24 July 2001
Release 1.1 substitutes release 1.0_new. This release has improvements to speed up the search in the most recent release of dbs.
The position of residues in (and out of) the helix are defined according
this nomenclature:
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:
N-terminal motifs
Ia = h-xpxhx
Ib = h-xpxph
IIa = hp-xpxhx
IIb = hp-xpxph
IIIa = hpp-xpxhx
IIIb = hpp-xpxph
C-terminal motifs
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.