Coincidentally, I use a way of keeping the contacts and the negs together, but not actually next to each other. I have my negs in paper sleeves (135, 120, 4x5) and the neg pages are inside archival storage boxes - the things that are used in document archives, having acid-free carton and stainless metal fixtures (no glue). I store those boxes horizontally, so the neg pages are flat, and then an archival board or foamboard divider with the contacts laid on that, or vice-versa.
The numbering of the neg sheets and the contacts match, and the total capacity of each box is relatively small, so matching the negs to contacts is pretty simple even though they are not in direct contact with each other. The archival boxes go on a metal shelving unit and stacking the boxes three high seems to be steady enough. The outside of the boxes gives plenty of space for clear labelling of the contents, however they sit on the shelf.