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About HB Plot
HB Plot is a new tool for exploring protein structure and function by
describing structure as a network of hydrogen bonding interaction. HB Plot
offers a simple way of analyzing protein secondary and tertiary structure.
Hydrogen bonds stabilizing secondary structural elements and those formed
between distant amino residues - defined as tertiary hydrogen bonds - can be
easily distinguished in HB Plot, thus, amino acid residues involved in
stabilizing protein structure and function can be identified. By analyzing
the network of tertiary interactions the possible spread of information
within a protein can be investigated as well.
The program distinguishes between main chain – main chain, main chain – side
chain and side chain – side chain hydrogen bonding interactions. Bifurcated
hydrogen bonds and multiple hydrogen bonds between amino acid residues; and
intra- and interchain hydrogen bonds are also indicated on the plots. Three
classes of hydrogen bondings are distinguished by color coding; short
(distance smaller than 2.5 Å between donor and acceptor), intermediate
(between 2.5 Å and 3.2 Å) and long hydrogen bonds (greater than 3.2 Å).
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