User:Stephen Mills/Secondary Structure: Sheets: Difference between revisions

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<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?

<scene ~~name~~='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>~~Click here~~ to ~~add hydrogen bonds for~~ the ~~mainchain (dashed lines)~~.~~</scene>~~ The hydrogen bonds connect backbone NH groups ~~and~~ C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

==H-bonds in Parallel Sheets==

Hydrogen bonds have now been added to the structure. The hydrogen bonds connect backbone NH groups of one strand with the C=O groups of another. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).

You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>

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If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.

==Anti-Parallel β-sheet==

@@ Line 25: / Line 25: @@
 <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels/6'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. What is the orientation of these groups with respect to the long axis of each strand? What the orientation of these groups with respect to the flat plane of the sheet?
+<br/><br/><br/><br/><br/><br/><br/><br/><br/><br/>
-<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'>Click here to add hydrogen bonds for the mainchain (dashed lines).</scene> The hydrogen bonds connect backbone NH groups and C=O groups. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).
+==H-bonds in Parallel Sheets==
+<Structure load='Tut_parallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb/5'/>
+Hydrogen bonds have now been added to the structure. The hydrogen bonds connect backbone NH groups of one strand with the C=O groups of another. The N-H group is the hydrogen bond donor, the oxygen in the C=O group is the acceptor (N-H--->O=C). Each hydrogen bond is approximately 3.0 Angstroms (0.3 nm) in length (measured between the N and the O).
 You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain (because of the almost fully extended conformation). The strands line up in the sheet so that the NH and C=O groups are parallel to plane of the sheet and lie opposite each other in pairs. This means that hydrogen bonds can be made between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_mainchain_labels_hb_z/5'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene>
@@ Line 37: / Line 40: @@
 If we apply this to all the strands (<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Parallel_sidechains_alt/2'>click here</scene>) you can see that all the sidechains above the plane of the sheet are purple, and all those below are blue.
 ==Anti-Parallel β-sheet==