Calculate the total number of intramolecular hydrogen bonds in T4 lysozyme (2LZM). Please be sure to count only the intramolecular hydrogen bonds; do not count any hyrdogen bonds between the protein and water molecules or between water molecules. Divide the total number of hydrogen bonds into the categories of main chain—main chain, side chain—main chain and side chain—side chain. Explain the relative abundance of each of these types in a typical protein structure. Did you notice anything odd in the report for the side chain—side chain category?
Run hydrogen bonding calculations for the
November 2017 PDBselect list. Now, that list is based on polypeptide chains, which may come in structures with other polypeptides and many water molecules. In order to simplify our analysis logic later, use an option of
gfp, the
-c option, to output only the specified chain. This option requires a five character input code, the four characters of the PDB ID and the one character chain ID, which is the full ID in the PDBselect file.
For your analysis, plot the total number of hydrogen bonds (remember, you don't have any water molecules in your structure files) as a function of chain length. A wrinkle that might help you here is that hbplus writes both of the number of residues and total number of hydrogen bonds to standard output for each calculation. When running hbplus over the PDBselect list, redirect standard out to a file (identified as hbplus-std-out-file later). To extract the pertinent data from that file, use the program hbcnt.
The PDBselect list does have just a few chains that are much longer than the rest, feel free to remove those couple long chains and replot to verify what you see. Still there, eh? What can you conclude about hydrogen bonding in proteins as a result?
Last updated at 08:39:49 on 2025-12-04.
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