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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
spinqualitylabelsall models PDB ID 3L79_514-525.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 1HHO_B_5-16.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image	spinqualitylabelsall models PDB ID 2QD3_A_346-357.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
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

• Alpha helix at Wikipedia.
• Secondary structure

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