136 A.E. Kister et al.
7.4.3 Defining of theβ-Strands and Loops
As mentioned above our Structural analysis is based on the information about
H-bonded residues. A pair ofβ-strands is determined as two fragments of
residues whose residues are connected by H-bonds between the main chain
atoms. The first residue in the segment to form an H-bond is considered to
be the first residue of the strand, while the residues that come before it in a
sequence are not involved in H-bonding and are, therefore, considered to be
part of a loop. Similarly, the last residue of an amino acid segment to form an
H-bond defines the end of the strand. Based on this analysis the strands in
the structure are consequently numbered starting from N-end of sequences.
The segments of residues between the strands are considered as the loops.
We do not consider here the conformation of loops. As known from the analysis
of all beta proteins some loops in the structures were observed in the helical
conformations.
Strands in barrel structures are numbered sequentially starting from the
N-end of the sequence. Barrel structures differ by the number of strands (“n”)
that form the cylinder. In the “All beta” class of SCOP database beta-barrel
structures are made from 4 to 8 strands.
Some strands in the mainβ-sheet have more than two adjacent strands.
These are termed “bifurcated strands.” More than half of the barrel structures
have at least one such bifurcated strand. As a result, they contain the so-called
“side”β-sheets in addition to the main barrelβ-sheet. So far as our goal is to
define what is common to all barrel structures, we eliminate the sideβ-sheets
from our analysis of supersecondary structures, and retain only the strands
that make up the mainβ-sheet. The strands in the “edited” barrel structures
are numbered sequentially starting from the N-end of the sequence.
Barrel structures differ by the number of strands (n∗) that form cylinder
structure. In the “All beta” class of SCOP database beta-barrel structures
contain 4–8 such strands.
7.4.4 Arrangement of the Strands in theβ-Sheet
The interstrand hydrogen bonds define the strand arrangement ofβ-sheet.
The H-bonds were calculated for all barrel structures. Figure 7.2 illustrates the
interconnection among strands in the 1bia structure: strand 1 is H-bonded to
strands 2 and 5, while strand 5 is bonded only to strand 1; strand 2 is bound
to strands 1 and 3, and strand 4 – to strand 3. Since strands 4 and 5 are not
connected to each other, 1bia is a partly open barrel. Arrangement of strands
of mainβ-sheet in the 1bia structure can be represented schematically as: 5-1-
2-3-4. Arrangement of strands in the beta barrels of different folds is presented
in the “Arrangement” column of Table 7.2.
Despite the large number of possible combination of strands in barrel struc-
tures, the number of different arrangements of strands is in reality very lim-
ited. For example, the theoretical number of strand combinations in the barrel