Helix-turn-helix (lambda repressor)
DNA binding is mediated by an 'inserted' alpha helix, as occurs in all three of our proteins

 

 

 

rendering options:
unsigned Jmol applet
signed Jmol applet
JSmol (HTML5 only) Works on iPad! But use 'low power' setting @ lower left
JSmol (WebGL)

Useful Link for Amino Acid Feels: http://blc.arizona.edu/courses/181Lab/surfaces/index.html

Repressor (a DIMER) with DNA

Color one monomer orange

Show monomer sidechain interactions (one helix & its carbons orange; other cyan

Gln44 and dA4 + dA24

Gln44 and adenine focus

Gln44 and both Lys4 interacting with bases

Gln44 and both Lys4 interacting with bases (slab)

image display faster sharper
Processor power (choose SMALLER number if everything is laggy):
8 (fast machine)   7  6  5  4  3  2  1 (iPad or pokey)
spacefill wire ball&stick cartoons fancy not flat
color atomno color cpk color structure

console
Instructions

Commands & Interactions
*To find out what atom you're looking at, hover the mouse over it. Amino acids will show up using 3-letter code (i.e. [GLY] = glycine); DNA begins [DT] for thymine, etc.

+Gray represents Hydrophobic. Lt. Purple represents Hydrophilic.

~~~Slab refers to a feature of this program. It allows you to move the molecule making parts of it "transparent" as you move it. This will allow you to better see interactions or lack there of.

General Instructions: To zoom in on the molecule right-click the mouse (Mac Users:Hold down control key and click) and on the drop-down menu select zoom and then the percentage. As well, if needed, certain atoms and parts of the protein can be selected and made a different color. To do this, right click (Mac Users:Hold down control key and click), select the color menu, and then select what you would like to color and what color you would like it to be.

Modified from work by SaraBCarey