my %h;
while ( defined ( $_ = <DATA> )){
  chomp;
  my ( $k, $v) = split ' ';
  push @{$h{$k}}, $v;
}

open my $fh1, '>', '/tmp/1.txt' or die;
open my $fh2, '>', '/tmp/2.txt' or die;

for my $k ( sort keys %h ) {
  my $c = @{$h{$k}};  
  for ( @{$h{$k}}){
    $c > 1 ? print $fh2 "$k\t$_\n" : print $fh1 "$k\t$_\n";
  }}
__DATA__  
protein1   stomach
protein2   head
protein3   muscle
protein3   heart
protein3   brain
protein4   leg
protein5   toes
protein5   mouth
protein6   ear
[download]