Backbone representations

THIS ARTICLE IS UNDER DEVELOPMENT AND IS CURRENTLY INCOMPLETE. Eric Martz 20:18, 19 September 2014 (IDT)

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 (balls) but the  backbone trace line  does not coincide with any of the covalent bonds in the main chain ().

Protein Main Chain Lets begin with (15 amino acids) 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 .

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