I'm not sure whether my question is appropriate or not. Let me clarify below.
I have found two mutations in HIV-1 gp41 interact with each other. So, I prepared a homology structure. Now, in Pymol I represent both amino acid position with colored spheres and it seems they are kind of close to each other. Then I choose different options among them in MESH surface it seems two nets from these amino acids are kind of interacting with each other. Can I interpret they this way two amino acids are interacting.
Please give me some idea, or link for self studies. I'm adding one figure of MESH surface for the two amino acids.
So you introduced your mutations and are getting close contacts upon visual inspection of your homology model. Depending on the modelling procedure used, it may or may not optimize the side chain rotamers of the mutated side chains - if you get clashes, they may be relieved by side chain rotamer changes.
If you have an energetically favorable interaction, e.g. hydrogen bonds or charge interaction, the distance between the two interacting atoms will be closer than the sum of the Van-der-Waals radii. To see whether the side chain actually clash, use the "measuring wizard" to actually measure interatomic distances - In homology modelling, I usually am worried about clusters of clashes there the interatomic distance is less than 0.8* the sum of the VdW radii, in this analysis, good hydrogen bonds still show up as clashes. The Mesh representation you use probably is a solvent accessible surface - this is the surface traced by "water molecules" (spheres of around 1.4Å rolled over the surface). So it will only show up in the interface if there are holes large enough to accommodate a water molecule.
The residue shown in orange in your image seems to be located on the surface of your structure, the blue one is rather buried. The two residues are clearly not in direct contact - if their effects influence each other, there are other residues between the two mutations. If the two mutations influence each other, this must be mediated by structural changes, e.g. shift of the backbone or rotamer changes in the intervening side chains.
CM viewer is the software by which you can check how does amino acid residues are interacting with its neighbouring residues.
In PyMOL. First of all represent those two amino acid residues ib sticks and then go to wizard option of control panel of PyMOL and select measu
So you introduced your mutations and are getting close contacts upon visual inspection of your homology model. Depending on the modelling procedure used, it may or may not optimize the side chain rotamers of the mutated side chains - if you get clashes, they may be relieved by side chain rotamer changes.
If you have an energetically favorable interaction, e.g. hydrogen bonds or charge interaction, the distance between the two interacting atoms will be closer than the sum of the Van-der-Waals radii. To see whether the side chain actually clash, use the "measuring wizard" to actually measure interatomic distances - In homology modelling, I usually am worried about clusters of clashes there the interatomic distance is less than 0.8* the sum of the VdW radii, in this analysis, good hydrogen bonds still show up as clashes. The Mesh representation you use probably is a solvent accessible surface - this is the surface traced by "water molecules" (spheres of around 1.4Å rolled over the surface). So it will only show up in the interface if there are holes large enough to accommodate a water molecule.
The residue shown in orange in your image seems to be located on the surface of your structure, the blue one is rather buried. The two residues are clearly not in direct contact - if their effects influence each other, there are other residues between the two mutations. If the two mutations influence each other, this must be mediated by structural changes, e.g. shift of the backbone or rotamer changes in the intervening side chains.
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