Calculate structure: Difference between revisions
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'''Domain 2 of chain A Glycogen Phosphorylase''' (<scene name='Calculate_structure/Domain_2/2'>Load Structure</scene>) - 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> | '''Domain 2 of chain A Glycogen Phosphorylase''' (<scene name='Calculate_structure/Domain_2/2'>Load Structure</scene>) - 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 lite</scene>, as four residue segments, the one residue segments in the summary below. (Remember to display the hbonds by running ''calculate hbonds structure'' from the console.) Only one segment has a residue colored blue, indicating a turn, and the other residues are colored as being part of a helix | * <scene name='Calculate_structure/Domain_2_3turns2/6'>High lite</scene>, as four residue segments, the one residue T segments in the summary below. (Remember to display the hbonds by running ''calculate hbonds structure'' from the console.) Only one segment has a residue colored blue, indicating a turn, and the other residues are colored as being part of a helix or sheet. Improve the view by displaying these <scene name='Calculate_structure/Domain_2_3turns3/7'>segments in isolation</scene>. See summary below for a description of each of these T: segments. | ||
* Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. 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, and that segment (822-825) is part of a | * Reveal the nature of the <scene name='Calculate_structure/Domain_2_4turn/2'>remaining T segments</scene>. 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, and that segment (822-825) is part of a 4-turn and two 5-turns. Displaying these <scene name='Calculate_structure/Domain_2_4turn2/5'>turns in isolation</scene> makes it easier to observe the hbonds. Using the residue numbers in the summary one can determine which residues make up the turns. At two places the β-turns overlap. 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 hbonds.). | ||
* Using the method used for myohemerytherin above, look for β-turns that have a Pro at position 3 but do not have hbonds. | * Using the method used for myohemerytherin above, look for β-turns that have a Pro at position 3 but do not have hbonds. | ||
'''SUMMARY of T's for Domain 2 of Chain A Glycogen Phosphorylase:'''(All other segments deleted.)<br> | '''SUMMARY of T's for Domain 2 of Chain A Glycogen Phosphorylase:'''(All other segments deleted.)<br> | ||
T : A:488_A:488 | T : A:488_A:488 488 (colored blue) is one residue between sheet & 3<sub>10</sub>-helix<br> | ||
T : A:495_A:495 | T : A:495_A:495 495 at the end of α-helix<br> | ||
T : A:525_A:526 β-turn 524-527<br> | T : A:525_A:526 β-turn 524-527<br> | ||
T : A:594_A:595 β-turn 593-596<br> | T : A:594_A:595 β-turn 593-596<br> | ||
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T : A:683_A:685 β-turn 682-685<br> | T : A:683_A:685 β-turn 682-685<br> | ||
T : A:694_A:695 β-turn 693-696<br> | T : A:694_A:695 β-turn 693-696<br> | ||
T : A:728_A:728 | T : A:728_A:728 728 first residue of an α-helix<br> | ||
T : A:747_A:750 β-turn 748-751<br> | T : A:747_A:750 β-turn 748-751<br> | ||
T : A:752_A:753 β-turn 751-754<br> | T : A:752_A:753 β-turn 751-754<br> | ||
T : A:773_A:773 | T : A:773_A:773 773 first residue in an α-helix <br> | ||
T : A:777_A:777 | T : A:777_A:777 777 part of same α-helix as 773<br> | ||
T : A:807_A:807 | T : A:807_A:807 807 part of an α-helix<br> | ||
T : A:822_A:825 | T : A:822_A:825 4-turn & two 5-turn 820-826<br> | ||
486-490,493-497,726-730,771-775,776-779,804-809; 524-527,593-596,610-613,633-636,636-639,668-671,675-678,682-685,693-696,748-751,751-754,820-826 | 486-490,493-497,726-730,771-775,776-779,804-809; 524-527,593-596,610-613,633-636,636-639,668-671,675-678,682-685,693-696,748-751,751-754,820-826 | ||
