User:Robert Dutnall/Sandbox 1 alpha helix
From Proteopedia
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::Right click to bring up an options menu | ::Right click to bring up an options menu | ||
| - | ==An | + | ==An α-helix== |
| - | + | ||
| + | This is a 19 amino acid chain in α-helical conformation. | ||
<Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/> | <Structure load='Tut_alpha_helix.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_load/1'/> | ||
| - | This is a 19 amino acid chain in alpha helical conformation. | ||
| - | 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_load'>Click here at any time to return to this view.</scene> | ||
| - | + | 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> | |
| - | + | 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> | |
| - | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/ | + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_ribbon/2'>Click here to add a ribbon to define the path of the mainchain. </scene> You should be able to see that is helical with a right-handed twist. |
| - | + | ||
| - | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/ | + | 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, <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_axis/1'>click here </scene>to zoom in and look down the helix axis from the N-terminal end. | ||
| + | |||
| + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_mainchain_label_hbonds/3'>Click here to zoom out again and add hydrogen bonds for the mainchain (dashed purple lines).</scene> 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 | More text here | ||
| + | |||
| + | <scene name='User:Robert_Dutnall/Sandbox_1_alpha_helix/A_helix_sidechains/2'>Click here to show the side chains again.</scene> 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? | ||
= = | = = | ||
Revision as of 17:10, 25 August 2011
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.
|
All the atoms are shown in this initial orientation (C = green; N = blue; O = red; S = yellow; H = white).
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?
