Try

#!/usr/bin/perl -w
use strict;

my %hash;
(!/^$/) && (push @{$hash{(split /\s+/,$_)[0]}}, (split /\s+/,$_)[1]) w
+hile(<DATA>);


open TMP1, '>duplicates.txt' or die;
open TMP2, '>distinct.txt' or die;

for my $key (keys %hash) {
   for (@{$hash{$key}}) {
    (@{$hash{$key}} > 1) ? print TMP1 "$key\t$_\n" : print TMP2 "$key\
+t$_\n" ;
   }
}

__DATA__
protein1   stomach
protein2   head
protein3   muscle
protein3   heart
protein3   brain
protein4   leg
protein5   toes
protein5   mouth
protein6   ear
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Please refer to combine duplicate entries for similar solutions.
Thanks..