The 3-atom fragments, about which the atom distributions are defined, are any three atoms - 1, 2 and 3 - in which atom 1 is covalently bonded to atom 2, and atom 2 is covalently bonded to atom 3.
Only atom 3 of the fragment is used for defining atom-atom contacts; contacts with atoms 1 and 2 in the fragment are ignored, though, of course, distributions around these atoms are defined when they are at position 3 in other fragments.
Atom-atom contacts between a probe atom and the fragment's atom 3 are deemed to occur if their centres are within the sum of their van der Waals radii plus 1.0A. Atoms from the same residue, or from residues i +/- 1 or i +/- 2 along the polypeptide chain are excluded from consideration to cut out, as far as possible, contacts due primarily to the contraints of the local secondary structure.