As worded, your question is almost impossible to understand. It would be really helpful if you could provide some more explanation and context. However, a "list of proteins obtained from ENCODE" could mean ChIP Seq data sets for proteins studied by ENCODE. In that case one could download called peaks or sites, and use BEDTools (intersectBed) to find overlaps, or bring the data into R and use bioconductor tools (i.e. GenomicRanges). There's also a wide variety of tools listed at UCSC.