Method 1 (used for the figures) identifies atom-atom contacts with Find Clashes/Contacts or its command equivalent, findclash.
With the proteins in the bound state:Method 2 first calculates buried surface area, then uses the resulting per-atom values (assigned as atom attributes) to identify interface atoms.Command: findclash #0.1 test #0.2 intersub true overlap -1 hb 0 make false select trueIn the findclash command, the overlap and hb parameters are adjustable, with values of 0.0-(–1.0) Å and 0.0 Å, respectively, recommended for finding contacts. An overlap cutoff of –1.0 identifies pairs of atoms with VDW surfaces up to 1.0 Å apart. When the command is instead used to find only clashes (unfavorable, too-close contacts), hb values > 0.0 help to exclude H-bonding atom pairs. The two sets of atoms are specified with model numbers (e.g. #0.1), but chain identifiers could have been used instead (e.g. :.a), and if water had not been deleted, the calculation could have been limited explicitly to protein (e.g. #0.1&protein or :.a&protein).
Command: namesel contacts
Command: ~select
Command: color yellow contacts�.1
Command: color hot pink contacts�.2
With the proteins in the bound state:Command: measure buriedArea #0.1 #0.2
Command: color yellow #0.1@/buriedSESArea>1
Command: color hot pink #0.2@/buriedSESArea>1The total buried area and details of the calculation are given in the Reply Log. Different cutoff values could be used, but in this case, atoms with > 1.0 Å2 of solvent-excluded surface area buried in the interface are similar to the set of atoms found in the method 1 example. Although solvent, ions, and ligands are not enclosed in the displayed surfaces, the buried-area calculation will include all specified atoms. Thus it is important to specify only the intended atoms; for example, if nonprotein atoms were present:
Command: measure buriedArea #0.1&protein #0.2&protein
Method 3 identifies where surfaces are close to one another and does not involve atoms.
With the proteins in the bound state and surfaces shown:Command: measure contactArea #0.1 #0.2 2.5 color yellow offset 0
Command: measure contactArea #0.2 #0.1 2.5 color hotpink offset 0These commands identify where the surfaces are within 2.5 Å of each other. Again, different cutoffs could be used, but 2.5 gave a result roughly similar to the preceding examples. The specifications in the contact-area command (e.g. #0.1) refer to the surface models, which happen to have the same model numbers as the corresponding atomic structures.