pot odds

You should precise the hands (with how much BB you have, he has, level, your specific hand and how he played before-his tendency etc..)

Usually, your pot odds should be bigger than the odds itself to make the call to win in the long run!

so, if i have flush draw on flop

35% chance of hitting

pot is 1000
bet is 400 to call which = 1400

35% of 1400 = 490

call?

You have ~35% chance to hit if you see turn and river.

If it's all-in, then 1400:400 = 3,5:1 = ~22% so yes, it's a call

If he would bet pot (all-in): 2000:1000 = 2:1 = ~33% so you could still call.

the strength of a draw depends on what alternatives you have - meaning: do you have any straight draw or backdoor straight draw? Can you win if you pair your hand on the latter streets?
So it really actually depends on what exactly you're holding and what the board is.
I'm not gonna give you PerusJamppa style mathematics because we both know we will never do this kind of math on the table
but he's right.

TL;DR: With the implied odds this is an easy call.
40% of the flop? You don't call that much for 9 outs unless the draw is strong. If it is strong go for it.

Odds are very important, but as you already figured out yourself we can sometimes call although we don't get the correct odds. That's due to the implied odds which should be taken into account.

Regarding the math:
If the pot is 1000 and he bets 500 you would need to call another 500 for a total pot of 2000. Divide the amount you have to call (500) by the total pot that would be the result (2000) and you have your pot odds. Next step would be to define your outs and get your win% that way.

Regards,
Asaban