142 A.E. Kister et al.
protein structures (the single exception was found in the proteins described
in the protein fold # 57, “Domain of alpha and beta subunits of F1 ATP
synthase-like” in SCOP database). It follows that the rule of two interlocked
pairs of strands can serve to distinguish of the sandwich and barrel structures.
7.4.11 Invariant Substructure at the Place of Distortion:
A Hydrophobic Tetrahedral
Analysis of residue content of the place of distortion revealed four conserved
positions in each subsheet. The residues at each such position across the wide
spectrum of barrel proteins all share certain sequence and structural proper-
ties. The four conserved positions of each subsheet can be said to represent
the invariant substructure of their respective subsheet. A specific chemical
characteristic of these positions is that at least three of the four conserved
positions in each subsheet are occupied exclusively by hydrophobic residues.
If we take the four conserved positions in either subsheet to be the ver-
tices of a closed geometrical figure then each subsheet will be seen to contain
an imaginary tetrahedral. Interestingly, the invariant substructures of the two
subsheets are essentially identical. The characteristic appearance of the invari-
ant substructure is a consequence of the fact that the pairs of residues in the
two strands that form the two opposite “faces” of the tetrahedral are located
one reside away from each other. Figure 7.4illustrates the invariant tetrahe-
dral of each subsheet. Note that residues at the positions s in one strand and
t in the other always share a hydrogen bond; the two upstream positionss+2
andt+ 2 complete the figure. A similar situation is obtained in the other
subsheet, where the four tetrahedral positions are p andp+2, r andr+2,
with an H-bond between residues at the p and r positions. Since at least three
of the four positions of each tetrahedral are always hydrophobic, the invariant
structures of the subsheets were termed “hydrophobic tetrahedras.”
Fig. 7.4.Two tetrahedrals form “tetralock” in the barrel structures