# Atoms that define distance constraints

**URL:** <https://ask.bioexcel.eu/t/atoms-that-define-distance-constraints/4420>\
**Category:** Uncategorized\
**Created:** [July 19, 2023, 7:44am UTC](https://ask.bioexcel.eu/t/atoms-that-define-distance-constraints/4420 "2023-07-19T07:44:53Z")\
**Posts on this page:** 2\
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**Author:** ![gautamd](https://avatars.discourse-cdn.com/v4/letter/g/da6949/32.png) [@gautamd](https://ask.bioexcel.eu/u/gautamd)\
**Post date:** [July 19, 2023, 7:44am UTC](https://ask.bioexcel.eu/t/atoms-that-define-distance-constraints/4420/1 "2023-07-19T07:44:53Z")

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When one defines distances between residues (for distance constraints) which atoms are chosen, for amino acids and for nucleotides (in DNA/RNA)?

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [July 19, 2023, 8:01am UTC](https://ask.bioexcel.eu/t/atoms-that-define-distance-constraints/4420/2 "2023-07-19T08:01:52Z")

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It all depends on how you define your restraints, i.e. the selection your make.

If selecting a full residue (giving the residue number), all atoms of that residue will be used.  
If you in addition define specific atoms, only those will be used.

For the format of the distance restraints check for example Box 4 of our Nature Protocol paper:

- S.J. de Vries, M. van Dijk and **A.M.J.J. Bonvin** [The HADDOCK web server for data-driven biomolecular docking.](https://www.nature.com/nprot/journal/v5/n5/abs/nprot.2010.32.html) _Nature Protocols_, _5_, 883-897 (2010).