The position of residues in (and out of) the helix are defined according
N4'-N'''-N''-N'-Ncap(the first residue of the helix)-N1-N2-N3- ... -C3-C2-C1-Ccap(the last residue of the helix)-C'-C''-C'''-C4'
Helix motifs consist of sequences in which specific classes of residues
are found at specific positions. The classes used in the motif description are:
h = hydrophobic residues (Ala, Val, Ile, Leu, Met, Phe, Trp, Cys, neutral His and the alkyl side-chain moieties of Arg and Lys);
p = polar (Gly, Ser, Thr, Asn, Gln, Asp, Glu, Lys, Arg and protonated His);
n = non-beta branched = not (Val,Ile, Thr, Pro);
x = indifferent
Here is the list of motifs describer by Aurora and Rose:
Ia = h-xpxhx
Ib = h-xpxph
IIa = hp-xpxhx
IIb = hp-xpxph
IIIa = hpp-xpxhx
IIIb = hpp-xpxph
IV = hxph-Gh
Va = hxpx-nxh
Vb = hxpx-nxph
VIa = hxxx-Gpxh
VIb = hxxx-Gpxph
VIIa = hxxx-Ppxh
VIIb = hxxx-Ppxph
The hyphen symbol (-) indicates the start of the helix (or the end, for C-terminal motifs).
As an example of explanation for the notation, Motif Ia starts at the N' residue with an hydrophobic residue, a polar residue is at the N1 position and an hydrophobic residue is at N3 position. Ncap and N2 positions can be occupied by any residue.