Molecular visualization of an idealized protein alpha helix

This web page uses the open-source Java Applet program Jmol, a proposed platform-independent replacement for Chime and Rasmol, neither of which is available in an OS X native version. You will need a relatively recent Java Virtual Machine to use it.

The buttons below are generally intended to be clicked in order.

This is an idealized alpha helix, via InsightII. The initial coloring is blue->red N-terminus to C-terminus. The second button highlights the C=O --- H-N i -> i+4 hydrogen bonding along the backbone in green. The third button emphasizes that approximately every fourth (3.6th/7.2th) residue lines up on one side of the helix. The spacefill button shows that there is no hole down the middle.

Click here for the same alpha helix in a real protein (the GCN4-DNA complex).

Click here for the idealized beta sheet.

Click here for the same beta sheet in the protein tendamistat.
Teaching resources. J. Kahn home page.