Node Size
Node Color
Ala, A
71.0788 Da | 7.8%
Very abundant, very versatile. More stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, and can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside.


BLOSUM matrices from NCBI and two Wikipedia articles ( Amino Acid and Proteinogenic Amino Acid ) are used for the underlaying data. Main motivation of this visualization is to see the big picture of amino acid world: their properties and relationship in a network setting.

BLOSUM matrix is a substitution matrix. In other words, it shows you if an amino acid can be placed instead of an other one. If the link between two amino acids are thick, it means that those amino acids are favored for replacement compared to the remaining ones. If there is no link, their substitution is not favored. However, you can play with the substitution score threshold to see the interactions in different levels. Please consult the BLOSUM Wikipedia article for further information.

Amino acid substitution can be different among distant (bird and mouse) or close (mouse and human) species. BLOSUM matrices are calculated for different levels of similarity between species and it is represented by percent identity. You can play with the BLOSUM % identity slider to see how substitution changes when the similarity between different species changes.

You can also change the color and size of each amino acid according to their properties, each time using a different methodology. Details of those properties and methodologies can be found in the Wikipedia articles mentioned above.

Some characteristic properties of amino acids are somewhat vague (like the hydrophobicity state of amino acids). I strongly recommend you to read about those properties from multiple resources to get a better understanding.

For any mistakes, suggestions, or appreciation please do contact me:

Implemented using the D3 library.

Ahmet Rasit Ozturk | |