User:Stephen Mills/Secondary Structure: Sheets: Difference between revisions
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<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. | <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' 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)''' | 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)''' Here are a couple of links that might help you figure this out. [http://www.nku.edu/~russellk/tutorial/peptide/peptide.html NKU tutorial] and [http://sbb.uvm.edu/~sje/351/sub2.3.html UVM COMET]. | ||
<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. | <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. | ||
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The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel. | The sheet shown below is composed of four strands. All the atoms are shown (C = green; N = blue; O = red; S = yellow; H = white). This is a mixed β-sheet. Some of the strands are parallel, some are antiparallel. | ||
<Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1'/> | <Structure load='Mixed_sheet.pdb' size='500' frame='true' align='left' caption='' scene='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_load/1' name='mixed_sheet'/> | ||
<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O). | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain/2' target='mixed_sheet'>Click here</scene> to show only the polypeptide mainchain of each strand (NH, Cα, and C=O). | ||
'''What is the orientation of each pair of strands (parallel or antiparallel)?''' | '''What is the orientation of each pair of strands (parallel or antiparallel)?''' | ||
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Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange. | Click below to highlight the strands in pairs (pair 1, pair 2 and pair 3). The carbon atoms will be highlighted in orange. | ||
<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1'>Pair 1.</scene> | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair1/1' target='mixed_sheet'>Pair 1.</scene> | ||
<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1'>Pair 2.</scene> | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair2/1' target='mixed_sheet'>Pair 2.</scene> | ||
<scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1'>Pair 3.</scene> | <scene name='User:Robert_Dutnall/Sandbox_1_sheets/Mixed_sheet_mainchain_pair3/1' target='mixed_sheet'>Pair 3.</scene> | ||
'''Write down your answers for pair 1, pair 2 and pair 3 to submit to your instructor.''' | '''Write down your answers for pair 1, pair 2 and pair 3 to submit to your instructor.''' | ||