140 A.E. Kister et al.
Fig. 7.3.The connection between the strands in two subsheets. (a) Two “short”
edge strands in different subsheets form a hydrogen bond contact. The strands a,
b, and c form one subsheet, while the strands k, m, n form another subsheet. The
strands a and k are the edge strands in these two subsheets. (b) One “long” edge
strand k forms H-bonds with the strands of both subsheets. The part at the begin-
ning of the strand k′is connected with the strand m of one subsheet and the part
k′′is connected with the strand a of another subsheet. (c) Two “long” edge strands
k and a form H-bonds with the strands of both subsheets. Residues of the k′part
of the strand k form H-bond contacts with the strand m, and a” parts of the strand
a. Residues of the k′′part of the strand k form H-bond contacts with the strand a′.
(d) Three “long edge strands k, m and a form H-bonds with the strands of both
subsheets
7.4.7 Classification of Barrel Based on the Strands Arrangement
The arrangements of the barrel strands in two subsheets of the mainβ-sheet
are shown in Table 7.2. It illustrates the arrangement of strands in the main
β-sheet of one representative structure of each protein folds. For example,
in the 1bia structure (fold # 40) the first subsheet contains mutually parallel
strands 1, 2 ′, and 5 (subsheet A), while the other subsheet is made of mutually
parallel strands 2′′, 3, and 4 (subsheet B) (Fig. 7.1).
It was shown that all proteins of a given fold share the same arrangement
of strands in the A and B subsheets. The arrangement of the strands in the
A and B subsheets in a given fold is different from that of other fold. For
example, the proteins in folds ## 48 and 49 have a similar arrangement of
the strands in theβ-sheet: 1-2-3-4-5-6; however the “strand compositions” of
“β-subsheets” A and B are different (see Table 7.2).
It is important to mention here that in our research the secondary structure
definition and the arrangement of the strands in the structures are based
mostly on the analysis of the H-bond contacts between the main chain atoms.
It follows that the information about the matrix of H-bond contacts between
residues of a barrel structure is sufficient to formally assign a given barrel
protein to its proper SCOP fold.