The second most popular a.a. side chain conformations
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The conformation of a protein's main chain is essentially defined by
pointing two dihedral angles - φ and ψ. A similar description applies
for amino acid (a.a.) side chains: if they contain singlets of bonds
around which parts of the molecule can rotate, these bonds the
characterising dihedral angles may vary. The question arises, oh what
are the most common values of these angles?

Analyse the distribution of side chain dihedral angles of the *second*
most abundant a.a. side chain in the PDB. Pick and a.a. to which side
chain conformation analysis applies (i.e. drop Gly and Ala from the
"popularity contest" - why?).

Questions you found a.a.:

- what is this a.a.?

- what are the side chain angle regions most commonly found in the
  PDB?  Why?

- whether the a.a. of the type you found, whose side chains are found
  have rare conformations? Why do these conformations occur? What is
  their biological significance? Are these errors in solving/describing
  structures or real facts of nature?

- What statistical parameters best describe your a.a. side chain angle
  distribution? Why?

Program:

This research requires a program that reads PDB archive files and
determines and outputs side chain torsion angles for the a.a. that
you are interested in.