Ramachandran

We already mentioned that there is a relation between the side chain and the backbone. In Bioinformatics 1 we discussed how steric hindrance makes β-branched residues good for β-strands, and how the entropy of water makes AMELKQ good α-helix residues.

We also learned that Asp, Asn and Ser are good at forming hydrogen bonds with the own backbone (and, partly, because of that are good for β-turns, and in general are bad for α-helices and β-strands.

In the next twenty plots you see each time four Ramachandran plots. These plots were determined for amino acids in well-solved protein structures (i.e. solved at high resolution and considered good structures by the PDBREPORT).

In each picture you see in the top left the Ramachandran plot for all residues that DSSP calls a α-helix, top right β-strand, bottom left turn (not the very specific β-turn, but turn in general), and bottom right loop.

Study these plots. Search for things that different residues have in common, and things where similar residues differ. Think about the difference in 'density' between the four secondary structures of one amino acid. Think about differences in spread in and around the preferred areas. While thinking about this think also about the entropy of water, about hydrogen bonds with the own backbone, etcetera.

• Ala (Click on the plots for an enlargement)

• Cys

• Asp

• Glu

• Phe

• Gly

• His

• Ile

• Lys

• Leu

• Met

• Asn

• Pro

• Gln

• Arg

• Ser

• Thr

• Val

• Trp

• Tyr

Feel free to look at these videos before or after answering the questions: , and .

Question 21:

• Which residues are seen most often around the left handed helix area?
• Which residue is most restricted overall?
• Compare the highly similar residues Asp and Glu. Try to explain both the coarse and the subtle differences.
• Look at proline and analyze the β-strand plot. You will see a few prolines in areas where they don't belong, like the helix area. Explain how they got there. Think about the fact that we did not make these plots by hand...
• What is 'wrong' with the contour lines of the island in the top-right corner of each plot (called left handed helix or +/+ area)? And why is this not an error?