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Suppose, the following is a diagram of a protein's polypeptide chain:

enter image description here

What does this diagram represent?

  1. What are the letters A, E, M, W, L, N, S, etc. represent? (I suppose these are amino acid codes. Right?)
  2. Which one is the c-alpha atom here?
  3. What are the sequence numbers i-2, i-1, i, i+1, i+2, etc. represent? Why there are negative and positive increments from i?

The following is a related diagram:

enter image description here

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    $\begingroup$ 1. Yes, 2. it's a schematic with a whole residue was a circle —from Voet and Voet IIRC. 3. Residue i is the one in focus, the reference. i-1 is the preceding residue. Have a gander at en.m.wikipedia.org/wiki/Turn_(biochemistry) where this type of relative notation is important. $\endgroup$ Aug 22 at 6:50
  • $\begingroup$ is this from a school or university assignment? $\endgroup$ Aug 24 at 2:31
  • $\begingroup$ @user3479780, this is not an assignment. this is a personal study for data analysis. $\endgroup$
    – user366312
    Aug 24 at 2:35
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  1. Yes, the letters are amino acids
  2. It's a schematic with a whole residue as a circle —possibly from Voet and Voet.
  3. Residue i is the one in focus, the reference. i-1 is the preceding residue. Have a gander at en.wikipedia.org/wiki/Turn_(biochemistry) where this type of relative notation is important.

The diagram shows how secondary structure (helices, sheets etc.) affect the distance between the residues. In a helix a residue 3 positions down will be close, but not in a sheet.

However, for assignment of secondary structure it may be easier to look at the φ and ψ angles:

  • α helix: phi=-57.8, psi=-47.0
  • π helix: phi=-57.1, psi=-69.7
  • 3.10 helix: phi=-74.0, psi=-4.0
  • β sheet: phi=-139, psi=+135

Although these have a range and you can get π bulges within α helices —important for conformation switching for pore opening (capsaicin binding to TRPV1 is a classic example).

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