Automated methods for identifying and characterizing
regular β-barrels from coordinate data have been developed
to analyze and classify various kinds of barrel structures
based on geometric parameters such as the barrel strand
number (n) and shear number (S). In total,
we find 1,316 barrels in the January 1998 release of Protein
Data Bank. Of 1,316 barrels, 1,277 barrels had an even
shear number, corresponding to 50 nonhomologous families.
The (βα)8 triose phosphate isomerase
(TIM) barrel (n = 8, S = 8) fold has
the largest number of apparently nonhomologous entries,
16, although the trypsin like antiparallel (n
= 6, S = 8) barrels (representing only three families)
are the most common with 527 barrels. Of all the protein
families that exhibit barrel structures, 68% are found
to be various kinds of enzymes, the remainder being binding
proteins and transport membrane proteins. In addition,
the layers of side chains, which form the cores of barrels
with S = n and S = 2n,
are also analyzed. More sophisticated methods were developed
for detecting TIM barrels specifically, including consideration
of the amino acid propensities for the side chains that
form the layers. We found that the residues on the outside
of the eight stranded parallel β-barrel, buried by
the α-helices, are much more hydrophobic than the residues
inside the barrel.