Biochemistry Problem Set: X-Ray Question

  Choose the Best-Fit R-Group:

Residue 2:    A   B   C   D
Residue 3:    A   B   C   D
Residue 4:    A   B   C   D

Five Amino Acid Residues in an Electron Density Map.
The Jmol image shows a short polypeptide, of sequence Gly-X-X-X-Gly, within its electron density map. The segment of a protein structure is initially shown as an Ala pentapeptide displayed as Backbone with beta carbons (if appropriate) and colored CPK. The meshwork surrounding the chain simulates the electron density contour from an X-Ray diffraction experiment.

Use the buttons (Labeled A-D) at the right of the model to find the best-fit amino acid residue at each of the three positions (residues 2, 3, and 4). The buttons leave each amino acid selected so that any combination of Display or Color can be used until another amino acid is selected.
(Please note: All 12 of the amino acid possibilities are falsely labeled, "ALA", however, a click on individual atoms will correctly identifiy that atom on the window status line. Note: In newer versions of Firefox, the status bar has been removed. You can identify an atom by mouse roll-over (~1 sec delay). If you want a permanent label, right-click to bring up the menu, go to the "set-picking" menu, and select "label". Changing the background to black may make it easier to see the label.
Submit your proposed best-fit sequence along with an explaination of your approach. Feel free to submit an image of the fitted electron density with your problem set.