292 S.S. Wijmenga, B.N.M. van Buuren/Progress in Nuclear Magnetic Resonance Spectroscopy 32(1998)287-387 Cytosine Thymine Uracil Guanine i+1 Fig 1. Structure and atom numbering in nucleic acids, according to the IUPAC/UB guidelines 61, of the five common bases(pyrimidines C,T and U; purines G and A)(A), and of the B-D-deoxy )riboses(B and C).(B)also shows the torsion angles in the sugar-phosphate backbone(a, B, 6, e and $)and the glycosidic torsion angle x( the exact definition is given in the text), a designation of the chain 5 to 3 direction and the unit numbering in a polynucleotide chain. (C) shows the puckering of the two most common B-D-(deoxy )ribose sugar ring conformations, the C2'-endo(or S-type )and the C3'-endo(or N-type)conformati subsequently going into more detail. Finally, we 4.1.Overview of short distances and their general iscuss their derivation from NOESY spectra and characteristics their use as constraints in simulated annealing protocols In Table 1 we have summarized the short distancessubsequently going into more detail. Finally, we discuss their derivation from NOESY spectra and their use as constraints in simulated annealing protocols. 4.1. Overview of short distances and their general characteristics In Table 1 we have summarized the short distances Fig. 1. Structure and atom numbering in nucleic acids, according to the IUPAC/IUB guidelines [61], of the five common bases (pyrimidines C, T and U; purines G and A) (A), and of the b-D-(deoxy)riboses (B and C). (B) also shows the torsion angles in the sugar–phosphate backbone (a, b, g, d, « and z) and the glycosidic torsion angle x (the exact definition is given in the text), a designation of the chain 59 to 39 direction and the unit numbering in a polynucleotide chain. (C) shows the puckering of the two most common b-D-(deoxy)ribose sugar ring conformations, the C29-endo (or S-type) and the C39-endo (or N-type) conformations. 292 S.S. Wijmenga, B.N.M. van Buuren/Progress in Nuclear Magnetic Resonance Spectroscopy 32 (1998) 287–387