Helices in Proteins
From Proteopedia
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Each of the three examples below is a decapeptide fragment extracted from an actual protein structure in the [[PDB]]. They are shown using the same scale, for a better comparison (as a consequence, zoom in the Jmol applets is disabled). | Each of the three examples below is a decapeptide fragment extracted from an actual protein structure in the [[PDB]]. They are shown using the same scale, for a better comparison (as a consequence, zoom in the Jmol applets is disabled). | ||
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<Structure name='jmol_3' load='3L79_514-525.pdb' size='260' scene='Helices_in_Proteins/3_10_helix_start/1' /> | <Structure name='jmol_3' load='3L79_514-525.pdb' size='260' scene='Helices_in_Proteins/3_10_helix_start/1' /> | ||
| - | <br /><scene name='Helices_in_Proteins/3_10_helix_start/1' target='jmol_3'>scene 1</scene> | ||
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<Structure name='jmol_a' load='1HHO_B_5-16.pdb' size='260' scene='Helices_in_Proteins/Alpha_helix_start/1' /> | <Structure name='jmol_a' load='1HHO_B_5-16.pdb' size='260' scene='Helices_in_Proteins/Alpha_helix_start/1' /> | ||
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<Structure name='jmol_p' load='2QD3_A_346-357.pdb' size='260' scene='Helices_in_Proteins/Pi_helix_start/3' /> | <Structure name='jmol_p' load='2QD3_A_346-357.pdb' size='260' scene='Helices_in_Proteins/Pi_helix_start/3' /> | ||
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3<sub>10</sub> | 3<sub>10</sub> | ||
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<br />φ = -49°, ψ = -26° | <br />φ = -49°, ψ = -26° | ||
<br />[[3l79]]: 514-525 | <br />[[3l79]]: 514-525 | ||
| + | <br /><scene name='Helices_in_Proteins/3_10_helix_start/1' target='jmol_3'>scene 1</scene> | ||
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3.6<sub>13</sub> | 3.6<sub>13</sub> | ||
<br />3.6 residues/turn | <br />3.6 residues/turn | ||
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<br />1hho chain B: 5-16 | <br />1hho chain B: 5-16 | ||
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4.4<sub>16</sub> | 4.4<sub>16</sub> | ||
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Revision as of 19:40, 16 June 2014
Helical conformations in proteins
This page illustrates the 3 most common helical conformations (among secondary structures) found in proteins.
Each of the three examples below is a decapeptide fragment extracted from an actual protein structure in the PDB. They are shown using the same scale, for a better comparison (as a consequence, zoom in the Jmol applets is disabled).
To re-align the 3 models, reload this page.
| 310 helix | alpha helix | pi helix | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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310
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3.613
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4.416
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The alpha helix is by far the most common helix. Note that it is a right-handed helix when formed with the common L-amino acids[1][2][3]. (It is left-handed when formed with D-amino acids[1][2][3].) When viewed from either end, right-handed helices turn clockwise when followed away from you.
See Also
- Alpha helix at Wikipedia.
- Secondary structure
References
- ↑ 1.0 1.1 Novotny M, Kleywegt GJ. A survey of left-handed helices in protein structures. J Mol Biol. 2005 Mar 25;347(2):231-41. PMID:15740737 doi:10.1016/j.jmb.2005.01.037
- ↑ 2.0 2.1 Jourdan F, Lazzaroni S, Mendez BL, Lo Cantore P, de Julio M, Amodeo P, Iacobellis NS, Evidente A, Motta A. A left-handed alpha-helix containing both L- and D-amino acids: the solution structure of the antimicrobial lipodepsipeptide tolaasin. Proteins. 2003 Sep 1;52(4):534-43. PMID:12910453 doi:http://dx.doi.org/10.1002/prot.10418
- ↑ 3.0 3.1 Moradi M, Babin V, Roland C, Darden TA, Sagui C. Conformations and free energy landscapes of polyproline peptides. Proc Natl Acad Sci U S A. 2009 Dec 8;106(49):20746-51. Epub 2009 Nov 18. PMID:19923435 doi:10.1073/pnas.0906500106
