Protein Dimer

Question

[M]

i have a dssp file and i want recognize aminoacides that play role in dimerization how can i understand it only by using dssp information like as acc number? please help me

Answer 1

[João Rodrigues]

DSSP gives you (solvent) accessibility only. If you want residues that play a role in dimerization, and assuming you are looking at the structure of a dimer, you should look for those residues that are buried in the complex structure and exposed in the free form. Another, perhaps easier way of knowing which residues are interacting is to calculate which residues are close in 3D space in the complex structure (between chains).

Now, to predict the dimer interface from a monomeric structure only is not so trivial. Using DSSP, you can look at accessible residues above a certain threshold of accessibility (say, 15% either backbone or side-chain) and then use them for docking calculations (e.g. HADDOCK allows definition of which residues are involved in the interaction).

I could use much more information to help you better.. and a better title would also improve your chances of having better answers.