I have read that Ramachandran plots are used to identify secondary structures of proteins. Also, alpha helices and beta strands cluster around specific regions of the plot which gives us the information about how much of these structures are present in the protein. But, it seems intuitively unreasonable. I can't convince myself "why there can't be other structures with the same torsion angles as alpha helices or beta sheets". Am I missing something?

  • $\begingroup$ Perhaps you are missing time with a suitable text book. Try Dickerson and Geis. Long out of print but you might pick up one second-hand if it isn’t in your university library. And this list can hardly respond to your intuition, other than to suggest you do not put too much trust in it. $\endgroup$ – David Jan 12 at 20:37
  • $\begingroup$ Thanks Dave!!!! $\endgroup$ – incredible sulk Jan 13 at 5:47
  • $\begingroup$ There is some information on Ramachandran Plots that you may find useful in an answer I posted to another question. $\endgroup$ – David Jan 17 at 13:48
  • $\begingroup$ The problem with your question is that you do not quote a source, so it is impossible to know what is meant by Ramachandran plots being used to identify secondary structure of proteins. Why? Because a Ramachandran plot made up of all the amino acids in a protein requires knowledge of the dihedral angles of each amino acid, and so can only be plotted for a protein if its 3D structure is known — in which case the secondary structure is evident as it is defined in terms of repeating dihedral angles. So what do you mean? Some kind of blind recognition quiz? You need to clarify your question. $\endgroup$ – David Jan 17 at 13:54

Its not true that the Ramachandran plot will determine the secondary structure of an amino acid.

Ramachandran plots show the sterically allowed phi/psi angles of an amino acid. As such nearly all non-glycine amino acids are in alpha/beta spaces. Random coil segments of structure consist mostly of alpha and beta conformation amino acids in nonsense orders. (alpha/beta/beta/alpha/alpha and etc)

The dihedral angles repeated in a pattern over a several consecutive amino acids create secondary structure (N>4 or 7 for helices - strands need other strands forming sheets).

  • $\begingroup$ Okay. That was helpful! Thank you! $\endgroup$ – incredible sulk Jan 13 at 5:48
  • $\begingroup$ So, is it possible for two amino acids to have the same sterically allowed phi/psi angles ? $\endgroup$ – incredible sulk Jan 13 at 6:33
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    $\begingroup$ all the amino acids except for glycine have pretty much the same allowed phi/psi angles :) . glycine, having a hydrogen on the alpha carbon rotates much more freely. IN a polypeptide the allowed angles will change depending on the rest of the peptide... this is not as predictable.. $\endgroup$ – shigeta Feb 27 at 19:22

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