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Electrostatics and hydrophobicity

The p53 core domain bound to DNA (PDB 1TSR), in four requests.

1. Open the structure

open 1tsr, keep only chain B and the DNA, and show them as cartoons

open 1tsr
hide #1 target acs; cartoon #1/B,E,F

The entry has three copies of the domain (chains A, B, C); chain B is the one on the DNA (chains E and F).

The p53 core domain as a cartoon on the DNA double helix
The p53 core domain as a cartoon on the DNA double helix

2. Electrostatic potential

show the protein as a surface colored by electrostatic potential

cartoon hide #1/B
coulombic #1/B

Red is negative, white neutral, blue positive. ChimeraX warns that Ser 96 lacks an atom, so the potential near it is approximate.

The domain as a surface coloured red to blue by Coulombic potential
The domain as a surface coloured red to blue by Coulombic potential

3. Hydrophobicity

color the surface by hydrophobicity instead

mlp #1/B surfaces #1.3

Molecular lipophilic potential on the same surface: hydrophobic patches orange, polar ones teal.

The same surface coloured teal to orange by hydrophobicity
The same surface coloured teal to orange by hydrophobicity

4. Which face binds the DNA

back to electrostatics, and make the DNA gray so the positive face it binds stands out

coulombic #1/B surfaces #1.3
color #1/E,F gray

The positively charged face of the domain lies against the phosphate backbone.

Electrostatic surface with the DNA in gray against its positive face
Electrostatic surface with the DNA in gray against its positive face
The same view, rotating
The same view, rotating