Java uses properties files because Java code gets compiled into binary format and therefore making any code changes becomes difficult. By removing configuration values ot a text file, Java enables people to change the confioguration without recompiling.
PHP, on the other hand, is not compiled into binary. Therefore, the PHP files are always editable by a a plain text editor. Most PHP apps handle confguration options by placing them into a separate PHP file with lots of comments describing each setting. And the settings are directly made to variables. Then any PHP code that needs those settings includes that file and then uses the variables. For an example of this, look at the settings.php file that comes with Drupal.