Hi Hunter, > 1. how to find those hydrophobic residues PISA will also tell you this - you just need to look at the hydrophobic residues which are highlighted and have a buried surface area (BSA) value in the PISA output. You can take these residues and plot them in your favourite pdb viewer (CCP4mg, PyMol, etc)
As for confirming their importance - the only definative test IS site-directed mutagenesis. However, before you dash off and order your primers, Rosetta/Robetta has an in-silico alanine scanning mutatgenesis server which may help direct your efforts: http://robetta.bakerlab.org/alascansubmit.jsp HTH David 2009/8/19 Haitao ZHANG <crystalc...@gmail.com>: > Hi, everybody > I have a crystal structure as homodimer, from which residues in the dimer > interface need to be identified. Using PISA on the EBI website, > residues involved in forming hydrogen bonds, salt bridges, disulfide bonds > and covalent bonds could be identified. But hydrophobic interaction could > also play an essential role on the dimer stablization. So does anybody know: > 1. how to find those hydrophobic residues (software or on-line-server) > 2. how to confirm that whether they play a role in the dimerization, except > for site-mutation. > > Thanks a lot! > > Hunter -- ============================ David C. Briggs PhD Father & Crystallographer http://drdavidcbriggs.googlepages.com/home Skype: DocDCB ============================
