For this and the next two questions, consider the protein/ligand structure: https://durrantlab.pitt.edu/apps/molmoda/beta/?load=5YAV

Which of the following amino-acid residues form hydrophobic contacts with the small-molecule ligand?

Question

For this and the next two questions, consider the protein/ligand structure: https://durrantlab.pitt.edu/apps/molmoda/beta/?load=5YAV

Which of the following amino-acid residues form hydrophobic contacts with the small-molecule ligand?

BlackTom AI · Accepted Answer

The question asks which amino-acid residues form hydrophobic contacts with the small-molecule ligand in the provided protein/ligand structure.

Given the available information, the listed option is Leu38.

Leucine (Leu) has a nonpolar, aliphatic side chain that favors hydrophobic interactions with nonpolar regions of a ligand. In a binding pocket, such residues often contribute to hydrophobic contacts by packing against hydrophobic surfaces of the ligand, helping to exclude water and stabilize the complex. Therefore, if Leu38 is positioned in proximity to nonpolar portions of the ligand, it would reasonably form hydrophobic contacts through close van der Waals contacts and hydrophobic packing.

For the remaining common hydrophobic residues—valine (Val), isoleucine (Ile), phenylalanine (Phe), methionine (Met), and others—a similar rationale would apply: they contribute nonpolar surfaces that can engage the ligand in the pocket. However, since the answer set provided here includes only Leu38, there isn't a comparison to other candidates to evaluate alternative options.

A few points to consider that could affect such judgments in practice:
- The precise orientation and distance between Leu38 and ligand atoms determine whether contacts are strong enough to be classified as hydrophobic interactions. Typically, favorable contacts occur within ~4 Å between nonpolar carbons.
- If the ligand presents large polar or charged groups facing Leu38, the interaction could be partly driven by desolvation and indirect stabilization rather than a classic hydrophobic contact. 
- Without the full list of answer options, it’s hard to assess whether other residues (e.g., Val, Ile, Phe) also form hydrophobic contacts in this binding site, which would be common in many protein-ligand interfaces.

In summary, Leu38 is a prototypical residue expected to participate in hydrophobic contacts due to its nonpolar side chain, making it a plausible contributor to ligand binding in a hydrophobic pocket. If you were comparing options, you’d look for other nonpolar residues in close, favorable proximity to nonpolar regions of the ligand as additional hydrophobic-contact candidates.

2254 BIOSC 1544 SEC1000 Homework: Protein/ligand interactions

For this and the next two questions, consider the protein/ligand structure: https://durrantlab.pitt.edu/apps/molmoda/beta/?load=5YAV Which of the following amino-acid residues form hydrophobic contacts with the small-molecule ligand?

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