Backbone representations
From Proteopedia
Backbone representations are simplified 3D depictions of proteins or nucleic acids that enable the polymer chain structure to be seen. In proteins, a simple backbone trace connects alpha carbons (shown as balls in the initial scene) but the backbone trace line does not coincide with any of the covalent bonds in the main chain.
Protein Main ChainLets begin with all atoms of a small alpha helix (15 amino acids)[1] The atoms and bonds are colored by element: C H O N.
Protein Backbone TraceBackbone 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.
Smoothed Protein Backbone TraceA smoothed backbone trace is another common backbone representation. Here, the smoothed backbone trace is green .
Ribbon Backbone TracePerhaps the most common protein backbone representation is the ribbon. 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 ExampleNow lets look at a small protein domain (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.
Alpha Helices, Beta Strands , Loops .
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See Also
- Introduction to molecular visualization
- Secondary structure which has links to other pages with details on alpha helices, beta sheets, and turns.