I guess you could try extracting JUST the loop residues into PDBs with a script and clustering those.
If you have constant sequences, then the loop residues ought to be on constant line numbers, so you can use something like:
for each PDB
Then you can try clustering those. The new files will have the old file names embedded so you can translate them back…
If you have nonconstant sequences then you can do something slightly fancier with sed/awk/grep where you search for the right residue number in the right column – either way it should be a one-liner to extract the needed residues into their own PDB file.