Amphipathic beta-strand
The sequence clusters that
mapped to beta-strands were short and diverse, and there was no clear
point of division between them. However, there are clearly two extremes
among the patterns: amphipathic and hydrophobic.
A 3-residue stretch defined the category into which each cluster fell.
If there were three non-polar residues in a row, the cluster was placed
in the hydrophobic set; if the middle position preferred polar or had
no preference, it was called amphipathic. The highly heterogeneous nature
of the two beta-strand motifs may reflect the importance of non-local
interactions.
Amphipathic beta-strand:
The amphipathic beta-strand clusters have a 1-3 pattern of conserved non-polar
sidechains, followed by a different set of conserved residues for each
individual cluster in the motif. Position 5 (see Fig) was found to have
preferences for Pro, Asp, Arg/Lys, His, or strictly polar in 5 separate
clusters, and each case correlated strongly with beta-sheet structure.
Many members of the shortest clusters were found not in beta-sheets but
in short loops between helices. The non-polar periodicity of 2 is a strong
helix breaker. We found no beta-strand clusters where the amphipathic
pattern extended beyond 2 hydrophobic groups. The third alternating hydrophobic
position is only weakly conserved in some of these clusters; sometimes
that position prefers a proline.
