The first attack you make in a given turn has no penalty to hit. Each subsequent attack you make accrues some cumulative attack penalty (AP) which will apply to future attacks made in the same turn. The value of the penalty that's added is the AP of the equipment or body part you attack with. Unless otherwise noted, an attack has an AP of -3. This is the AP for missile attacks as well as any other attack where an -3 isn't stated. Your attack penalty resets to 0 at the end of each turn (not just your own).