A helical wheel is a type of plot or visual representation used to illustrate the properties of alpha helices in proteins on a 360 degree map with respect to the side of the helix. 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. Thus we can say that a helix can be represented in its so called wheel presentation.
This representation is conceptually easily grasped, but tends to obscure the distance along the helix; residues 0 and 18 are exactly aligned on this diagram, but are actually separated in space by 27 Å. This is so because numbering the helix beginning with residue #0 simplifies some calculations. Note that distances along helices are measured from the first residue, but, in effect, do not count the first residue. Thus, the length of a four-residue helix is 4.5 Å, not 6 Å.
Constructing the helical wheel alpha helix (Helical wheel projection)
In constructing helical wheel plot first place the first amino acid denoted as #0 at 0° then the second denoted as #1 = 100° and so on….
Residue #0 = 0° –> #1 = 100° –>#2 = 200° –>#3 = 300° –> #4 = 400° = 40° –> #5 = 140° –>
#6 = 240° –> #7 = 340° –> #8 = 440° = 80° –> 9# = 900° (from first) = 180°.
These angles can be plotted on a circle. Doing so results in a representation that corresponds to the view looking down the long axis of the helix. (Note that the rotation is clockwise as the residue number increases). Helical wheel diagram is given below.
So, analyzing a peptide in α -helical form onto a plane along the helix axis allows for the circular distribution of the amino acid side chain direction away from the center. This analysis may reveal that if the first amino acid is hydrophobic, and then amino acid at positions 4, 5, 8, 11, 12 and 15 are hydrophobic and the rest hydrophilic, the helix obtains an amphipathic character, with the one side of the helix being hydrophobic and the other side being hydrophilic.
Therefore, one can conclude that the distribution of hydrophobic residues follows the loose rule that every 3rd and/or 4th residue is hydrophobic in nature. This arrangement is more common in alpha helices within the globular proteins, where one side of the helix is facing toward the hydrophobic core and one side is facing 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 region and coiled coil motifs.
Now different helical wheel generator are used to study alpha helices