To do what you want with cluster :

1) Input file : bed file of the two TFs binding site with a field refering to the TF. ex :

chr1    100 150  TF1
chr1    180 230  TF2
chr1    250 280  TF1
chr1    950 1000 TF2

2) Find clusters within a reasonable window (for instance 500 bp).

bedtools cluster -d 500 -i in.bed > out.bed
cat out.bed
chr1    100 150  TF1     1
chr1    180 230  TF2     1
chr1    250 280  TF1     1
chr1    950 1000 TF2     2

3) check the number of TF1 and TF2 in each cluster. you can do that in bash, python, or even excel. I'll do it in R in this case :

clusters=read.table("out.bed", colClasses =c("factor", "numeric", "numeric", "factor", "factor"), col.names = c("chrom", "start", "end", "TF", "clust"))
by(clusters$TF, clusters$clust, summary)

clusters$clust: 1
TF1 TF2 
  2   1 
---------------------------------------------------------------------------------- 
clusters$clust: 2
TF1 TF2 
  0   1

4) Find the clusters that have 2 TF1 in it and one TF2 in it. Once again, I'll use R, but you can use something else.

by(clusters$TF, clusters$clust, function(x) (summary(x)[1]==2 & summary(x)[2]==1))

clusters$clust: 1
[1] TRUE
---------------------------------------------------------------------------------- 
clusters$clust: 2
[1] FALSE