 So the problem with showing you snorkeling and anti snorkeling in a single structure is that there are too many fluctuations And there might just be one or two residues that exhibit that property The advantage of trying to find a numerical measure such as literally measuring this angle is that I can't create averages either an average in a Molecular simulation or maybe averages of structures now 20 years ago That wasn't particularly useful because we only had a handful of primary protein structures today we have hundreds if not thousands and That means that not only are there enough structures available The resolution is starting to become so high that we definitely see the side chains snorkeling and in many cases We might even see the lipids they interact with I'll show you this first in a simple simulation so this is just two examples of methionine side chain and an arginine side chain and The exact values here are not important But you see how there is in particular for the arginine. There is a clear snorkeling effect What do I mean by n-terminal and c-terminal? Well There are two sides to this helix right if I put the helix to the membrane There is the beginning of the helix and there is the end of the helix and it turns out they're not quite identical if you look at a helix and Let's say that we go from the n side to the c side so in the direction of the sequence If you look at that bond from the c-alpha to the c-beta In general that bond points just so slightly towards the n-terminal Again, when we first look at it, it might look like it's stretching straight out, but it is pointing a bit backwards The structure down here which side is the n-terminus? Well, we can see that Do you see that that bond is pointing that way? So the n-terminus here the start of the chain is at the bottom and this helix is pointing up that means that if I now take this light scene that would like to point outwards if I put this close to the n-terminus Well, I'm already pointing a little bit in the right direction after the first bond So it's going to be easier for the arginine to be located close to the n-terminus Then it is to put it at the c-terminus because at the c-terminus here I first the first bond by definition goes a bit in the wrong direction and then I would have to snorkel in the other direction And that's one more effect There will be systematic patterns in the occurrence of amino acids and membrane proteins We'll look at that in a second, but I need to show you tryptophan2