Calculate structure: Difference between revisions
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The second T in the myohemerytherin summary is identified as segment A:68_A:69. <scene name='Calculate_structure/Turn_67/5'>This turn</scene> serves to illustrate that most often 4-turns (β-turns) are identified in the summary by their two central residues. Most of the β-turns in myohemerythrin are exceptions to this generalization, but in glycogen phosphorylase (below) it does hold in the majority of cases. Since Proteopedia uses Jmol 11.8, ''calculate hbonds structure'' does not function in the green link, so in order to display the hbonds after clicking a green link the user must run the ''calculate hbonds structure'' command in the console. One can see that the hbond is between residues 67 and 70 making it a 4-turn, and the values for the phi and psi angles of residues 2 and 3 make it a class I β-turn. Notice, however, that part of residues 67 and 68 are colored white rather than blue. The first T is identified by a two residue segment, but the two residues, A:65_A:66, are the last two in the <scene name='Calculate_structure/Turn_63/2'>turn</scene>. Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 4-turn and the torsional angles classify it as type I β-turn. As shown by their coloration the first two residues also qualify as α-helix and are displayed as such since a helix has priority over a turn. The last T identifies a three residue segment indicating a <scene name='Calculate_structure/Turn_114/2'>5-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (4-turn and type II β-turn) and between 114 and 118 (5-turn). A β-turn is nested in a 5-turn. Residue 114 is part of the 3<sub>10</sub>-helix so it is not colored blue. | The second T in the myohemerytherin summary is identified as segment A:68_A:69. <scene name='Calculate_structure/Turn_67/5'>This turn</scene> serves to illustrate that most often 4-turns (β-turns) are identified in the summary by their two central residues. Most of the β-turns in myohemerythrin are exceptions to this generalization, but in glycogen phosphorylase (below) it does hold in the majority of cases. Since Proteopedia uses Jmol 11.8, ''calculate hbonds structure'' does not function in the green link, so in order to display the hbonds after clicking a green link the user must run the ''calculate hbonds structure'' command in the console. One can see that the hbond is between residues 67 and 70 making it a 4-turn, and the values for the phi and psi angles of residues 2 and 3 make it a class I β-turn. Notice, however, that part of residues 67 and 68 are colored white rather than blue. The first T is identified by a two residue segment, but the two residues, A:65_A:66, are the last two in the <scene name='Calculate_structure/Turn_63/2'>turn</scene>. Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 4-turn and the torsional angles classify it as type I β-turn. As shown by their coloration the first two residues also qualify as α-helix and are displayed as such since a helix has priority over a turn. The last T identifies a three residue segment indicating a <scene name='Calculate_structure/Turn_114/2'>5-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (4-turn and type II β-turn) and between 114 and 118 (5-turn). A β-turn is nested in a 5-turn. Residue 114 is part of the 3<sub>10</sub>-helix so it is not colored blue. | ||
The two remaining T's have one residue segments, and these could possibly be a 3-turn with that | The two remaining T's have one residue segments, and these could possibly be a 3-turn, but displaying <scene name='Calculate_structure/Turns_84_100/1'>backbone</scene> with hbonds reveals that they are 4-turn with some of the other residues also being part of a helix which has priority over a turn. Both of these turns are class I β-turn. | ||
There are two β-turns that are not detected by DSSP, and they are both class IVB which do not have a hbond. They are located at residues 5-8 and 88-91. | There are two β-turns that are not detected by DSSP, and they are both class IVB which do not have a hbond. They are located at <scene name='Calculate_structure/Turns_5_88/1'>residues 5-8 and 88-91</scene>. Run ''calculate hbonds structure'' to confirm that there are no hbonds in these turns. | ||
'''SUMMARY for Myohemerytherin:'''<br> | '''SUMMARY for Myohemerytherin:'''<br> | ||
