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I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file:

HELIX    4   4 MET A 255  ILE A  265  1                                  11    

SHEET    2   B 2 ILE A 253  MET A 255 -1  N  ILE A 253   O  ILE A 248           

Now, as I understand the documentation, this means there is an alpha helix starting from residue "MET A 255" to the residue "ILE A 265". There is also a beta strand from "ILE A 253" to "MET A 255". We see that the alpha helix and beta strand share the residue "MET A 255".

The documentation describes these as:

  • "Name of the initial residue."
  • "Name of the terminal residue of the helix."

The wording suggests that the "initial" residue is included, but I'm unsure of whether or not the "terminal" residue would be included.

Question: Should I consider this residue as belonging to both the alpha helix and beta strand? Or should I consider the "terminal" residue as not belonging to the secondary structure element? (Or something else?)

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ive seen records like this although it does not seem possible as alpha and beta have distinct ramachandran coordinates. i'll try to look at the structure and post an answer/opinion. a quick way around this is to find the phi/psi values for the amino acids in question and make the call yourself. –  shigeta Aug 1 '12 at 16:46

1 Answer 1

This is almost more a philosophical question about how you would like to define helices and sheets, which I would argue is not so well defined. shigeta mentions that they have well defined ramachandran coordinates, but that's for the central residues. Terminal residues are far more flexible. The more traditional definition is along the lines of the DSSP algorithm, i.e. what is their main-chain hydrogen bonding pattern.

The DSSP algorithm is a bit conservative about assignments, often leaving out the first and last residues in both sheets and helices. In deposited structures, you can compare author annotations to DSSP and STRIDE and see the authors will often assign longer runs than either. And I have certainly seen structures where a residue is annotated as both, especially when it lies at the junction between two secondary structure elements.

Looking at the structure, residues 254 and 255 are clearly hydrogen bonding into a beta-sheet on one side and an alpha helix on the other, so I see no reason they shouldn't be annotated into both.

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