Not sure what your problem is, but that's way to much code :D

I think you want something like this:

#!/usr/bin/env perl

use strict;
use warnings;

our %code;

while (<>){
    chomp;
    my @tokens = split " ", $_;
    my $protein = shift @tokens;
    for my $token (@tokens) {
        $code{$token} = $protein;
    }
}

foreach my $key (sort keys %code){
    print "$key\t$code{$key}\n";
}
[download]

Using this input file:

A ABC DEF GHI JKL
B QRS TUV WXY
C EYE LUV YOU
[download]

I get this result:

ABC    A
DEF    A
EYE    C
GHI    A
JKL    A
LUV    C
QRS    B
TUV    B
WXY    B
YOU    C
[download]