Hydrogen Bond Plot 
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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.



Program features


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).


When using this program, please cite:

Z. Bikadi, L. Demko and E. Hazai
Functional and structural characterization of a protein based on analysis of its hydrogen bonding network by hydrogen bonding plot
Arch. Biochem. Biophys. 461, 225-234 (2007)

I. K. McDonald and J. M. Thornton
Satisfying Hydrogen Bonding Potential in Proteins
JMB 238, 777-793 (1994)