For most purposes, QuickViews' DISPLAY Contacts menu will give the desired contact-decorated surface display more easily and quickly. Its Contact-Decorated Surface Controls offer a number of rendering options not available in Advanced Explorer's Contact-Decorated Surfaces inteface, which was developed earlier. You are advised to get thoroughly familiar with QuickViews DISPLAY Contacts before learning how to use Advanced Explorer's Contact-Decorated Surfaces inteface. The latter (i) should be used only when the former cannot produce the desired result, and (ii) will require some familiarity with Chime's command language.
The example displays produced in the Tutorial below can be much more easily generated in QuickViews' DISPLAY Contacts. Capabilities of Advanced Explorer's Contact-Decorated Surfaces inteface that are absent in QuickViews are:
Follow this procedure to generate an exemplary contact surface:
Start a new PE session showing 1B07. Use the PE Site Map to go to Advanced Explorer, then Contact-Decorated Surfaces. Enter :a in the "surface on" slot. Enter :b in the "contacted by" slot. Press the [Make] button. Zoom in.
The dark surface represents the solvent-accessible surface of the "receptor" (chain A), which is a Src Homology type 3 domain (SH3 domain).
The lighter zone on the dark surface represents the portion close enough to the "ligand" to be bonded to it, the "contact surface". The "ligand" (chain C) is a regulatory peptide.
The coloring of the contact surface gives an overview of the bonding pattern. Four large magenta spots show the positions of the closest contacts. Each large magenta spot represents a hydrogen bond. You'll also see 3 white hydrophobic pockets, accomodating Pro4, Val7, Pro8 in the ligand.
Check Hide noncontact "receptor" surface and press the [Make] button again. This hides most of the receptor surface -- only the contact surface remains visible. Rotate it -- now you can see the "back side" (the side facing in towards the receptor) since it is no longer covered with the remainder of the receptor surface.
Now check Show bonded "receptor" atoms (selecting O/N) and press the [Make] button again. The contact surface is now transparent. On the "receptor" side of the surface are now shown (as small spheres) "receptor" oxygen and nitrogen atoms close enough to "ligand" oxygen and nitrogen atoms to be hydrogen bonded (3.5 Angstroms or closer). Whether they are actually hydrogen bonded is up to you to judge. You can click on any atom to identify it, and you can use the commands "set picking distance" or "set picking monitor" to report distances between pairs of atoms clicked with the mouse. (The aliases for these commands are "spd" and "spm".)
Select C/S/X (carbon, sulfur) instead of O/N, and press the [Make] button again. On the "receptor" side of the surface are now shown "receptor" carbon and sulfur atoms close enough to "ligand" carbon or sulfur atoms to be van der Waals-bonded (4.5 Angstroms or closer). Whether they are actually engaged in hydrophobic interactions is up to you to judge. Also shown are receptor atoms other than carbon, sulfur, oxygen or nitrogen (e.g. metals) that are within 4.5 Angstroms of any ligand atom. You can click on any atom to identify it.
You have now seen an example of a contact surface. More detailed visual analysis of noncovalent bonding interactions can be performed with the Noncovalent Bond Finder.
It is not necessary to have distinct ligand and receptor for a contact surface to be useful. For example, you can select an arbitrary segment of a protein, and examine its contacts with the remainder of the protein. To see such an example, with 1b07 still loaded, click the [Hide] button and then issue these commands:
r none s all bb 0.3 s 179-183 co greenThis highlights a segment, residues 179-183, buried in the middle of the complex. Now specify for receptor "not 179-183" and for ligand "179-183", and generate the various contact surfaces. Not all of the atoms bonded to this segment come from chain A -- we didn't exclude chain C from the "receptor" so it contributes to the surface. :a and not 179-183
The surface generated here is a water-accessible surface generated with a rolling probe. A spherical probe 1.4 Angstroms in radius (the conventional radius for a sphere approximating water) is rolled over the surface of the "receptor". The probe is rolled in parallel loops spaced 0.8 Angstroms apart. The resulting surface represents all contacts of the probe surface with the receptor surface.
When the "noncontact" surface of the receptor is hidden, the edge of the receptor's "contact" surface is 4.1 Angstroms from the closest ligand atom. The edge is gray. Portions of the "contact" surface closer to ligand atoms are in turn lighter gray, white, pale magenta, and magenta. Gray to white regions are often involved in hydrophobic interactions, while magenta regions are often involved in hydrogen bonds.
The atoms making up the "Receptor" and "Ligand" are arbitrary, and are defined by the expressions in the respective slots on the control panel. The terms "rec" and "lig" are defined when a contact surface is generated.
select rec color chainwhich using aliases can be simplified to
s rec coc
While hydrogen bond acceptors and donors are likely to be primarily nitrogen or oxygen, any atoms other than carbon and sulfur are shown as Possible Hbond Donors/Acceptors (PHDA). Ligand PHDA within 3.5 Angstroms of receptor PHDA are considered to be within hydrogen bonding distance.
For hydrophobic interactions, ligand carbon or sulfur within 4.5 Angstroms of receptor carbon or sulfur atoms are shown as being within bonding distance.
"X": ligand atoms other than oxygen, nitrogen, carbon, or sulfur (e.g. metals) within 4.5 A of any receptor atom are shown.
O/N, when selected, shows oxygen and nitrogen atoms in the receptor that are within bonding distances of ligand atoms; C/S/X shows carbon, sulfur, or any non-O/N atoms in the receptor that are within bonding distances of ligand atoms.
After generating the O/N or C/S/X displays, the resulting sets of receptor atoms within bonding distances of ligand atoms may be selected with the terms bron (Bonded Receptor O/N) or brcs. Thus, for example, after generating the O/N image, you can color likely-bonded receptor oxygen atoms atoms green and all other receptor oxygens red by issuing these commands:
s rec and oxygen coe s bron and oxygen co green
The following terms are defined during the creation of a contact surface if the relevant categories are requested. These terms can be used in 'select' commands.