Backbone representations: Difference between revisions

Revision as of 20:13, 19 September 2014

Backbone representations are simplified 3D depictions of proteins or nucleic acids that enable the polymer chain structure to be seen.

Here is a small alpha helix (15 amino acids)^[1] In the , all atoms are shown, 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, 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.

@@ Line 5: / Line 5: @@
 ==Protein Main Chain==
-Here is a small alpha helix (15 amino acids)<ref>Residues 23-37 from [[1pgb]].</ref> In the <scene name='59/599354/Helix/1'>initial scene</scene>, all atoms are shown.
+Here is a small alpha helix (15 amino acids)<ref>Residues 23-37 from [[1pgb]].</ref> In the <scene name='59/599354/Helix/1'>initial scene</scene>, all atoms are shown, colored by element:
+<font style="font-size:150%;">{{Template:ColorKey_Element_C}}
+{{Template:ColorKey_Element_H}}
+{{Template:ColorKey_Element_O}}
+{{Template:ColorKey_Element_N}}</font>.
-*First, we'll simplify by <scene name='59/599354/Helix/2'>hiding the hydrogen atoms</scene>. [[Hydrogen]] atoms make up almost exactly 50% of the atoms in proteins.
+*First, we'll simplify by <scene name='59/599354/Helix/2'>hiding the hydrogen atoms</scene>. [[Hydrogen in macromolecular models|Hydrogen]] atoms make up almost exactly 50% of the atoms in proteins.
 *Next, we'll simplify by <scene name='59/599354/Helix/3'>hiding the amino acid side chains</scene>. 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, and the second, the carboxyl carbon with its double-bonded oxygen (double bonds not shown). We could also <scene name='59/599354/Helix/4'>hide the oxygen atoms</scene>, leaving only the atoms that are part of the '''main chain''', also called the backbone.