Talk:Alpha helix

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Contents 1 List of figures: Alpha_helix 1.1 Initial view 1.2 alpha helix 1.3 right-handed helix 1.4 hydrogen bonds 1.5 3.6 residues per turn 1.6 kink in a helix 1.7 proline 1.8 the helix in crambin 1.9 C-terminal end 1.10 Jmol commands: buttons etc 1.10.1 side chains 1.10.2 ON 1.10.3 OFF 1.10.4 carbonyl oxygen 1.10.5 amino group 1.10.6 increase the sphere radii 1.10.7 phi and psi 1.10.8 show helical axes with rockets 1.11 Summary 1.11.1 coordinates used 2 3D scenes

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

• do a manual check: https://proteopedia.org/cgi-bin/getfrozenstructure?abb78d56d3e07a4e0290a8783dcb8b58
• 1FIA: https://proteopedia.org/cgi-bin/getfrozenstructure?edfb4ce39cfe73bccb63eb7f6261b144
• 3NIR: https://proteopedia.org/cgi-bin/getfrozenstructure?9366550c976e80068b9dc9648aff81c5

3D scenes

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