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?)