HydrogenBonds

Usage of Hydrogen Bond Constraints

Application of hydrogen bond constraints is optional, though not recommended in the absence of experimental evidence, such as detection of scalar couplings across hydrogen bonds, or measurement of amide proton exchange rates.

In the absence of direct experimental evidence hydrogen bonds can be inferred from the preliminary structures (for example, if found in >50% of structures in the ensemble). The corresponding hydroden bond constraints can then be used to generate more consistent structure ensembles. Keep in mind that this procedure carries a risk of introducing bias in the resulting structrures.

Hydrogen Bond Constraints for Cyana

Each hydrogen bond is defined by a pair of upper and lower distance constraints. This is an example hbond.upl for hydrogen bond upper bounds:

13 VAL  H      59 VAL  O       2.00
13 VAL  N      59 VAL  O       3.00

This is an example hbond.lol for lower bound restraints:

13 VAL  H      59 VAL  O       1.80
13 VAL  N      59 VAL  O       2.70

Both upper and lower distance constraints can be generated with the 'Hbonds' command in CYANA. See also the Hbonds.cya macro in the demo/tasks folder of the CYANA installaion directory.

The default bounds in CYANA are 1.8-2.0 and 2.7-3.0 A. Other values can be chosen for compatibility with alternative software, such as CNS and Xplor.

Hydrogen Bonds Report

A report on hydrogen bonds in the selected structures can be generate with the 'structures hbonds' command. Note that the default criteria for considering a particular donor-acceptor pais as hydrogen bonded may be different from the default constraint bounds.

The same report is also generated by the overview.cya macro at the end of structure calculation. For an example see the Cyana wiki overview page.