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DivineSolutions

Guide 05 · Structure

Reading
a helical wheel

How to read the wheel diagram in Sequence Studio, and what it can and can’t tell you.

Reading time
2 min
Sections
4
Updated
On this page4 sections

Looking down a helix

In an α-helix each residue sits about 100° around the axis from the one before it, and 3.6 residues make a full turn. A helical-wheel projection looks down that axis and places residue n at (n − 1) × 100°, counting from the first. Drawing a line from each residue to the next traces the star you see in Sequence Studio.

Fig. 1 · Helical wheel

Computed from the sequence

1 · Leu · hydrophobicL12 · Leu · hydrophobicL23 · Gly · hydrophobicG34 · Asp · acidicD45 · Phe · hydrophobicF56 · Phe · hydrophobicF67 · Arg · basicR78 · Lys · basicK89 · Ser · polarS910 · Lys · basicK1011 · Glu · acidicE1112 · Lys · basicK1213 · Ile · hydrophobicI1314 · Gly · hydrophobicG1415 · Lys · basicK1516 · Glu · acidicE1617 · Phe · hydrophobicF1718 · Lys · basicK18

Hydrophobic Polar Basic (+) Acidic (−)

Fig. 1. The first 18 residues of LL-37, numbered in sequence order, 100° apart. Leu2, Ile13 and the phenylalanines gather on one face, and the arrow points to it. LL-37 is studied as an amphipathic helix in membrane-like environments.

Color is chemistry

Each residue takes the color of its side-chain class:

Amber
Hydrophobic. Here the class also includes glycine and proline.
Green
Polar.
Blue
Basic. Lysine and arginine are positively charged at neutral pH; histidine (side-chain pKa about 6.5) is mostly neutral.
Red
Acidic: negatively charged at neutral pH.
Gray
Non-standard residues, such as Aib or 2-naphthylalanine.

The arrow

The arrow is the hydrophobic moment: the vector sum of each residue’s hydropathy pointing out from its position. If hydrophobic residues cluster on one side of the wheel, the arrow points to that face and is long; an even mix gives a short arrow. Amphipathic helices, such as many antimicrobial peptides, show strong moments.

A caveat

The projection assumes an ideal α-helix. Short peptides, proline-rich sequences and many of the peptides we list don’t form stable helices, so for them the wheel is a consistent way to picture the sequence rather than a claim about its structure.