The Ramachandran plots of glycine and pre-proline

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>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<jats:sub>i+1</jats:sub> or O atom is sandwiched between the two H<jats:sup>α</jats:sup> atoms of glycine. We show that the shape of the 5 distinct regions of density (the α, α<jats:sub>L</jats:sub>, β<jats:sub>S</jats:sub>, β<jats:sub>P</jats:sub> and β<jats:sub>PR</jats:sub> 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<jats:sub>i-1</jats:sub>···C<jats:sup>δ</jats:sup>H<jats:sup>δ</jats:sup> <jats:sub>i+1</jats:sub> weak hydrogen bond. This is analogous to the CO<jats:sub>i-1</jats:sub>···NH<jats:sub>i+1</jats:sub> hydrogen bond that stabilizes the γ region in the generic Ramachandran plot.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion</jats:title> <jats:p>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.</jats:p> </jats:sec>