The DNA double helix
(or at least about 1/10 th of a complete turn)
Stacked G:C and A:T base pairs
This figure looks down the axis of the helix at a G:C pair (red) over an A:T pair (green). The top pair is twisted 34 degrees relative to the pair below. The glycosidic bonds to the sugars are labeled "dR".
The is considerable overlap of the bases, but due to the twist it is not complete . As you can guess, the extent of over lap depends on the particular nucleotide sequence.
Since both sugars, and thus phosphates, are linked to the base pairs on the same side of the helix axis, the two phosphodiester chains are closer together at the lower left (the minor grove) than they are at the upper right (the major grove).
Add the sugars and phosphates and you have nucleotides
In this Java enabled display you can rotate the two pairs to get an idea of the 3D structure of the DNA helix. I have removed all H atoms except those involved in the base pairing.
Looking at the bases edge-on you see how parallel they are in the stack, and the four sugars show up well as pentagons, almost perpendicular to the bases.
The four phosphates are on the outside of the helix (I removed the two non-ester oxygen atoms from each phosphate). They are as far apart as they can be, which minimizes the electrostatic repulsion which tends to separated the strands. On the outside they can form H bonds with water, and are partially screened by a slight excess of positive ions clustered around them. There are a number of water molecules that are fairly tightly bound to the DNA , but they are not shown here.