Hello everyone,
I have a question about the YASARA software.
I want to discover the hydrophobic interactions between some protein residues. These interactions are not linked to the interest residue as you can see in picture 1 compared to picture 2. Can someone explain to me what is the problem?
Thank you.
Satyendra Singh
Distance cutoff: The hydrophobic interactions may not be detected if the distance cutoff used in the analysis is too large. In YASARA, you can adjust the distance cutoff for hydrophobic interactions in the "Hydrophobic" tab of the "Contacts" menu. Try decreasing the distance cutoff to see if this helps link the interactions to the interest residue. Other interactions taking precedence: YASARA may be detecting other types of interactions (e.g. hydrogen bonds, salt bridges) that take precedence over the hydrophobic interactions and prevent them from being linked to the interest residue. You can try adjusting the settings for other types of interactions to see if this helps. Water molecules: Hydrophobic interactions can be influenced by the presence of water molecules. If the analysis is not taking into account the water molecules in the system, this could affect the detection of hydrophobic interactions. In YASARA, you can use the "Water" tab in the "Contacts" menu to adjust the settings for water molecules. Residue selection: It's possible that the interest residue is not being included in the selection for hydrophobic interactions. Double check that the interest residue is included in the selection you're using for the analysis.
It's difficult to say for sure without more information or seeing the specific data and settings you're using in YASARA. However, here are a few possible reasons why the hydrophobic interactions may not be linked to the interest residue in your analysis:
I hope this helps!
0 votes
0 thanks
More Meriem El Fessikh's questions See All
Similar questions and discussions