NAME Hbond - locate possible hydrogen bonds in a protein structure SYNOPSIS hbond -options files DESCRIPTION Hbond is a program to read in Brookhaven format files and to calculate all the possible hydrogen bonds and other sidechain interactions of interest. The output from hbond is a file with a .hbd extension that is primarily meant to be used as input for joy. If you want to use the file for other purposes it is important that you understand the assumptions used to define the hydrogen bonds. It is your responsibility to make sure that the input Brookhaven file is o.k., i.e. it should not have alternate atoms, explicit hydrogen atoms, etc; preprocessing of the Brookhaven file with pdb2atm(1) is recommended. The following options to hbond are available: -h Print a help message on the standard output. -v Be verbose in what is reported to the user, this is mainly of use to see what is actually being read by hbond. -V Print the version number of hbond on the standard output. WHAT IS A HYDROGEN BOND ? In the interests of simplicity, a hydrogen bond (or analogous interaction) is flagged if the distance between the two participants in the interaction are less than a set distance apart (usually 3.5). For disulphide bonds the criteria is that the two sulphur atoms are less than 3.0 apart (note, this is a generous cutoff). Due to the larger Van der Waal's radius of sulphur atoms a 4.0 cutoff is used for interactions involving this element type. No check is made on the lower bound of the distance. Interactions to HETATM records are always calculated. Some interactions also have the relevent angles calculated, however this has no influence as to whether an atom pair occurs in this file (and is considered as a hydrogen bond). Note that angles that are undefined are written as 999.99. For mainchain to mainchain hydrogen bonds, energies are calculated as in the paper of Kabsch and Sander. The following points may need to be considered before you use the program. The first is that the amide sidechains of asparagine and glutamine are assumed to be undetermined ( i.e. you can swap the NH2 and O atoms freely), thus both atoms are considered as donors and acceptors. The second point is that the y atom of cysteine is considered to be a possible donor and acceptor atom, additionally the d sulphur of methionine is an acceptor. Finally, the protonation state of an acidic residue (aspartic acid and glutamic acid is considered as undefined), i.e. it can be protonated and so again either of the oxygen atoms can be both donors and acceptors. Finally, (again) no interactions between residues are considered for atoms in residues closer than two residues from the central residue. Because of the nature of the cutoff, it is likely that not all the interactions reported are likely to be real hydrogen bonds. However, the definition is rigid and easily defendable. Other methods are likely to produce lists of hydrogen bonds that are simply subsets of the ones reported by hbond. However, it is relatively easy either to write a program that will select out the hydrogen bonds from the .hbd file, or to change the cutoffs internally within the program. FORMAT OF THE .hbd FILE The .hbd file contains a small header, whether HETATM records were included in the analysis. There the follows a list of the possible interactions, listed one per line, with the donor listed first followed by the acceptor atom. The format for the data in the .hbd file is (FORTRAN format): 1X, I3, 1X, A5, 1X, A1, 1X, A, 1X, A3, 1X, I3, 1X, A5, 1X, A1, 1X, A, 1X, A3, 1X, A3, 1X, I4, 1X, F4.2, 1X, F4.2, 1X, F6.2, 1X, F6.2 Where the fields are; the index of the first residue, the number of the donor residue, the chain-name of the donor residue, the residue type of the donor residue, and the atom type of the donor atom; this is followed by a similar set of values for the acceptor atom. This information is followed by the class of the hydorgen bond (see table below), an integer indicating the soacing of the donor and acceptor atoms (can be negative), the distance between the donor and acceptor atoms, the distance between the hydrogen atom and the acceptor (see below for how hydrogen positions are calculated), the angle between the donor, hydrogen and acceptor and finally the angle between the donor, acceptor and carbonyl carbon. An example of a .hbd file is: # produced by hbond, version 1.0c (2.3b) # parameterized for 600 residues, 20 atoms per residue, and 500 hetatoms # # coordinate data taken from file 2ptn.atm # number of atoms = 1610 # number of residues = 221 # number of chains = 2 # chain 1 extent from 1 to 4, of length 5 # chain 2 extent from 5 to 221, of length 216 # number of hetatoms = 1 # # criteria for hydrogen bond definition :- # donor-acceptor distance cutoff (oxygen and nitrogen) = 3.50 # donor-acceptor distance cutoff (sulphur) = 4.00 # hydrogen-acceptor distance cutoff = none # angular criteria applied = none # energy criteria applied = none # include HETATM records = T # include WATER records = T # #----- Donor ----- ---- Acceptor --- ------- Geometry ------ - Energy - #index - res - atm index - res - atm typ span Dd-a Dh-a <d-H-N <a-O=C kJ/mol 1 16 I N 120 142 G O MM 119 3.29 9.99 999.99 999.99 999.99 1 16 I N 121 143 N O MM 120 3.03 9.99 999.99 999.99 999.99 1 16 I N 174 194 D OD1 SN 173 2.72 9.99 999.99 120.26 * 999.99 1 16 I N 174 194 D OD2 SN 173 3.48 9.99 999.99 81.36 * 999.99 2 17 V N 169 189 D O MM 167 2.82 1.85 166.93 166.76 -3.01 4 19 G N 2 17 V O MM -2 3.42 3.40 83.36 71.35 .97 5 22 C N 133 155 L O MM 128 3.08 9.99 999.99 999.99 999.99 5 22 C SG 133 155 L O SO 128 3.52 9.99 999.99 89.43 999.99 5 22 C SG 134 156 K O SO 129 3.41 9.99 999.99 75.51 999.99 5 22 C SG 135 157 C SG DS 130 2.04 9.99 999.99 999.99 999.99 The hydrogen bonds are classified using the following scheme: center; l l. class meaning MM mainchain to mainchain MH mainchain to hetero atom MW mainchain to water SO sidechain to mainchain CO SN sidechain to mainchain NH SS sidechain to sidechain SH sidechain to hetero atom SW sidechain to water DS disulphide CAVEATS Please bear in mind what the program is meant to do, before blindly using its output. The program is likely to be changed in the near future. The main limit you are likely to encounter is a maximum numer of residues of 500. SEE ALSO pdbseq(1), joy(1). RELEASE LEVEL This document describes hbond version 0.7 and later.