Backbone representations: Difference between revisions

Revision as of 20:09, 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.

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 1: / Line 1: @@
-<StructureSection load='1pgb' size='400' side='right' caption='' scene=''>
+Backbone representations are simplified 3D depictions of proteins or nucleic acids that enable the polymer chain structure to be seen.
-==Main Chain==
+<StructureSection load='' size='400' side='right' caption='' scene='59/599354/Helix/1'>
-<scene name='59/599354/Helix/1'>all atoms</scene>
-<scene name='59/599354/Helix/2'>no h</scene>
+==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.
+*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.
+*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.
+==Protein Backbone Trace==
-<scene name='59/599354/Helix/3'>no sides</scene>
-<scene name='59/599354/Helix/4'>no o</scene>
 <scene name='59/599354/Helix/5'>backbone</scene>