How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?

Question

We are working on an algorithm to assign proteins only on the basis of alpha-carbons.

My teacher told me to draw a diagram to represent hydrogen bonds only on the basis of alpha-carbons.

I showed him the following picture:

He said this picture doesn't count, as this diagram shows all the atoms.

I couldn't figure out how to do this without showing oxygen, non-alpha-carbon, and nitrogen atoms.

How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?

Answer 1

There are three options:

1. it's a badly phrased Ramachandran plot question
2. it's a question aimed at the describing the properties of different SS
3. it's a trick question

φ & ψ can be used to classify SS (cf. Ramachandran plot), these are however proper dihedrals, so require 4 atoms, which you lack.

The sequential Cαs in a strand are increasingly distant by 3–4Å, while in a helix there's a periodicity every 3–4 residues. The images you were given are likely to remind you that between two strands in a sheet the Cαs are ~5Å away from the other strand, but the order is different —the indices will increase together in parallel strands, but not in anti-parallel strands.

A C-alpha trace has the issue that the residues are often not known (UNK is technically represented as homoalanine, but is an unknown) and the resolution is > 4Å. Any SS allocation will be highly inaccurate making it a trick question.