Protein Structure and its Classification - Essays in Bioinformatics - page 110

folds are roughly paralleled by Frequently Occurring Domains (FODs) in the SCOP
database and by highly populated regions of fold space in FSSP.
Predominantly Alpha-Domains -helix that runs

parallel to the helix axis, the residue side-chains form ridges separated by grooves, and
helices pack together so that the ridges of one helix fit into the grooves of the other. The
average interaxial distance of packed helices is 9.4Å, which means that inter-helix contact
is made by the side chain ends. The relative angle between the helical axes depends upon
which ridges and grooves are intercalated. The most common arrangement has the ridges
formed by every fourth residue on one helix fitting into the grooves formed from every
fourth residue on the other helix in which case the angle is ~50 o . Other characteristic angles
are observed, the second most common being ~20 o which arises when the ridges of one
helix formed from each third residue fit into the grooves formed by every forth residue on
the other helix [[9].
Four-helix Bundle The most frequent

α - α Packing On any surface of an α

α -helical domain in globular proteins is the

four-helix bundle, which is made up of two -hairpins. It occurs in proteins as disparate as

cytochrome b 562 [58] and the tobacco mosaic virus protein coat [59]. Sequential helices are
packed together at an angle of ~20 o and can be either anti-parallel as in hemerythrin (figure
15) or parallel as in human growth hormone.
Globin Fold The globin fold occurs in the mammalian oxygen binding proteins,
haemoglobin and myoglobin, and other related proteins such as the phycocyanins [12, 60-
61]. It is a bundle of eight helices usually labelled A to H, in which sequential helices are
not adjacent (except for G and H) and are arranged to form a pocket for a heme group. The
helices are packed at angles of around 50 o .

α

Figure 15. a) Schematic diagram of a four-helix-
bundle. b) Raswin cartoon of Hemerythrin, chain
C, 2hmz [62]. CATH : 1,20,120,50. (alpha, up-
down bundle, 4-helix bundle) SCOP : alpha, four-
helical up-and-down bundle ( CATH description to
topology level, SCOP description to fold level)

Figure 16 Raswin cartoon of horse heart
myoglobin, 1ymb [12]. For clarity pairs of
consecutive helices are shaded differently. CATH :
1,10,490,10 (alpha, orthogonal bundle, globin-like)
SCOP : Alpha, globin- like.