First of all, the calculator is entirely wrong. The only way to know how many calories your body uses is to measure every day for a period of several months. Track every calorie you eat and your median weekly weight. Then you'll be able to calculate your maintenance calories, i.e., the number of calories you need to eat per day to maintain your current weight. You can use online calculators for a very rough guess to start with, but everyone is different, and it's best to track calories anyway if you're serious about fitness.
After that's done, you need to understand that "bulking" is not a useful or necessary thing to do, unless your goal is to gain fat. You can build muscle while in a calorie deficit. All that matters is that you're getting enough protein, not eating in TOO much of a deficit (100-300 calories below your maintenance level is fine), and doing the work to break down the muscle (i.e., lifting heavy weights).
Also, at 31, be aware that you can only gain about 2-3 pounds (.9-1.3 kg) of muscle per year MAX. All other weight you may gain from "bulking" is fat. You're simply too old to make the kinds of insane gains that a 15-20 year-old could. If you want to do something about this, the only (legal) solution is to talk to a men's health physician about HRT.
Finally, once you understand all of the above, no, it doesn't matter where your protein comes from. You could drink protein powder all day, eat no other source of protein, and still gain muscle. It has all the amino acids you need. And 1 gram of protein per pound (1 lb = .45 kg) of muscle is MORE than enough for anyone. You should be eating 165 g protein per day at the most; really, 150 g will be fine and should be easily doable.
It is very hard to not eat enough protein. In your daily estimate, it sounds like you're only accounting for the obvious animal-based proteins, when there is likely protein in many of the other things you eat (such as bread or milk). Take this example: Chug two protein shakes in the morning and you're already at 50 g protein. Three eggs and a piece of toast is another 23. A tall glass of milk is another 16 g. Add an extra egg white to your eggs and that's another 5. This is not even an especially large breakfast for most active men (it's about 770 calories), and afterward you'd only need 56 more grams of protein in the entire rest of your day. A nice, large chicken breast for lunch will get you basically there, and you haven't even had dinner yet.
The main reason bodybuilders like protein powder is that it's a low calorie AND convenient way of getting protein that tastes decent (it's also often the cheapest). They want to watch their calories so that they don't gain fat, but they also need to get enough protein within their calorie limit. Chicken breast is also very low in calories, but it's high in time and effort to cook. Eggs take less time and effort, but are high in calories. Same with milk. Egg whites are drinkable from the carton, but don't taste super good and need to be refrigerated. Protein powder, on the other hand, is super convenient and does the exact same thing inside your body as the others, so why not use it?
(BTW, if you're a total newbie, i.e., never lifted before, then you should expect to gain a lot more than 3 pounds of muscle in your first year at any age. But only in your first year. After that, 2-3 pounds or .9-1.3 kg of muscle per year max for a 31 year-old. And I do want to stress that's the max, and after 35 gains diminish even faster. Still, that's 10-20 pounds or 4.5-9 kg of solid muscle by the time you're 40, which will look great if you stay trim. Many people don't realize the insane difference that just 10 pounds of muscle will make in your appearance.)