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.
Smoothed Protein Backbone Trace
A is another common backbone representation. Here, the smoothed backbone trace is green .
Ribbon Backbone Trace
Perhaps the most common backbone representation is the . Here the ribbon is violet , the standard secondary structure color for alpha helices.
Backbone Trace
