User:Stephen Mills/Secondary Structure: Sheets: Difference between revisions
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==H-bonds in antiparallel sheets== | ==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'/> | <Structure load='Tut_antiparallel_bsheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1' name='anti_Hbonds'/> | ||
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). | 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' target='anti_Hbonds'>Click here to zoom in to show some of the hydrogen bonds more clearly.</scene> | ||
<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these. | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_hbonds/1' target='anti_Hbonds'>Click here to zoom out again.</scene> You should notice that all of the NH and C=O groups that lie between strands are involved in hydrogen bonds. Only the groups on the edges of the sheet do not have hydrogen bond partners, but if this sheet were part of a larger protein, other residues would supply groups to hydrogen bond to most if not all of these. | ||
Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name=' | Two of the strands in this sheet are connected by a β-turn. <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_turn/2' target='anti_Hbonds'>Click here</scene> to show the β-turn. The carbon atoms of the amino acids that define the turn have been colored orange. The turn allows a segment of polypeptide to reverse direction in a short distance. In this case it also allows two strands to interact in an antiparallel fashion. <scene name='46/463272/Antipara_mainchain_turn_zoom/1' target='anti_Hbonds'>Click here to zoom in on the turn and reorient it to show more clearly.</scene> '''Is this a Type I or Type II β-turn? (Write down your answer so you can submit it to your instructor)''' | ||
<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion. | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Antipara_mainchain_sidechains/1' target='anti_Hbonds'>Click here to zoom out again.</scene> In this view, some of the residues at the turn have been omitted and you are looking roughly edge-on to the flat plane of the sheet. Sidechains have been added and the atoms of each amino side chain have been colored blue or purple in an alternating fashion. | ||
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. | ||