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Revision as of 21:35, 25 June 2011 by Uskat (talk | contribs) (Visualisation of the Mutation)

General Information

SNP-id rs121907968
Codon 485
Mutation Codon Trp -> Arg
Mutation Triplet gTGG -> CGG

Pysicochemical Properities

First of all, we explored the amino acid properties and compared them for the original and the mutated amino acid. Therefore we created the possible effect that the mutation could have on the protein.

Trp Arg consequences
aromatic, polar, hydrophobic, neutral positive charged, polar, hydrophilic Trp is very big, because of two aromatic rings in its structure. Furthermore, it is hydrophobic, whereas, Arg is a hydrophilic amino acid. Therefore, the changes in the 3D structure might be extreme and delete the function of the protein.

Visualisation of the Mutation

In the next step, we created the visualization of the muation with PyMol. Therefore we created a picture for the original amino acid, for the new mutated amino acid and finally for both together in one picture whereas the mutation is white colored. The following pictures display that the mutated amino acid Arginine looks very different to Tryptophan. Tryptophan has two huge aromatical rings. Contrary, Aspartate is also a long amino acid and forks at the end of the rest. Furthermore, Arginige is also orientated in a completly different direction. Because of the aromatical rings the differences between these two amino acids is realy huge. Therefore, the amino acids will probably cause drastical effects on protein structure and function.

picture original aa picture mutated aa combined picture
Amino acid Tryptophan
Amino acid Arginine
Picture which visualize the mutation

Subsitution Matrices Values

PAM 1 Pam 250 BLOSOUM 62
value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution
2 2 (Arg) 0 (all, except Arg, Phe, Ser, Tyr) 2 2 (Arg) 0 (all, except Arg, His, Leu, Phe, Ser, Tyr) -3 2 (Tyr) -4 (Asn, Asp, Pro)

PSSM analysis

self-information expected self-information
Trp 13 99
Arg -6 0

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary Structure Mutation Analysis


Comparison with the real structure:

Mutation at position 485
Mutation at position 485 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
R Non-neutral 7 96%

A detailed list of all possible substitutions can be found [here]

SIFT Prediction

SIFT Matrix:
Each entry contains the score at a particular position (row) for an amino acid substitution (column). Substitutions predicted to be intolerant are highlighted in red.

Sift legend.png
485 sift.png.png

SIFT Table
Threshold for intolerance is 0.05.
Amino acid color code: nonpolar, uncharged polar, basic, acidic.
Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction.

Predict Not ToleratedPositionSeq RepPredict Tolerated

PolyPhen2 Prediction

HumDiv prediction
HumVar prediction