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 .

• 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 backbone representation is the . Here the  ribbon is violet , the standard secondary structure color for alpha helices.

• Here is the .

• Here the .

Backbone Trace