my @aminos = qw( A R N D C E Q G H I L K M F P S T W Y V );

# now A-R is the same as R-A in terms of interactions but if we
# only use one we need a sort so use both, duplicate data but lose sort....
my @a_a;
for my $a1(@aminos) {
    for my $a2(@aminos) {
        push @a_a, ["${a1}_${a2}", (join '', sort $a1,$a2)];
    }
}

# now prepare our lookup table for interactions
my %interactions;
for my $a_ref( sort{ $a->[1] cmp $b->[1] }@a_a ) {
    $interactions{$a_ref->[0]} = rand;
}

my @chains = map{ [(@aminos)x25] } 0..5;

my $interact;
for my $ca_i( 0.. $#chains-1 ) {
    for my $cb_i( $ca_i+1 .. $#chains ) {
        print "Comparing chain $ca_i to $cb_i\n";
        for my $res_a( @{$chains[$ca_i]} ) {
            for my $res_b( @{$chains[$cb_i]} ) {
                $interact = $res_a . '_' .$res_b;
                print "\t$interact => $interactions{$interact}\n";
            }
        }        
    }
}