Atoms that define distance constraints

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

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: