Stereo Vision Exam Questions

   

Molecules are three-dimensional entities and stereo-vision of images on paper and on the screen is one of the most powerful, intuitive ways to appreciate that. We have practiced stero-vision in this course; here are a number of situations that require spatial awareness.

   

2002

This divergent stereo-view shows a trace of connected C^α atoms of a protein domain (the VH domain of the anti-Fluorescein antibody 4-4-20, 4FAB.PDB) and a wireframe representation of all its tryptophan sidechains.

Write down the label of the tryptophan that is a conserved element of the hydrophobic core of this domain.

2002

This divergent stereo-view shows a trace of connected C^α atoms of a Pleckstrin PH domain, 1PLS.PDB

Trace the backbone from the N-terminus to amino acid 52 with pencil or pen in one of the images.

I wouldn't ask this type of question any longer - the drawing task seems a bit convoluted for the actual skill it is supposed to test.

2003

This divergent stereo-view shows selected helices from 1A2J.pdb (DsbA).

The figure was generated with the following RasMol commands:

set background white
set stereo -5
select all
color white
restrict helix and backbone 
wireframe 90
select glu,asp
color [80,80,80]

Mark on this sheet the position of those Asp or Glu residues that are positioned to interact favourably with the helix dipole. If there are several plausible residues in a helix, mark the one closest to the correct terminus.

2003

This divergent stereo-view shows a trace of connected backbone atoms – N, C^α, C and O – as well as the cysteine sidechains of the four disulfide bridges, of the pea defensin 1JKZ.pdb.

Trace the disulfide bonded cysteine sidechains in one of the stereoviews of this picture.