Backbone representations

Protein Main Chain

Lets begin with (15 amino acids)^[1] The atoms and bonds are colored by element: C H O N.

• First, we'll simplify by . Hydrogen atoms make up almost exactly 50% of the atoms in proteins.

• Next, we'll simplify by . What remains is called the main chain. Each amino acid's main chain atoms are N-C-C, where the first C is the alpha carbon (shown as a ball), and the second, the carboxyl carbon with its double-bonded oxygen (double bonds not shown). We could also , leaving only the atoms that are part of the main chain, also called the backbone.

Protein Backbone Trace

: Now we'll draw a  yellow line  between alpha carbons (balls). This line is called a  backbone trace . Note that the backbone trace does not follow any actual covalent chemical bonds -- it simply connects alpha carbon positions, thereby simplifying the representation.

• makes the backbone trace even clearer.

• Here is the .

Smoothed Protein Backbone Trace

A is another common backbone representation. Here, the  smoothed backbone trace is green .

• Here is the .

Ribbon Backbone Trace

Perhaps the most common protein backbone representation is the . Here the  ribbon is violet , the standard secondary structure color for alpha helices. As you can see, the ribbon is a smoothed backbone trace expanded in width. The arrowhead at one end points to the carboxyl terminus.

• Here is the .

• Here the .

Protein Domain Example

Now lets look at a (1pgb). This domain contains the alpha helix used above, but also contains a small beta sheet made of four beta strands, plus loops (regions that are neither alpha helix nor beta strand) connecting the helices and strands. The helices and strands are represented as ribbons, while the "ropes" connecting them are smoothed backbone traces. This type of representation is properly called a secondary structure schematic, but is called a cartoon in Jmol and its family of ancestral visualization programs (RasMol, Chime). Arrowheads point towards the carboxy terminus.

• A such a ribbon representation is with a spectral sequence of colors from the amino (N) terminus to the carboxy (C) terminus. (Proteins are synthesized by adding amino acids to the C terminus.) This color scheme is called N->C Rainbow. Notice how the arrowheads point towards the C terminus.

• Next, lets :

Alpha Helices,  Beta Strands ,  Loops .

• For comparison, here are .

• Here are the , without the ribbon.

• A simple for this small domain.

• The domain .

• The .