It is crucial to realize that the form of DNA is dynamic. You should not think of it as something static; I am not aware of there being any regions in the genome that are permanently in A- or Z-form.

To my understanding, conversion of DNA from the default B-form to A-form primarily happens as a response to dehydration, presumably to protect the DNA. I am thus not sure that A-form is really something you need to worry about; if you are looking for protein-DNA interactions in happily growing cells, I think you can safely ignore A-DNA.

Because Z-DNA forms a left-hand helix (as opposed to the right-hand A- and B-DNA), the formation of Z-DNA happens in response to negative supercoiling. Some work was done long ago on predicting the propensity of different DNA sequences to form Z-DNA when negatively supercoiled (Ho et al., 1986). I am not aware of a tool that you can download, though.

However, I think it is fairly safe to assume that most DNA is in B-form most of the time. If the protein you are interested binds to B-form DNA, I think you are on bit of a wild goose chase here.

This database predicts non-B DNA structures

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.

But be careful. Lars Juhl Jensen is absolutely right, you need to be very careful in interpreting a prediction