Structure : Make H Bond Restraints
Create Hydrogen Bond Restraints
This popup allows the user to make simple distance-based hydrogen bond
restraints for structure determination. These restraints are essentially the
same as other distance restraints, although a single hydrogen bond is usually
restrained with a complementary pair of restraints: one restraint is between
the hydrogen and the acceptor atom site (usually a backbone carbonyl oxygen in
proteins) and the other is between donor and acceptor heavy atoms (e.g.
between protein backbone amide nitrogen and carbonyl oxygen). This combination
of restraints work together to give an energy minimum for the restraint when
the donor, hydrogen and acceptor atoms are co-linear; a known optimum for
hydrogen bonds.
To make hydrogen bond restraints the user first selects various options from
the upper pulldown menus: a restraint set that groups the h-bond restraints
with other restraint lists, an H-bond type restraint list that the individual
restraints are place in, and a molecular system to specify which set of atoms
the restraints are between.
Next the “New H Bond Type” should be checked, but the default “N-H..O=C” is
already set for polypeptide backbone H-bonds. The various default distances can
be adjusted to specify what the restrained values will initially be, although
the user can make manual adjustments (including by setting and propagating new
defaults) afterwards. The “Lower Limit”, “Target” and “Upper Limit” distances
refer to the separation between the hydrogen and its acceptor. The distance
between the donor heavy atom and the acceptor atom are made automatically
based on the “X-H” bond length setting. Specifically, the target distance for
the heavy atoms’ restraint will be the hydrogen to acceptor distance plus
the bond length. Also, the upper and lower limits for these atoms will follow
the same proportions as the hydrogen to acceptor values; the values will be
the same fractions of the target distances.
Hydrogen bond restraints can be added using [Add New] and then setting the
Atom A and Atom B values by double clicking in the table and selecting the
required atom sites. Note that generally the user only needs to set the
hydrogen to acceptor restraints. The heavy atoms’ restraint is made afterwards
by pressing the [Make Co-linear Restraints] button. It notable that this
function will actually add any missing restraint of a co-linear pair.
Evidence
This system relies upon the user having a reasonable and unbiased judgement
about the location of hydrogen bond in a molecular structure. Whenever H-bond
restraints are made the user should always be aware of the evidence for
particular hydrogen bond. It is possible to get nice looking but otherwise
fictitious structures by using hydrogen bond restraints too liberally.
Often H-bond evidence often comes from knowledge of protein secondary
structure (particularly alpha-helix for i to i+4 links ), which in turn can be
deduced using chemical shift data, for example using DANGLE, or confident
comparative modelling of protein homologues. Also, there are some NMR
experiments that will exploit spin couplings over hydrogen bonds themselves.
Whatever the source of confidence about hydrogen bonds, using them as
restraints generally requires that consistency with any other structural data
is checked, for example by violation analysis. With NOE data for example it is
prudent to generate initial protein structures without any H-bond information
and only add-in H-bond restraints if they would be consistent with the initial
NOE-derived conformations. In this way ‘low evidence’ hydrogen bonds can be
added to improve the later stages of structure refinement without having an
undue influence of the general fold of a structure.
Main Panel
Restraint Set: Selects which restraint set the selected, or new, hydrogen bond restraint list resides in
H Bond List: Selects which hydrogen bond restraint list to display; may be set to “<New>” to put restraints in a new list
MolSystem: Selects which molecular system (group of chains) to make restraints for; sets which atoms are available for selection
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
H Bonds Table
Allows the setup of individual hydrogen bond restraints
Default Distances
1.73: Set the lower distance limit, in Angstrom, to apply to new hydrogen bond restraints; each limit may be subsequently adjusted
2.2: Set best-fit/target distance, in Angstrom, to apply to new hydrogen bond restraints; each limit may be subsequently adjusted
2.7: Set the upper distance limit, in Angstrom, to apply to new hydrogen bond restraints; each limit may be subsequently adjusted
1.0: The distance between the hydrogen and its covalently bound partner atom; user to make co-linearity restraints
New H Bond Type: Selects which kind of hydrogen bond is being made, with respect to the kinds of atoms involved
Hydrogen Bond Restraints
Table 1 |
Atom A |
The donor hydrogen atom involved in the hydrogen bond restraint (Editable) |
Atom B |
The acceptor atom involved in the hydrogen bond restraint (Editable) |
Lower Limit |
The lower distance bound value for the restraint, in Angstrom (Editable) |
Target Distance |
The best-fit/target distance for the hydrogen bond restraint, in Angstrom (Editable) |
Upper Limit |
The upper distance bound value for the restraint, in Angstrom (Editable) |
Add New: Add a new hydrogen bond restraint to the selected list; the acceptor and donor atoms etc. are set subsequently
Delete Selected: Delete selected hydrogen bond restraint from the list
Set Default Distances: Set the selected hydrogen bond restraints to have the default upper, lower and target distances
Delete List: Delete the whole hydrogen bond restraint list
Make Co-linear Restraints: Make any complementary restraints which restrain co-linearity of X-H..Y bonds