<?php

$array = array('A','B','C','D','E','F','G','H','I');
$seperation = 3;
$assoc = array(); // stores result

for($i = 0; $i+$seperation < count($array); $i++) {
   $assoc[$array[$i]] = $array[$i + $seperation];
}

print_r($assoc);

Array
(
    [A] => D
    [B] => E
    [C] => F
    [D] => G
    [E] => H
    [F] => I
)