachandran plot is a fundamental tool in the analysis of protein structures. Of the 4 basic types of Ramachandran plots, the interactions that determine the generic and proline Ramachandran plots are well understood. The interactions of the glycine and pre-proline Ramachandran plots are not. RESULTS: In glycine, the ψ angle is typically clustered at ψ = 180° and ψ = 0°. We show that these clusters correspond to conformations where either the N(i+1 )or O atom is sandwiched between the two H(α) atoms of glycine. We show that the shape of the 5 distinct regions of density (the α, α(L), β(S), β(P )and β(PR )regions) can be reproduced with electrostatic dipole-dipole interactions. In pre-proline, we analyse the origin of the ζ region of the Ramachandran plot, a region unique to pre-proline. We show that it is stabilized by a CO(i-1)···C(δ)H(δ)(i+1 )weak hydrogen bond. This is analogous to the CO(i-1)···NH(i+1 )hydrogen bond that stabilizes the γ region in the generic Ramachandran plot. CONCLUSION: We have identified the specific interactions that affect the backbone of glycine and pre-proline. Knowledge of these interactions will improve current force-fields, and help understand structural motifs containing these residues.