Email updates

Keep up to date with the latest news and content from BMC Structural Biology and BioMed Central.

Open Access Highly Accessed Open Badges Research article

The Ramachandran plots of glycine and pre-proline

Bosco K Ho1* and Robert Brasseur2

Author affiliations

1 Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, San Francisco, CA 94107, USA

2 Centre de Biophysique Moléculaire Numérique, 2 Passage des déportés, B-5030 Gembloux, Belgium

For all author emails, please log on.

Citation and License

BMC Structural Biology 2005, 5:14  doi:10.1186/1472-6807-5-14

Published: 16 August 2005



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.


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 Ni+1 or O atom is sandwiched between the two Hα atoms of glycine. We show that the shape of the 5 distinct regions of density (the α, αL, βS, βP and βPR 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 COi-1···CδHδi+1 weak hydrogen bond. This is analogous to the COi-1···NHi+1 hydrogen bond that stabilizes the γ region in the generic Ramachandran plot.


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.