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

pulldown Restraint Set: Selects which restraint set the selected, or new, hydrogen bond restraint list resides in

pulldown H Bond List: Selects which hydrogen bond restraint list to display; may be set to “<New>” to put restraints in a new list

pulldown MolSystem: Selects which molecular system (group of chains) to make restraints for; sets which atoms are available for selection

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

H Bonds Table

Allows the setup of individual hydrogen bond restraints

Default Distances

float 1.73: Set the lower distance limit, in Angstrom, to apply to new hydrogen bond restraints; each limit may be subsequently adjusted

float 2.2: Set best-fit/target distance, in Angstrom, to apply to new hydrogen bond restraints; each limit may be subsequently adjusted

float 2.7: Set the upper distance limit, in Angstrom, to apply to new hydrogen bond restraints; each limit may be subsequently adjusted

float 1.0: The distance between the hydrogen and its covalently bound partner atom; user to make co-linearity restraints

pulldown 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)

button Add New: Add a new hydrogen bond restraint to the selected list; the acceptor and donor atoms etc. are set subsequently

button Delete Selected: Delete selected hydrogen bond restraint from the list

button Set Default Distances: Set the selected hydrogen bond restraints to have the default upper, lower and target distances

button Delete List: Delete the whole hydrogen bond restraint list

button Make Co-linear Restraints: Make any complementary restraints which restrain co-linearity of X-H..Y bonds

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