Protein Side Interaction Assay

I was to compare the two peptides using pull down assay.  So, first, the peptides were made with a GST fusion tag.  The pull-down assay would have the GST tag bind to GS beads and the peptide would bind to the NS3 Helicase which would be added to see how much affinity the peptide had to the NS3 Helicase.  The affinity would be tested by SDS-PAGE and Western Blot.  The experimental peptide had the same affinity as the control peptide.  I decided to make another control using the GST Tag by itself to see if the GST tag had any side interactions with the NS3 Helicase.  There was none.