3.2 The Algorithm
The algorithm for locating hydrogen bonds involves two steps. Firstly,
finding the positions of the hydrogens, and secondly, calculating the
hydrogen bonds. An interaction is counted as a hydrogen bond if (i) it is
between a listed donor and acceptor (Table II) and (ii) the angles and
distances formed by the atoms surrounding the hydrogen bond lie within
the set criteria. If the donor and acceptor are only one or two covalent
bonds apart, the interaction is not counted as a hydrogen bond.
Cysteines are treated specially. Any two Cysteines which have their
sulphur atoms within three Angstroms (this distance can be changed using the
command line arguments) are defined as Cystines, and treated separately.
In principle, Cystines can accept two bonds but cannot donate.
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Table II - List of Hydrogen Bond Donors and Acceptors
Donors
1. N (ie Main Chain NHs of recognised residues)
2. CYH SG, HIS NE2, HIS ND1, LYS NZ, ASN ND2, GLN NE2, ARG NE, ARG NH1,
ARG NH2, SER OG, THR OG1, TYR OH, TRP NE1
3. Recognised donors of non-standard recognised molecules
4. Nitrogen atoms in unrecognised molecules
5. Oxygen atoms of recognised water molecules
Acceptors
1. O (ie Main Chain COs of recognised amino - not imino - acid residues)
2. CYH SG, CSS SG, ASP OD1, ASP OD2, GLU OE1, GLU OE2, HIS ND1, MET SD,
ASN OD1, GLN OE1, SER OG, THR OG1, TYR OH
3. Recognised acceptors of non-standard recognised molecules
4. Oxygen atoms in HETATM molecules (including waters)
Atoms that may act as both donors and acceptors under the -X or -x options
1. HIS CD2, HIS CE1, ASN OD1, ASN ND2, GLN OE1, GLN NE2
Non-Standard Recognised Molecules
1. Standard Nucleotides C, A, U, G, T, also ATP.
2. Coenzymes COA, FMN, HEM, NAD
3. Small Molecules MTX, ACE, FOR
4. Amino Acids AIB, PHL, SEC, ALM, MPR, FRD, LYM, GLM, PPH, PGL, OLE, ABA,
NLE, B2V, B2I, B1F, BNO, B2A, B2F, IVA, LOV, STA, PVL, CAL, PHA, DCI,
AHS, CHS, MSE, ETA, PCA, ASX, GLX, UNK, CYH, CSS
These can be listed with the -P option.
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Received on Mon May 24 2004 - 08:53:00 PDT
