In this section of the practical you will investigate what can be learned from looking at the Ramachandran plots representing some protein structures. First look at your lecture notes to refresh your mind about what a Ramachandran plot is!
The PDBsum website provides a lot of information about each known protein structure. All known structures are stored in various on-line databases including PDBsum and referred to by a 4-character PDB code e.g. 3PAT, 4FXN etc. Information available on PDBsum includes a Ramachandran plot which shows the phi and psi angles of each of the amino acids in the structure. To go to the PDBsum website click here.
You are going to investigate two protein structures: parvalbumin (PDB code 3PAT) and an immunoglobulin binding domain (PDB code 1IGD). If you can, work in pairs, so that one of you investigates each structure.
For the structure you are investigating, type the 4 character PDB code into the box and click the 'Find' button. You should be taken to a page showing information about the protein, including a schematic ribbon diagram in the top left hand corner, and a Ramachandran plot on the right hand side with 'Procheck' above it.
First look at the ribbon diagram. What type of structure is this? Where would you expect the phi and psi angles for this protein to be? Then click on the Ramachandran plot to get an enlarged image. There is one blue square to represent the phi and psi angle of each residue in the protein. Is the distribution what you expected based on the secondary structure?
Now compare the Ramachandran plots for the two structures. In addition to the difference in secondary structures of the two proteins, there is also a difference in quality of the two structures. Can you see differences between the two Ramachandran plots which reflect the qualities of the two structures?