Helix

Helixes (AAColor coloring, "cartoon thin" view).

Helix is one of three types of secondary structure in Foldit. The other types are sheet and loop.

In its ideal form, a helix appears like a coiled cylindrical spring with its sidechains pointing outward. Ideal helixes usually have hydrogen bonds between every fourth amino acid in the helix.

Some times the prefix "alpha" is added, so you might see "alpha helix" or "α-helix". The "alpha" reflects the fact that helixes were the first type of protein structure discovered.

The Foldit view options "Show Bonds" (basic GUI) or "Show Bonds (helix" (advanced GUI) can be used to visualize helix bonds. In the advanced GUI, the "cartoon" or "cartoon thin" protein view options show helixes with the coiled shape seen in the example on this page.

An ideal helix has one turn of the coil for every 3.6 amino acids.

Certain amino acids have a tendency to form helixes, while others tend not to. Those that often (but not always) form helixes are methionine, alanine, leucine, uncharged glutamate, and lysine ("MALEK" in the amino-acid 1-letter codes). Those that do not easily form helixes include proline, glycine, and aspartate. Proline, however, may be found at the beginning of a helix.

Helixes as Part of Larger Structures

Editor's note: this section is interesting, but it's perhaps a bit on the technical side for most.

Coiled-coil α helixes are highly stable forms in which two or more helixes wrap around each other in a "supercoil" structure. Coiled coils contain a highly characteristic sequence motif known as a heptad repeat, in which the motif repeats itself every seven residues along the sequence. The first and especially the fourth residues (known as the a and d positions) are almost always hydrophobic (the fourth residue is typically leucine) and pack together in the interior of the helix bundle. In general, the fifth and seventh residues (the e and g positions) have opposing charges and form a salt bridge stabilized by electrostatic interactions. Fibrous proteins such as keratin and myosin often adopt coiled-coil structures, as do several dimerizing proteins. A pair of coiled-coils - a four-helix bundle - is a very common structural motif in proteins. For example, it occurs in human growth hormone and several varieties of cytochrome. The Rop protein, which promotes plasmid replication in bacteria, is an interesting case in which a single polypeptide forms a coiled-coil and two monomers assemble to form a four-helix bundle.

See Alpha helix in wikipedia