Calculate structure: Difference between revisions

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The user is urged to use the above directions to perform the calculate structure command so that the resulting display can be compared with the summary below. After running the commands the segments displayed as α-helices and 310-helices can easily be associated with peptide segments in the summary.

The turns need some additional explanation because as you can see in the summary the segments labeled with a T do not contain the same number of residues. The second T in the summary is identified as segment A:68_A:69. This turn (Display with green link below) 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. Displaying the hbonds after clicking the green link as described below shows that the first residue is hydrogen bonded to the last residue of the turn. This bond qualifies it as a 4-turn, and the phi and psi angles of residues 2 and 3 (Directions [[Psi_and_Phi_Angles#More Detail on Psi and Phi |to display these angles]]) make it a class I β-turn. Notice, however, that part sof 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 turn (Display with green link below). Displaying the hbond shows that residues A:63-A:66 qualifies 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 ~~ones that contain~~ one residue could possibly be a 3-turn with that one residue being the central residue of the turn, but it could also be a residue of a 4-turn with some of the other residues also being part of a helix which has priority over a turn. This seems to be the case for the turns that are ~~marked~~ as ~~being at~~ A:86_A:86 and A:110_A:110. As described ~~below~~ the summary often identifies β-turns (4-turns) with the two interior residues, but in the case of A:86_A:86 (Display with green link below) residue A:85 is part of an α-helix so it is included as part of that helix. In the case of A:110_A:110 (Display with green link below) A:110 and A:113 are hydrogen bonded which qualifies it for a 4-turn, and the phi and psi angles of A:111 and A:112 qualify it for a class I β-turn. Turns identified as A:65_A:66 and A:68_A:69 are examples of 4-turns and β-turns that are identified by their two central residues. Use the green links as before to show that the hbonds are between the terminal residues. Both of them are class I β-turns.

The turns need some additional explanation because as you can see in the summary the segments labeled with a T do not contain the same number of residues. The second T in the summary is identified as segment A:68_A:69. This turn (Display with green link below) 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. Displaying the hbonds after clicking the green link as described below shows that the first residue is hydrogen bonded to the last residue of the turn. This bond qualifies it as a 4-turn, and the phi and psi angles of residues 2 and 3 (Directions [[Psi_and_Phi_Angles#More Detail on Psi and Phi |to display these angles]]) make it a class I β-turn. Notice, however, that part sof 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 turn (Display with green link below). 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

The two remaining T's have one residue segments, and these could possibly be a 3-turn with that one residue being the central residue of the turn, but it could also be a residue of a 4-turn with some of the other residues also being part of a helix which has priority over a turn. This seems to be the case for the turns that are identified as A:86_A:86 and A:110_A:110. As described above the summary often identifies β-turns (4-turns) with the two interior residues, but in the case of A:86_A:86 (Display with green link below) residue A:85 is part of an α-helix so it is included as part of that helix. In the case of A:110_A:110 (Display with green link below) A:110 and A:113 are hydrogen bonded which qualifies it for a 4-turn, and the phi and psi angles of A:111 and A:112 qualify it for a class I β-turn.

SUMMARY:(Key for the structural components is '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 310-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.)

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T : A:110_A:110     <scene name='Calculate_structure/Turn_110/1'>Display turn</scene>

G : A:111_A:114

T : A:115_A:117

T : A:115_A:117     <scene name='Calculate_structure/Turn_114/1'>Display turn</scene>

Show structure of <scene name='Calculate_structure/Domain_2/2'>domain 2 of chain A glycogen phosphorylase</scene>

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 The user is urged to use the above directions to perform the calculate structure command so that the resulting display can be compared with the summary below. After running the commands the segments displayed as α-helices and 3<sub>10</sub>-helices can easily be associated with peptide segments in the summary.
-The turns need some additional explanation because as you can see in the summary the segments labeled with a T do not contain the same number of residues. The second T in the summary is identified as segment A:68_A:69. This turn (Display with green link below) 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. Displaying the hbonds after clicking the green link as described below shows that the first residue is hydrogen bonded to the last residue of the turn. This bond qualifies it as a 4-turn, and the phi and psi angles of residues 2 and 3 (Directions [[Psi_and_Phi_Angles#More Detail on Psi and Phi |to display these angles]]) make it a class I β-turn. Notice, however, that part sof 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 turn (Display with green link below). Displaying the hbond shows that residues A:63-A:66 qualifies 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 ones that contain one residue could possibly be a 3-turn with that one residue being the central residue of the turn, but it could also be a residue of a 4-turn with some of the other residues also being part of a helix which has priority over a turn.  This seems to be the case for the turns that are marked as being at A:86_A:86 and A:110_A:110. As described below the summary often identifies β-turns (4-turns) with the two interior residues, but in the case of A:86_A:86 (Display with green link below) residue A:85 is part of an α-helix so it is included as part of that helix. In the case of A:110_A:110 (Display with green link below) A:110 and A:113 are hydrogen bonded which qualifies it for a 4-turn, and the phi and psi angles of A:111 and A:112 qualify it for a class I β-turn. Turns identified as A:65_A:66 and A:68_A:69 are examples of 4-turns and β-turns that are identified by their two central residues. Use the green links as before to show that the hbonds are between the terminal residues. Both of them are class I β-turns.
+The turns need some additional explanation because as you can see in the summary the segments labeled with a T do not contain the same number of residues. The second T in the summary is identified as segment A:68_A:69. This turn (Display with green link below) 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. Displaying the hbonds after clicking the green link as described below shows that the first residue is hydrogen bonded to the last residue of the turn. This bond qualifies it as a 4-turn, and the phi and psi angles of residues 2 and 3 (Directions [[Psi_and_Phi_Angles#More Detail on Psi and Phi |to display these angles]]) make it a class I β-turn. Notice, however, that part sof 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 turn (Display with green link below). 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
+The two remaining T's have one residue segments, and these could possibly be a 3-turn with that one residue being the central residue of the turn, but it could also be a residue of a 4-turn with some of the other residues also being part of a helix which has priority over a turn.  This seems to be the case for the turns that are identified as A:86_A:86 and A:110_A:110. As described above the summary often identifies β-turns (4-turns) with the two interior residues, but in the case of A:86_A:86 (Display with green link below) residue A:85 is part of an α-helix so it is included as part of that helix. In the case of A:110_A:110 (Display with green link below) A:110 and A:113 are hydrogen bonded which qualifies it for a 4-turn, and the phi and psi angles of A:111 and A:112 qualify it for a class I β-turn.
 SUMMARY:(Key for the structural components is '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 3<sub>10</sub>-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.)<br>
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 T : A:110_A:110    &nbsp;&nbsp;&nbsp; <scene name='Calculate_structure/Turn_110/1'>Display turn</scene><br>
 G : A:111_A:114<br>
-T : A:115_A:117<br>
+T : A:115_A:117 &nbsp;&nbsp;&nbsp; <scene name='Calculate_structure/Turn_114/1'>Display turn</scene><br>
 Show structure of <scene name='Calculate_structure/Domain_2/2'>domain 2 of chain A glycogen phosphorylase</scene>

Calculate structure: Difference between revisions

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