Hi Pinky,

1. I would not say that they are binding sites in the case of transcription factors or the protein you are doing IP with.

   With ChIP experiments you pull down DNA-fragments attached to protein. Now, if that particular protein is pulled down along with its interactors, then basically you are also sequencing those DNA fragments which are bound to its interactor proteins, which were pulled down during your ChIP experiment.

2. I didn't understand the meaning of "distance between binding sites"

1. Yes, the peaks are the putative binding sites, but not all the binding sites are functional (some of them are very weak bindings)
2. Are you saying the distance between binding sites and the promoters? You can use annotate them by homer http://homer.salk.edu/homer/ngs/annotation.html