Mutation P01112 at position 3: E → W (E3W)

Overview
Predicted structure (AF):
AF-P01112-F1-model_v4
Uniprot entry:
P01112
Gene:
HRAS
Protein length:
189 residues
Mutation:
E → W
Mutation position:
3
D2Deep Prediction:
1.000
Overall confidence:
0.217
Pred. interpretation:
Pathogenic based on D2Deep prediction
 
Benign
Pathogenic
Scores that are greater than or equal to 0.5 are considered "Pathogenic", while scores that are less than 0.5 are considered "Benign".
Sequence difference
1 2 3 4 5 6 7 8
Original M T E Y K L V V
Target M T W Y K L V V
Predicted original structure
Differences at amino acid level
Feature Original «E» Target «W»
Name Glutamate (Glutamic acid) (Glu) Tryptophan (Trp)
Molecular Formula C5H9NO4 C11H12N2O2
Residue Formula C5H7NO3 C11H10N2O
Molecular Weight 147.130 204.230 (+57.100)
Residue Weight 129.120 186.220 (+57.100)
Hydrophobicity index at pH 2 Neutral Very Hydrophobic
Hydrophobicity index at pH 7 Hydrophilic Very Hydrophobic
Charge Neutral Neutral
Solutibility 0.720 1.060
Structure Image Original Structure Target Structure
Description Glutamic acid (Glu) is similar to aspartic acid and is highly soluble in water. Tryptophan (Trp) can break down in the human gut. Also, it can convert into vitamin B3.
Predicted structures comparison

About these 3D Structures: The 3D structure representations of both original and target sequences (trimmed to 400 residues, from 1 to 189) will be modeled using the ESM Metagenomic Atlas tools. ESM Metagenomic Atlas is a web-based tool for protein structure prediction that uses deep learning methods to predict protein folding and structure from protein sequences.

Below the plots, you will find additional details on how to interpret the biophysical results.

Differences at biophysical features

About these plots: These plots have been generated by using Bio2Byte predictors to plot both the original and target sequences.

About how to use the plot controls located at the right side of each plot
By default, no tools are selected, but you can hover over the plot lines to view the tooltip information.
  • Pan: Use the hand icon to drag and move the plot area.
  • Zoom In/Out: Click the magnifying glass icons to zoom in or out on the plot. You can also use the box zoom tool to select a region to zoom into.
  • Wheel Zoom: Use your mouse wheel while hovering over the plot to zoom in and out smoothly.
  • Save: Click the disk icon to download the current plot as a PNG image.
  • Reset: Click the reset icon (circular arrow) to restore the plot to its original view.
  • Help: Click the question mark icon to open the official Bokeh documentation in a new tab for more details about plot controls.
  • Hover: Click the tooltip icon to enable hover tooltips, which show detailed information about data points when you move your mouse over them.
All plot are generated using the library Bokeh.
Biophysical features
Interpretation of the biophysical features

The predictions reflect 'emerging' properties, so what the sequence is capable of, not necessarily what it will do in a particular context, for example when it adopts a specific fold.

DynaMine Backbone Dynamics
  • > 1.0 Membrane spanning regions
  • 0.80 - 1.0 Rigid conformations
  • 0.69 - 0.80 Context dependent
  • < 0.69 Flexible regions
DynaMine Side Chain Dynamics

Higher values mean more likely rigid. These values are highly dependent on the amino acid type (e.g. Trp is rigid, Asp is flexible).

DynaMine Conformational Propensities
  • Sheet: Beta sheets consist of β-strands connected laterally by hydrogen bonds, forming a pleated sheet.
  • Helix: Alpha helices are right-handed coiled structures stabilized by hydrogen bonds.
  • Coil: Coil regions lack regular secondary structure and are flexible.
  • ppII: Polyproline II, a left-handed helical structure found in proline-rich regions.

Higher values indicate higher propensities for each structural element.

EFoldMine Early Folding Propensity

Values above 0.169 indicate residues likely to start the protein folding process, based on local interactions.

DisoMine Disorder Prediction

Values above 0.50 indicate likely disordered residues.

Agmata Beta-Sheet Aggregation Propensity

Values are divided by 20 from the original. Peaks indicate residues likely involved in beta-sheet aggregation.