User:Robert Dutnall/Sandbox 1 alpha helix
From Proteopedia
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== Biochemistry Tutorial #2 - Secondary Structure == | == Biochemistry Tutorial #2 - Secondary Structure == | ||
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All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). | All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white). | ||
| - | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here to show only the polypeptide mainchain (NH, Cα, and C=O). | + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain/3'>Click here </scene>to show only the polypeptide mainchain (NH, Cα, and C=O). |
Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/3'>Click here to see if you were correct.</scene> | Identify the N- and C-termini. <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label/3'>Click here to see if you were correct.</scene> | ||
Revision as of 17:27, 25 August 2011
"?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar"
Biochemistry Tutorial #2 - Secondary Structure
Blah, blah, blah
Note: in these tutorials, the images are 3D interactive images. You can manipulate them as you wish to get a better view of the molecules.
You can rotate the structure by holding down the right mouse button and dragging.
Other things you can do:
- To rotate: left drag
- To Zoom: scroll button or shift + left drag
- To Translate: ctrl + right drag
- Right click to bring up an options menu
An α-helix
This is a 19 amino acid chain in α-helical conformation.
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All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white).
to show only the polypeptide mainchain (NH, Cα, and C=O).
Identify the N- and C-termini.
You should be able to see that is helical with a right-handed twist.
Click the "toggle spin" button in the box to stop the structure from rotating.
Now use your mouse to rotate the structure to look down the helix axis. If you have any problems with finding this view, to zoom in and look down the helix axis from the N-terminal end.
The hydrogen bonds connect the backbone NH groups and C=O. The N-H group is the donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). More text here
The atoms of each amino side chain have been colored light blue to show them more clearly.
What is the general orientation of the side chains with respect to the helix axis?
