Assignment8

Using Molecular Viewer to see the features of Protein Structure
- To familiar with RasMol
- To understand protein structure features by RasMol commands
- Deadline - 1/2/2002

1. Make a GIF picture of the PDB file that you find in assignment 7
by RasMol. Display it in cartoon form and color it by structure.
Please make the orientation of the molecule just like the molecule
in the picture of assignment 7 - 2.

Ans:

2. Residues Glu173 and Arg177 are possible to form an ion pair
(salt-bridge). (a) Draw a zoom-in picture of this pair. Show these
two residues in sticks and color with cpk. The rest of protein in
backbone form. (b) Measure the distance between Glu173A.OE and
ARG177A.NH.

Ans:

(a)

(b)3.64埃

3. Show a protein fragment with residues 622 to 699 only. Show them
in cartoon form and color with temperature.

Ans:

4. Make a stereo picture for only the atoms within 6.0 Angstrom of
Phe721. Show this residue in green color, others in cpk and all
the residues in wireframe 0.1 format.

Ans: