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 psi angle is typically clustered at psi = 180 degrees and psi = 0 degrees. We show that these clusters correspond to conformations where either the Ni+ 1 or O atom is sandwiched between the two H-alpha atoms of glycine. We show that the shape of the 5 distinct regions of density ( the alpha, alpha(L), beta(S), beta(P) and beta(PR) regions) can be reproduced with electrostatic dipole- dipole interactions. In preproline, we analyse the origin of the zeta region of the Ramachandran plot, a region unique to preproline. We show that it is stabilized by a COi-l center dot center dot center dot (CH delta)-H-delta (i+l) weak hydrogen bond. This is analogous to the COi-1 center dot center dot center dot NHi+ 1 hydrogen bond that stabilizes the gamma 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.