If you only want to change certain lines in a file, also take a look at Tie::File, which makes this very easy:

use strict;
use Tie::File;
tie @lines, 'Tie::File', $filename
  or die "Couldn't open $filename : $!";

for my $line (@lines) {
  if ($line =~ /LEU\b/) {
    s/    (.*)/$z3leu  $z2leu  $z1leu   $1/
  }
};
[download]

That's it.

For an alternative, you could run Perl as a pipeline by redirecting the output of the following into a new file:

perl -pe "/LEU\b/ and s/    (.*)/$z3leu  $z2leu  $z1leu   $1/"
[download]