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 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.
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 Jmo and its family of visualization programs (RasMol, Chime). Arrowheads point towards the carboxy terminus.
Alpha Helices,
Beta Strands ,
Loops .
- For comparison, here are .
- Here are the , without the ribbon.
- A simple for this small domain.
