Calculate structure: Difference between revisions

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* There are two T segments that contain one residue, <scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and <scene name='Calculate_structure/Turn_110/6'>T : A:110_A:110</scene> (β-turn 110-113; 110 is blue, 111-113 are part of a 310-helix.).

* There are two T segments that contain two residues, <scene name='Calculate_structure/Turn_63/4'>T : A:65_A:66</scene> (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and <scene name='Calculate_structure/Turn_67/7'>T : A:68_A:69</scene> (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).

* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/2'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 310-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.

* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/3'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 310-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.

* 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.

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T : A:110_A:110   <scene name='Calculate_structure/Turn_110/6'>Display beta-turn</scene>

G : A:111_A:114

T : A:115_A:117   <scene name='Calculate_structure/Turn_114/2'>Display turns</scene>

T : A:115_A:117   <scene name='Calculate_structure/Turn_114/3'>Display turns</scene>

Key - '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 310-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.

=== Identify turns using resourses at RCSB ===

There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do Open home page of PDB]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First one, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second one, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn, and then if you click the mouse the one residue turn will appear in the Jmol applet. If secondary structure annotations other than DSSP are used, β-turns classes VIa1, VIa2, and VIb may be identified, see myohemerytherin ~~below~~. If you select one of the other annotations of secondary structure, you will discover 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&params.showJmol=true Open myohemerytherin at sequence page with Jmol open];   [http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2MHR&chainId=A Open sequence and Secondary structure page]</ref>

There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do Open home page of PDB]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First one, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second one, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn, and then if you click the mouse the one residue turn will appear in the Jmol applet. If secondary structure annotations other than DSSP are used, β-turns classes VIa1, VIa2, and VIb may be identified, see myohemerytherin above. If you select one of the other annotations of secondary structure, you will discover 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&params.showJmol=true Open myohemerytherin at sequence page with Jmol open];   [http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2MHR&chainId=A Open sequence and Secondary structure page]</ref>

=== Domain 2 of chain A Glycogen Phosphorylase ===

Calculate structure: Difference between revisions

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@@ Line 39: / Line 39: @@
 * There are two T segments that contain one residue, <scene name='Calculate_structure/Turn_84/2'>T : A:86_A:86</scene> (β-turn 84-87; 84 & 85 are part of a helix, 86 is colored blue & 87 is white.) and <scene name='Calculate_structure/Turn_110/6'>T : A:110_A:110</scene> (β-turn 110-113; 110 is blue, 111-113 are part of a 3<sub>10</sub>-helix.).
 * There are two T segments that contain two residues, <scene name='Calculate_structure/Turn_63/4'>T : A:65_A:66</scene> (β-turn 63-66; 63 & 64 part of a helix, 65 & 66 are blue.) and <scene name='Calculate_structure/Turn_67/7'>T : A:68_A:69</scene> (β-turn 67-70; 70 is part of a helix, 67 & 68 are white & blue, 69 entirely blue.).
-* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/2'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 3<sub>10</sub>-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.
+* The last T is a three residue segment, <scene name='Calculate_structure/Turn_114/3'>T : A:115_A:117</scene> (β-turn 114-117, 4-turn 114-118; 114 is part of a 3<sub>10</sub>-helix, 115-117 & part of 118 are blue, 118 is partially white.). A β-turn is nested in a 4-turn.
 * 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.
@@ Line 53: / Line 53: @@
 T : A:110_A:110  &nbsp;&nbsp;<scene name='Calculate_structure/Turn_110/6'>Display beta-turn</scene><br>
 G : A:111_A:114<br>
-T : A:115_A:117  &nbsp;&nbsp;<scene name='Calculate_structure/Turn_114/2'>Display turns</scene><br>
+T : A:115_A:117  &nbsp;&nbsp;<scene name='Calculate_structure/Turn_114/3'>Display turns</scene><br>
 Key - '''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>
 === Identify turns using resourses at RCSB ===
-There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do Open home page of PDB]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First one, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second one, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn, and then if you click the mouse the one residue turn will appear in the Jmol applet. If secondary structure annotations other than DSSP are used, β-turns classes VIa1, VIa2, and VIb may be identified, see myohemerytherin below. If you select one of the other annotations of secondary structure, you will discover 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&params.showJmol=true Open myohemerytherin at sequence page with Jmol open]; &nbsp;&nbsp;[http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2MHR&chainId=A Open sequence and Secondary structure page]</ref>
+There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do Open home page of PDB]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First one, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second one, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn, and then if you click the mouse the one residue turn will appear in the Jmol applet. If secondary structure annotations other than DSSP are used, β-turns classes VIa1, VIa2, and VIb may be identified, see myohemerytherin above. If you select one of the other annotations of secondary structure, you will discover 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&params.showJmol=true Open myohemerytherin at sequence page with Jmol open]; &nbsp;&nbsp;[http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2MHR&chainId=A Open sequence and Secondary structure page]</ref>
 === Domain 2 of chain A Glycogen Phosphorylase ===