Helical wheel

A helical wheel is a type of plot or visual representation used to illustrate the properties of alpha helices in proteins.

An example of an amino acid sequence plotted on a helical wheel. Aliphatic residues are shown as blue squares, polar or negatively charged residues as red diamonds, and positively charged residues as black octagons.

The sequence of amino acids that make up a helical region of the protein's secondary structure are plotted in a rotating manner where the angle of rotation between consecutive amino acids is 100°, so that the final representation looks down the helical axis.

Polarity and Characteristics

The plot reveals whether hydrophobic amino acids are concentrated on one side of the helix, usually with polar or hydrophilic amino acids on the other. This arrangement is common in alpha helices within globular proteins, where one face of the helix is oriented toward the hydrophobic core and one face is oriented toward the solvent-exposed surface. Specific patterns characteristic of protein folds and protein docking motifs are also revealed, as in the identification of leucine zipper dimerization regions and coiled coils. This projection diagram is often called and "Edmundson wheel" after its inventor.[1]

Drawing Helical Wheels

Helical wheels can be drawn by the HELIQUEST server and subsequently downloaded.[2] The helixvis package for the R programming language can also be used to draw customized helical wheels.[3]

gollark: Or, I guess, for full monke™ any technology.
gollark: I feel like you're drastically underestimating how bad life is without any modern technology.
gollark: Well, I do care about that, because having a worse economy means people's quality of life is generally worse.
gollark: I do think it would be good for cities to be split out into somewhat smaller cities with better land prices/traffic/etc, though.
gollark: Entirely anecdotally, I live in [RURAL AREA REDACTED] and don't like it because there is *nothing to do here*. Generally speaking, cities being less city-y would probably reduce productivity a lot which would be bad.

References
  1. Schiffer M, Edmundson AB (1967). "Use of helical wheels to represent the structures of proteins and to identify segments with helical potential". Biophysical Journal. 7 (2): 121–35. Bibcode:1967BpJ.....7..121S. doi:10.1016/S0006-3495(67)86579-2. PMC 1368002. PMID 6048867.
  2. Gautier, R; Douguet, D; Antonny, B; Drin, G (2008). "HELIQUEST: a web server to screen sequences with specific alpha-helical properties". Bioinformatics. 24 (18): 2101–2102. doi:10.1093/bioinformatics/btn392. PMID 18662927.
  3. Wadhwa, R; Subramanian, V; Stevens-Truss, R (2018). "Visualizing alpha-helical peptides in R with helixvis". Journal of Open Source Software. 3 (31): 1008. Bibcode:2018JOSS....3.1008W. doi:10.21105/joss.01008.

Further reading
  • Mount DM (2004). Bioinformatics: Sequence and Genome Analysis (2 ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN 0-87969-712-1.
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