In order to survey the genome-wide trends in
amino acid compositions of the organism groups,
all of the proteins were examined in the amino
acid composition space, where each protein can be
plotted at a point according to its composition.17
The distribution of proteins in the 20-dimensional
amino acid composition space may be visualized
by projecting it on a plane, which is defined by
two unit vectors. One of them is taken as the unit
vector pointing from an average amino acid composition
of GHA to that of GNO, and the other vector
points from an average composition of GHA to that
of GTH. Two kinds of amino acid compositions,
one on the protein surface and the other in the
protein interior, are considered. Residues on the
protein surface and in the interior were judged
based on model structures provided in the GTOP
database.16