![]() The generic Ramachandran plot was first explained by Ramachandran and co-workers in terms of steric clashes. The generic and proline Ramachandran plots are now well understood but the glycine and pre-proline Ramachandran plots are not. There are four basic types of Ramachandran plots, depending on the stereo-chemistry of the amino acid: generic (which refers to the 18 non-glycine non-proline amino acids), glycine, proline, and pre-proline (which refers to residues preceding a proline ). The φ-ψ angles cluster into distinct regions in the Ramachandran plot where each region corresponds to a particular secondary structure. It provides a simple view of the conformation of a protein. The Ramachandran plot is the 2d plot of the φ-ψ torsion angles of the protein backbone. Knowledge of these interactions will improve current force-fields, and help understand structural motifs containing these residues. We have identified the specific interactions that affect the backbone of glycine and pre-proline. NH i+1 hydrogen bond that stabilizes the γ region in the generic Ramachandran plot.We show that it is stabilized by a CO i-1 In pre-proline, we analyse the origin of the ζ region of the Ramachandran plot, a region unique to pre-proline. 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. 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. In glycine, the ψ angle is typically clustered at ψ = 180° and ψ = 0°. The interactions of the glycine and pre-proline Ramachandran plots are not. Of the 4 basic types of Ramachandran plots, the interactions that determine the generic and proline Ramachandran plots are well understood. The Ramachandran plot is a fundamental tool in the analysis of protein structures.
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