Ramachandran plot

In

One might expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot, but the effect of side chains is small.[5] In practice, the major effect seen is that of the presence or absence of the methylene group at Cβ.^[5] Glycine has only a hydrogen atom for its side chain, with a much smaller van der Waals radius than the CH₃, CH₂, or CH group that starts the side chain of all other amino acids. Hence it is least restricted, and this is apparent in the Ramachandran plot for glycine (see Gly plot in gallery) for which the allowable area is considerably larger. In contrast, the Ramachandran plot for proline, with its 5-membered-ring side chain connecting Cα to backbone N, shows a limited number of possible combinations of ψ and φ (see Pro plot in gallery). The residue preceding proline ("pre-proline") also has limited combinations compared to the general case.

More recent updates

The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was determined (myoglobin, in 1960^[6]), although the conclusions were based on small-molecule crystallography of short peptides. Now, many decades later, there are tens of thousands of high-resolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank (PDB). Many studies have taken advantage of this data to produce more detailed and accurate φ,ψ plots (e.g., Morris et al. 1992;^[7] Kleywegt & Jones 1996;^[8] Hooft et al. 1997;^[9] Hovmöller et al. 2002;^[10] Lovell et al. 2003;^[11] Anderson et al. 2005.^[12] Ting et al. 2010^[13]).

The four figures below show the datapoints from a large set of high-resolution structures and contours for favored and for allowed conformational regions for the general case (all amino acids except Gly, Pro, and pre-Pro), for Gly, and for Pro.^[11] The most common regions are labeled: α for α helix, Lα for left-handed helix, β for β-sheet, and ppII for polyproline II. Such a clustering is alternatively described in the ABEGO system, where each letter stands for α (and 3₁₀) helix, right-handed β sheets (and extended structures), left-handed helixes, left-handed sheets, and finally unplottable cis peptide bonds sometimes seen with proline; it has been used in the classification of motifs^[14] and more recently for designing proteins.^[15]

While the Ramachandran plot has been a textbook resource for explaining the structural behavior of peptide bond, an exhaustive exploration of how a peptide behaves in every region of the Ramachandran plot was only recently published (Mannige 2017^[16]).

The

One can also plot the dihedral angles in polysaccharides (e.g. with CARP).^[19]

Gallery

• 
  Ramachandran plot for the general case; data from Lovell 2003
• 
  Ramachandran plot for Glycine
• 
  Ramachandran plot for Proline
• 
  Ramachandran plot for pre-Proline

Software

• Web-based Structural Analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB
• Web-based tool showing Ramachandran plot of any PDB entry
• MolProbity web service that produces Ramachandran plots and other validation of any PDB-format file
• SAVES (Structure Analysis and Verification) — uses WHATCHECK, PROCHECK, and does its own internal Ramachandran Plot
• STING
• Pymol
  with the DynoPlot extension
• VMD, distributed with dynamic Ramachandran plot plugin
• WHAT CHECK, the stand-alone validation routines from the WHAT IF software
• UCSF Chimera, found under the Model Panel.
• Sirius
• Swiss PDB Viewer
• TALOS
• Zeus molecular viewer — found under "Tools" menu, high quality plots with regional contours
• Procheck
• Neighbor-Dependent and Neighbor-Independent Ramachandran Probability Distributions^[13]
• See also PDB for a list of similar software.

References

Further reading

• Richardson, J.S. (1981). "The Anatomy and Taxonomy of Protein Structure". Anatomy and Taxonomy of Protein Structures. Advances in Protein Chemistry. Vol. 34. pp. 167–339.
  PMID 7020376., available on-line at Anatax^{[permanent dead link}
  ]
• Branden, C.-I.; Tooze, J. (1991), Introduction to Protein Structure, Garland Publishing, NY,
  ISBN 0-8153-0344-0

External links

Wikimedia Commons has media related to Ramachandran plot.

• DynoPlot in PyMOL wiki
• Link to Ramachandran Plot Map of alpha-helix and beta-sheet locations
• Link to Ramachandran plot calculated from protein structures determined by X-ray crystallography compared to the original Ramachan.
• Proteopedia Ramachandran Plot