Helices in Proteins

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<Structure name='app_p' load='2QD3_A_346-357.pdb' size='260' scene='Helices_in_Proteins/Pi_helix_start/3' />
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Revision as of 08:19, 19 March 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
Drag the structure with the mouse to rotate


Drag the structure with the mouse to rotate
Drag the structure with the mouse to rotate

310
3 residues/turn
rise 0.20 nm/residue
helix pitch 0.60 nm
H bonds: Ni+3 → Oi
φ = -49°, ψ = -26°
3l79: 514-525

3.613
3.6 residues/turn
rise 0.15 nm/residue
helix pitch 0.54 nm
H bonds: Ni+4 → Oi
φ = -60°, ψ = -45°
1hho chain B: 5-16

4.416
4.4 residues/turn
rise ~0.115 nm/residue
helix pitch ~0.41 nm
H bonds: Ni+5 → Oi
φ = -55°, ψ = -70° (approx.)
2qd3 chain A: 346-357

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

References

  1. ↑ 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. ↑ 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. ↑ 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

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Angel Herraez, Eric Martz, Karsten Theis, Joel L. Sussman

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