These pages shows how to use python to extract a protein backbone's psi/phi torsion angles (ϕ,ψ) from a PDB file in order to draw a Ramachandran plot.

The Ramachandran plot is the 2d plot of the ϕ-ψ torsion angles of the protein backbone. It provides a simple view of the conformation of a protein. The ϕ-ψ angles cluster into distinct regions in the Ramachandran plot where each region corresponds to a particular secondary structure. 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 generic and proline Ramachandran plots are now well understood...

Quote from the introduction of Ho and Brasseur (2005), see references. See also other tools/programs for Ramachandran Plots.

• Step One - Calculating the angles (using MMTK or BioPython)
• Step Two - Drawing the Ramachandran Plot (using R via RPy)

The above page on drawing the plot loads a datafile from Lovell et al. (see references) which defines "allowed" and "favoured" regions, and uses this to colour the background of the diagram.

I tried to repeat the analysis by Lovell et al (2003) of their Top 500 high resolution PDB files to build the required density profile. However, my set of phi/psi angles didn't seem to match up all that closely (without even worrying about the data smoothing to generate the density profile). In the end, I was able to get in touch with the group and they sent me the relevant data files (which are now on their website).

References

GN Ramachandran et al. (1963). Stereochemistry of polypeptide chain configurations. J Mol Biol 7, 95-99. (PMID: 13990617)

GJ Kleywegt and TA Jones (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395-1400. (PMID: 8994966, website)

SC Lovell et al. (2003). Structure Validation by Cα Geometry: ϕ, ψ and Cβ Deviation. Proteins 50, 437-450. (PMID: 12557186, website)

BK Ho and R Brasseur (2005). The Ramachandran plots of glycine and pre-proline. BMC Structural Biology 5(14) (2005-09-09) (PMID: 16105172)

Python

 

Protein Data Bank (PDB)

 

The Molecular Modelling Toolkit (MMTK)

 

Biopython

 

The R Project

 

RPy (R from Python)