An ab initio quantum chemical analysis is performed on the intrinsic deformability of the DNA base amino groups and their role in the base stacking interactions and conformational variability observed in the DNA crystal structures. The present calculations, made at the HF/6-31G (NH2) and MP2/6-31G levels of theory, lead to results qualitatively different from the previous empirical potential studies and demonstrate limited applicability of the commonly used force fields. The amino groups of isolated DNA bases are nonplanar, and the deviation of the amino group hydrogens from the DNA base plane amounts to 0.1-0.5 angstrom. The largest amino group nonplanarity is found for guanine. In the case of cytosine containing complexes, modeling the isolated base pair, the amino group geometry is determined primarily by the intermolecular geometry of the hydrogen bonds. The flexibility of the amino groups facilitates optimization of the interaction energy under condition of nonplanar geometry of the complex. On the other hand, the DNA base amino groups are significantly nonplanar, if they participate in the interstrand bifurcated hydrogen bonds or in the interstrand contacts of amino groups. Both phenomena are observed in many DNA crystal structures. The nonplanar amino group geometry improves the interaction energy. It is demonstrated that the widespread idea of the interstrand repulsive amino group clashes in the DNA is not correct, because close contact between two amino groups results in an attractive interaction similar to that in the bifurcated hydrogen bonds. The only exception represents the steps having crystallographically identical base pairs. It is because attractive amino group interaction requires a highly asymmetric arrangement of the two amino groups, while any geometry with 2-fold symmetry is repulsive. The ab initio calculations are supplemented by an analysis of the contacts of amino groups in the available B-DNA crystals to show that the close amino group contacts are very frequent in the asymmetric steps. These close contacts are, however, absent in the central steps of the crystal structures with crystallographically identical strands. This finding agrees with the nonempirical calculations and shows that conformational variability of the symmetric steps is significantly restricted by the crystal packing forces.