How strongly do you want us to leave the terminals pointing out, and not buried?
It's okay if the terminals of your small peptide are buried or directed toward the target protein. These peptides might be hard to map directly onto a larger protein, but such high-scoring hotspots are still very informative.
That's a good question, though. Since I will be extending the "stub", I will ultimately need exposed termini -- but bkoep is correct; you don't need to worry about it. The most important thing for this puzzle is getting the side-chains to dock well at the SOD1 dimer interface. I can tweak the backbone after the fact for subsequent design, so designs with buried termini are still perfectly fine.
The scores for this puzzles have been adjusted and updated. See http://fold.it/portal/node/996740 .
One player pointed out that SOD1 is a metalloprotein (i.e. it has metal atoms as part of its structure -- one copper and one zinc per subunit). This is true, though they're not shown in this puzzle. I stripped out the metals for this puzzle because they're far from the region where we want our peptide to bind (the dimer interface), and because the puzzle would have required a little bit of extra setup on our part in order to make sure that Foldit didn't choke on the metals. The bottom line is that I was being a little bit lazy by leaving them out, but they wouldn't make a difference in this case!