spin once Magnify Reduce Cutaway view

Sharpness (slower but prettier)   Background:


Amino Acid vs. Protein

On the left is one subunit (monomer) of hemoglobin. For perspective, take a look at a single amino acid--histidine in this case, since this amino acid will be central to our later discussions.
reveal histidine  

To rotate, click and drag on it. This will help you to see the amino acid clearly. There's nothing like doing it yourself to get a sense of the molecule in 3D! (To zoom in or out, hold down the shift key while dragging down or up.)
You can do this with any image throughout this tutorial

In terms of scale, most proteins are made up of 100-400 amino acids.

entire protein

Representations of Proteins

In order to focus on different aspects of a structure, a number of ways of representing a 3-dimensional protein molecule have been developed. These are called

Spacefilling mode (initial view; atoms represented by spheres) is used to 'realistically' represent the actual space taken up by a protein and its parts) Note that all internal detail is invisible, but you get a real feel for the surface of the protein.

Sticks mode (used to emphasize side chains of the amino acids and the precise position of individual atoms) Note our buddy histidine again.

Rockets mode (Provides a solid representation of the backbone elements of alpha helices and beta sheets; adds arrowheads to indicate N => C-terminal direction).

Ribbons mode (used to highlight secondary structure elements). A conceptual ribbon is wound through the backbone of the protein (consisting of the amino group, alpha carbon, and carboxyl group of each amino acid). Note how clearly you can see the alpha helices (coiled elements); it also gives you a quick grasp of the path the protein chain takes. Hemoglobin has no beta-sheet structure; these would appear as parallel, flattened ribbons.

His in helix Highlight the helix containing the histidine we've been watching.

Ball & stick mode Show the aforementioned histidine in a ball and stick representation.