Calculate structure: Difference between revisions
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* Can you locate the two turns that are not colored with blue traces and do not contain a hbond between the first and the last residues of the turn. There are two class VIb β-turns in myohemerytherin. | * Can you locate the two turns that are not colored with blue traces and do not contain a hbond between the first and the last residues of the turn. There are two class VIb β-turns in myohemerytherin. | ||
''' | '''Summary for Myohemerytherin:'''<br> | ||
G : A:12_A:14<br> | G : A:12_A:14<br> | ||
H : A:19_A:37<br> | H : A:19_A:37<br> | ||
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=== Identify turns using resourses at RCSB === | === Identify turns using resourses at RCSB === | ||
Use end note to open necessary sites.<ref>[http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=2MHR Open myohemerytherin at sequence page]; [http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2MHR&chainId=A Open sequence and Secondary structure page]</ref> Follow directions given above. If you select one of the other methods of secondary structure annotations, you will observe that class VIb β-turns are among the structures being annotated. | Use end note to open necessary sites.<ref>[http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=2MHR Open myohemerytherin at sequence page]; [http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2MHR&chainId=A Open sequence and Secondary structure page]</ref> Follow directions given above. If you select one of the other methods of secondary structure annotations, you will observe that class VIb β-turns are among the structures being annotated. | ||
=== Domain 2 of chain A Glycogen Phosphorylase === | === Domain 2 of chain A Glycogen Phosphorylase === | ||
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If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br> | If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br> | ||
After clicking on the above green link, open the console and run the script: <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center><br> | After clicking on the above green link, open the console and run the script: <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center><br> | ||
* <scene name='Calculate_structure/Domain_2_3turns2/6'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/8'>segments in isolation</scene>. (Remember to display the hbonds by running ''calculate hbonds structure'' from the console.) Only one segment has a residue colored blue, and the other residues are colored as being part of a helix or sheet. See summary below for a description of each of these T | * <scene name='Calculate_structure/Domain_2_3turns2/6'>High light</scene> each of the one residue T segments (''e.g.'' T : A:488_A:488) in the summary below along with a few residues on each side of the single residue. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/8'>segments in isolation</scene>. (Remember to display the hbonds by running ''calculate hbonds structure'' from the console.) Only one segment has a residue colored blue, and the other residues are colored as being part of a helix or sheet. See summary below for a description of each of these T segments. The only turns that these single residue segments are part of are involved helices. | ||
* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment 822-825 is part of a 4-turn and two 5-turns. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). | * Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Inspecting them for hbonds (after running ''calculate hbonds structure'' from the console) reveals that all but one of these T segments are part of β-turns with the β-turns overlapping at two locations, and that segment 822-825 is part of a 4-turn and two 5-turns. All but two of the segments have at least one residue colored blue (Nitrogens involved in hbonds are also colored blue for ease of identifying the atoms involved in the hbonds.). | ||
''' | '''Summary of T's for Domain 2 of Chain A Glycogen Phosphorylase:'''(All other segments deleted.)<br> | ||
T : A:488_A:488 488 (colored blue) is between a sheet & 3<sub>10</sub>-helix.<br> | T : A:488_A:488 488 (colored blue) is between a sheet & 3<sub>10</sub>-helix.<br> | ||
T : A:495_A:495 495 is at the end of α-helix.<br> | T : A:495_A:495 495 is at the end of α-helix.<br> | ||
