Choose the Best-Fit R-Group:
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.