Spin-systems are usually restricted to each amino acid in the peptide chain because there is no detectable proton coupling between each residue. N there is heteronuclear coupling between residues. In addition, the quality of the structures has also be improved by the availability of additional inter-proton distances. In all modern multi-dimensional NMR experiments the chemical shifts of one spin are associated with that of another spin by transfer of the magnetization between spins. Usually, but not always, dipolar coupling is only measured for pairs of protons.
Scalar coupling is used to transfer magnetization between all combinations of spins.
Determining which protons belong to the same spin system is accomplished by a variety of homonuclear and heteronuclear methods. Unless you can resolve peaks in the spectra it is very difficult to determine reliable inter-proton distances. In the homonuclear case, only proton-proton couplings can be elucidated by these experiments. This experiment gives peaks whose frequencies are those of two coupled spins. This is accomplished by the transfer of magnetization, in a sequential fashion from one proton to another, to another, etc.