Talk:Alpha helix

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Current revision (15:21, 3 September 2020) (edit) (undo)
 
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==List of figures==
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==List of figures: Alpha_helix==
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--[[User:Karsten Theis|Karsten Theis]] 01:16, 20 July 2019 (UTC)
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--[[User:Karsten Theis|Karsten Theis]] 15:21, 3 September 2020 (UTC)
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===Initial view===
===Initial view===
script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt
 +
Available on this page: User:Karsten_Theis/alpha_helix
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58
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===alpha helix===
===alpha helix===
script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/2.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/2.spt
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Available on this page: Alpha_helix
coords: same as Initial view
coords: same as Initial view
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===right-handed helix===
===right-handed helix===
script: https://proteopedia.org/wiki/scripts/77/778341/Ribbon/1.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Ribbon/1.spt
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Available on this page: User:Karsten_Theis/alpha_helix
coords: same as Initial view
coords: same as Initial view
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===hydrogen bonds===
===hydrogen bonds===
script: https://proteopedia.org/wiki/scripts/77/778341/Hbonds/2.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Hbonds/2.spt
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Available on this page: User:Karsten_Theis/alpha_helix
coords: same as Initial view
coords: same as Initial view
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===3.6 residues per turn===
===3.6 residues per turn===
script: https://proteopedia.org/wiki/scripts/77/778341/Wheel/1.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Wheel/1.spt
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Available on this page: User:Karsten_Theis/alpha_helix
coords: same as Initial view
coords: same as Initial view
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===kink in a helix===
===kink in a helix===
script: https://proteopedia.org/wiki/scripts/77/778341/Proline/4.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Proline/4.spt
 +
Available on this page: Alpha_helix
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144
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===proline===
===proline===
script: https://proteopedia.org/wiki/scripts/77/778341/Proline/5.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Proline/5.spt
 +
Available on this page: Alpha_helix
coords: same as kink in a helix
coords: same as kink in a helix
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===the helix in crambin===
===the helix in crambin===
script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap/1.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap/1.spt
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Available on this page: User:Karsten_Theis/alpha_helix
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5
coords: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5
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===C-terminal end===
===C-terminal end===
script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap_detail/2.spt
script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap_detail/2.spt
 +
Available on this page: User:Karsten_Theis/alpha_helix
coords: same as the helix in crambin
coords: same as the helix in crambin
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===Jmol commands: buttons etc===
===Jmol commands: buttons etc===
====side chains====
====side chains====
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jmolLink(' select 6-14:A and sidechain; spacefill 20%; wireframe 0.3; delay 0.8; select 4-16:A and backbone or 4-16:A.CB; restrict selected;\n ...
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select 6-14:A and sidechain; spacefill 20%; wireframe 0.3; delay 0.8; select 4-16:A and backbone or 4-16:A.CB; restrict selected;\n
====ON====
====ON====
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jmolLink(' stereo 5\n ...
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stereo 5\n
====OFF====
====OFF====
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jmolLink(' stereo off\n ...
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stereo off\n
====carbonyl oxygen====
====carbonyl oxygen====
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jmolLink(' select 6-10:A.O; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n ...
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select 6-10:A.O; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n
====amino group====
====amino group====
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jmolLink(' select 10-14:A.N; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n ...
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select 10-14:A.N; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n
====increase the sphere radii====
====increase the sphere radii====
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jmolLink(' select visible; spacefill 30%; delay 0.2; spacefill 40%; delay 0.2; spacefill 50%; delay 0.2; spacefill 60%; delay 0.2; spacefill 70%; delay 0.2; spacefill 80%; delay 0.2; spacefill 90%; delay 0.2; spacefill 100%; delay 1.8; spacefill 20%;\n ...
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select visible; spacefill 30%; delay 0.2; spacefill 40%; delay 0.2; spacefill 50%; delay 0.2; spacefill 60%; delay 0.2; spacefill 70%; delay 0.2; spacefill 80%; delay 0.2; spacefill 90%; delay 0.2; spacefill 100%; delay 1.8; spacefill 20%;\n
====phi and psi====
====phi and psi====
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jmolLink(' select 9-12:A; draw rama; restrict selected; restrict backbone; hbonds off\n ...
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select 9-12:A; draw rama; restrict selected; restrict backbone; hbonds off\n
====show helical axes with rockets====
====show helical axes with rockets====
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jmolLink(' select 58-61:A; structure turn; select 50-58:A; rockets on; select 60-69:A; rockets on;\n ...
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select 58-61:A; structure turn; select 50-58:A; rockets on; select 60-69:A; rockets on;\n
===Summary===
===Summary===
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Total of green links: 9 and total of Jmol buttons etc: 8
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Total of green links: 9
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 +
Total of Jmol buttons etc: 8
====coordinates used====
====coordinates used====
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*/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58
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*do a manual check: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58
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*/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144
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*1FIA: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144
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*/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5
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*3NIR: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5
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==3D scenes==
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<StructureSection load='' size='350' side='right' caption='' scene=''><scene name='77/778341/Ballstick/1'>77/778341/Ballstick/1</scene>
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<scene name='77/778341/Ballstick/2'>77/778341/Ballstick/2</scene>
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<scene name='77/778341/Ribbon/1'>77/778341/Ribbon/1</scene>
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<scene name='77/778341/Hbonds/2'>77/778341/Hbonds/2</scene>
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<scene name='77/778341/Wheel/1'>77/778341/Wheel/1</scene>
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<scene name='77/778341/Proline/4'>77/778341/Proline/4</scene>
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<scene name='77/778341/Proline/5'>77/778341/Proline/5</scene>
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<scene name='77/778341/Proline_cap/1'>77/778341/Proline_cap/1</scene>
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<scene name='77/778341/Proline_cap_detail/2'>77/778341/Proline_cap_detail/2</scene>
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</StructureSection>

Current revision

Contents

List of figures: Alpha_helix

--Karsten Theis 15:21, 3 September 2020 (UTC)

Initial view

script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt Available on this page: User:Karsten_Theis/alpha_helix

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58


alpha helix

script: https://proteopedia.org/wiki/scripts/77/778341/Ballstick/2.spt Available on this page: Alpha_helix

coords: same as Initial view


right-handed helix

script: https://proteopedia.org/wiki/scripts/77/778341/Ribbon/1.spt Available on this page: User:Karsten_Theis/alpha_helix

coords: same as Initial view


hydrogen bonds

script: https://proteopedia.org/wiki/scripts/77/778341/Hbonds/2.spt Available on this page: User:Karsten_Theis/alpha_helix

coords: same as Initial view


3.6 residues per turn

script: https://proteopedia.org/wiki/scripts/77/778341/Wheel/1.spt Available on this page: User:Karsten_Theis/alpha_helix

coords: same as Initial view


kink in a helix

script: https://proteopedia.org/wiki/scripts/77/778341/Proline/4.spt Available on this page: Alpha_helix

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144


proline

script: https://proteopedia.org/wiki/scripts/77/778341/Proline/5.spt Available on this page: Alpha_helix

coords: same as kink in a helix


the helix in crambin

script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap/1.spt Available on this page: User:Karsten_Theis/alpha_helix

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5


C-terminal end

script: https://proteopedia.org/wiki/scripts/77/778341/Proline_cap_detail/2.spt Available on this page: User:Karsten_Theis/alpha_helix

coords: same as the helix in crambin

Jmol commands: buttons etc

side chains

 select 6-14:A and sidechain; spacefill 20%; wireframe 0.3; delay 0.8; select 4-16:A and backbone or 4-16:A.CB; restrict selected;\n

ON

 stereo 5\n

OFF

 stereo off\n

carbonyl oxygen

 select 6-10:A.O; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n

amino group

 select 10-14:A.N; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4;\n

increase the sphere radii

 select visible; spacefill 30%; delay 0.2; spacefill 40%; delay 0.2; spacefill 50%; delay 0.2; spacefill 60%; delay 0.2; spacefill 70%; delay 0.2; spacefill 80%; delay 0.2; spacefill 90%; delay 0.2; spacefill 100%; delay 1.8; spacefill 20%;\n

phi and psi

 select 9-12:A; draw rama; restrict selected; restrict backbone; hbonds off\n

show helical axes with rockets

 select 58-61:A; structure turn; select 50-58:A; rockets on; select 60-69:A; rockets on;\n

Summary

Total of green links: 9

Total of Jmol buttons etc: 8

coordinates used

3D scenes

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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