Get a single number representing the contact probability between a pair of genomic loci using HiC data
The fundamental unit of a Hi-C contact is the nearest restriction enzyme cut site.
This is where each mate in a read pair from a Hi-C library comes from and is mapped to when converting sequencing data into a contact matrix.

Because the distance to the nearest cut site is variable at different genomic positions, and depth of coverage of any single locus is typically low, contacts are aggregated into bins and "normalized" to account for differences in cut site densities within those bins.
This normalization transforms the raw contact matrix into something resembling a stochastic transition matrix, where you can think of the elements of that matrix as "what is the probability that at any moment in time bin $i$ is in contact with bin $j$".

So the probability you're looking for is the $(i, j)$th element of the normalized contact matrix, where bins $i$ and $j$ contain your regions of interest.
If your regions straddle the bin boundaries, you may want to average those bins.

You get to pick the resolution of the contact matrix, but if you select a resolutiong that's too small, you run the risk of making your matrix too sparse and having no contact between those loci.
If you pick one that's too large, your matrix elements aren't really informative for your question at hand.

Given your 500-5000 bp range and median of 1 kbp, it may make sense to pick a resolution between 1 kbp and 5 kbp and use that.