Calculate structure: Difference between revisions

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'''Myohemerytherin''' (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>)

* Locate any β-turns that are not being displayed by blue trace because there is not a hbond between the first and the last residues of the turn. Remember that you can confirm the presence of this type of β-turn by showing the presence of a Pro at position three. (Hover the cursor over the trace to display the name and number of the residues.) There are two class VIb β-turns in myohemerytherin.

* There are two T segments (<scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> and <scene name='Calculate_structure/Turn_110/2'>T : A:110_A:110</scene>) that contain one residue, and ~~that one~~ residue in both of ~~them is~~ the ~~only one not~~ involved in a helix which has priority over a turn. Both of these turns are class I β-turn.

* There are two T segments (<scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (run ''calculate hbonds structure'' in the console to show the hbonds) and <scene name='Calculate_structure/Turn_110/2'>T : A:110_A:110</scene>) that contain one residue, and the other three residue in both of the turns are involved in a helix which has priority over a turn. Both of these turns are class I β-turn.

* There are two T segments ~~(and <scene name='Calculate_structure/Turn_67/6'>T : A:68_A:69</scene>)~~ that contain two residues. ~~Residues #63 and #64~~ of <scene name='Calculate_structure/Turn_63/3'>T : A:65_A:66</scene> are part of a helix as well as the β-turn.

* There are two T segments that contain two residues. The first two residues of the β-turn marked by<scene name='Calculate_structure/Turn_63/3'>T : A:65_A:66</scene> are #'s 63 and 64, these two are part of a helix as well as the β-turn, and therefore only #'s 65 and 66 are part of the T segment. The middle two residues (68 and 69) of the β-turn marked by <scene name='Calculate_structure/Turn_67/6'>T : A:68_A:69</scene> are not part of a helix, but residue #70 is. Notice that part of residues 67 and 68 are colored white rather than blue. Both turns are class I.

* The ~~second~~ T ~~in the myohemerytherin summary is identified as segment~~ A:68_A:69~~. This turn~~</scene> ~~serves to illustrate that most often 3-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 ''calculate hbonds structure'' does not function in the green links of Proteopedia using Jmol 11.8, the ''calculate hbonds structure'' command must be run in the console to display the hbonds after clicking a green link.) One can see that the hbond is ~~between residues 67 and 70 making it a 3-turn (β-turn), and if the values for the phi and psi angles of residues 2 and 3 were displayed one could confirm it as a class I~~. Notice that part of residues 67 and 68 are colored white rather than blue.

* The last T identifies a three residue segment indicating a <scene name='Calculate_structure/Turn_114/2'>4-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (3-turn and type II β-turn) and between 114 and 118 (4-turn). A β-turn is nested in a 4-turn. Residue 114 is part of the 3<sub>10</sub>-helix, and part of residue 118 is colored white.

* The first T is identified by a two residue segment, A:65_A:66, but these two residues are ~~the last two in the turn</scene>. Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 3-turn (β-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'>4-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (3-turn and type II β-turn) and between 114 and 118 (4-turn). A β-turn is nested in a 4-turn. Residue 114 is part of the 3<sub>10</sub>-helix ~~so it~~ is ~~not~~ colored ~~blue~~.

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@@ Line 39: / Line 39: @@
 '''Myohemerytherin'''  (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>)
 * Locate any β-turns that are not being displayed by blue trace because there is not a hbond between the first and the last residues of the turn. Remember that you can confirm the presence of this type of β-turn by showing the presence of a Pro at position three. (Hover the cursor over the trace to display the name and number of the residues.) There are two class VIb β-turns in myohemerytherin.
-* There are two T segments (<scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> and <scene name='Calculate_structure/Turn_110/2'>T : A:110_A:110</scene>) that contain one residue, and that one residue in both of them is the only one not involved in a helix which has priority over a turn. Both of these turns are class I β-turn.
+* There are two T segments (<scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (run ''calculate hbonds structure'' in the console to show the hbonds) and <scene name='Calculate_structure/Turn_110/2'>T : A:110_A:110</scene>) that contain one residue, and the other three residue in both of the turns are involved in a helix which has priority over a turn. Both of these turns are class I β-turn.
-* There are two T segments (and <scene name='Calculate_structure/Turn_67/6'>T : A:68_A:69</scene>) that contain two residues. Residues #63 and #64 of <scene name='Calculate_structure/Turn_63/3'>T : A:65_A:66</scene> are part of a helix as well as the β-turn.
+* There are two T segments that contain two residues. The first two residues of the β-turn marked by<scene name='Calculate_structure/Turn_63/3'>T : A:65_A:66</scene> are #'s 63 and 64, these two are part of a helix as well as the β-turn, and therefore only #'s 65 and 66 are part of the T segment. The middle two residues (68 and 69) of the β-turn marked by <scene name='Calculate_structure/Turn_67/6'>T : A:68_A:69</scene> are not part of a helix, but residue #70 is. Notice that part of residues 67 and 68 are colored white rather than blue. Both turns are class I.
-* The second T in the myohemerytherin summary is identified as segment A:68_A:69. This turn</scene> serves to illustrate that most often 3-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 ''calculate hbonds structure'' does not function in the green links of Proteopedia using Jmol 11.8, the ''calculate hbonds structure'' command must be run in the console to display the hbonds after clicking a green link.)  One can see that the hbond is between residues 67 and 70 making it a 3-turn (β-turn), and if the values for the phi and psi angles of residues 2 and 3 were displayed one could  confirm it as a class I. Notice that part of residues 67 and 68 are colored white rather than blue.
+* The last T identifies a three residue segment indicating a <scene name='Calculate_structure/Turn_114/2'>4-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (3-turn and type II β-turn) and between 114 and 118 (4-turn). A β-turn is nested in a 4-turn. Residue 114 is part of the 3<sub>10</sub>-helix, and part of residue 118 is colored white.
-* The first T is identified by a two residue segment, A:65_A:66, but these two residues are the last two in the turn</scene>. Displaying the hbond shows that it is between residues A:63-A:66 which qualifies it for a 3-turn (β-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'>4-turn</scene>. ''Calculate hbonds structure'' shows hbonds between 114 and 117 (3-turn and type II β-turn) and between 114 and 118 (4-turn). A β-turn is nested in a 4-turn. Residue 114 is part of the 3<sub>10</sub>-helix so it is not colored blue.