<?php

$str = "user1 A
user2 B
user4 C
user2 D
user1 E";

$lines = explode("\n", $str);

$arr = array();

foreach($lines as $line) {
    list($user, $letter) = explode(" ", $line);
    $arr[$user][] = $letter;
}

var_dump($arr);

array(3) {
  ["user1"]=>
  array(2) {
    [0]=>
    string(2) "A
"
    [1]=>
    string(1) "E"
  }
  ["user2"]=>
  array(2) {
    [0]=>
    string(2) "B
"
    [1]=>
    string(2) "D
"
  }
  ["user4"]=>
  array(1) {
    [0]=>
    string(2) "C
"
  }
}