User:Stephen Mills/Secondary Structure: Sheets: Difference between revisions
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<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds. | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antiparallel_mainchain_labels/1'>Click here to start the structure spinning again.</scene> Look at the structure carefully and identify the mainchain NH and C=O groups. In each strand the mainchain NH and C=O groups point to opposite sides of the mainchain. The strands line up in the sheet so that these NH and C=O groups are parallel to plane of the sheet and lie opposite each other so that they can make hydrogen bonds. | ||
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<scene | ==H-bonds in antiparallel sheets== | ||
<Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'/> | |||
I'll reset the structure and add hydrogen bonds. 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). | |||
You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene> | You should be able to see that the mainchain NH and C=O groups are involved in hydrogen bonds between the strands of the sheet. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds_z/1'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene> | ||
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The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue. | The side chains are approximately perpendicular to the flat plane of the sheet. Along each strand, the side chains alternate direction (above the plane, below the plane, above the plane...) so you should be able to see that all the sidechains above the plane of the sheet are purple, and all those below are blue. | ||
==A mixed β-sheet== | ==A mixed β-sheet== | ||