PDs don't target ships, although they may hit ships while aiming for something else.
Anacondas have two Small hardpoints on the lower rear of the ship, near the thrusters. These are probably what's chewing on you.
Point defense fire looks pretty different from other projectiles. It's a stream of little streaks of light with a greenish tint . When it's been a while since I've had missiles or mines coming after me, and the PDs on my Anaconda suddenly fire past the canopy, I sometimes think for a sec that I've encountered one of the rarer PowerPlay weapons or some strange new tech
The best angle to attack from is going to be different depending on how your ship and the Anaconda are set up. If he has all lasers up front, multicannons on his Small rear HP's, and your shields are 100%, his multis are the lowest threat to you.
Above and behind is generally best, because he can hit you with maybe two weapons, some of the time, while you have a clean shot straight at his Power Plant. In the upcoming 1.4 update, Power Plant destruction will no longer automatically blow up the ship, but it will probably still be the target of choice.
I don't recommend hanging out dead-ahead of an Anaconda for long, but... it's actually not the most dangerous place to be. Yesterday, I noticed that there's a 'sweet spot' ahead and to either side, where (assuming most of the 'conda's weapons are turreted), ALL BUT ONE of the big guy's guns can track and hit you! (The one that cannot is the medium HP on the opposite side, blocked by the hull) That is:
0-1 Huge (a fixed weapon like Plasma Accelerator won't hit here, but gimballed or turreted Cannons might, and...)
3-4 Large (there are 3 Large HPs, but the Huge may be underequipped with a Class 3 weapon for wider coverage/less power drain)
1 Medium
2 Small
Here's a rough illustration using a random screenshot I had (click to view full-size)
The red-zones are approximate and should be equal sizes, but they show the general area. Don't sit there unless you like high repair bills