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I want to know if I am reading the venn diagram correctly and why there are discrepancies in the diagrams.

I'm trying to determine which amino acids are considered hydrophobic and I am using this diagram suggested by my teacher from Amino acid properties and consequences of subsitutions.

venn

From the diagram I've determined that A, G, C, T, V, I, L, F, W, Y, H, K, M are hydrophobic.

My problem is when I visit other sources I do not get the same results. Using Amino Acid Table I determines that A, G, I, L, M, F, P, W, Y, V were hydrophobic:

table

Furthermore, there is even another different venn diagram from Decoding the Building Blocks of Life from the Perspective of Quantum Information

venn2

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1 Answer 1

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Polarity and hydrophobicity are not discrete phenomena and, therefore, categorizing amino acids as such has some measure of arbitrariness, especially at edge cases. It all depends on one’s definition.

Other properties have similar problems. Charge depends on pH. And what is the cut-off between “large” and “medium” sides chains?

What is, in my opinion, more important than memorizing charts/diagrams/etc (unless you have an exam) is understanding why different amino acids have these properties. For example, why can threonine or tyrosine be classified as both hydrophobic and polar? Why can cysteine or serine, which are classified as uncharged, act as strong nucleophiles in enzymatic reactions?

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  • $\begingroup$ What search terms should I use to research which amino acids can be classified into multiple properties? $\endgroup$ Mar 12, 2018 at 13:55
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    $\begingroup$ @JohnnyJohnston — You don't seem to understand the remark in the answer about "understanding why different amino acids have these properties". You need to look at the structures, look at the classifications, and then use your knowledge of chemistry to see how they apply. If your chemistry is inadequate for this, you need to remedy that deficiency before you can proceed further. Let us know and we can recommend some reading. $\endgroup$
    – David
    Mar 12, 2018 at 14:23
  • $\begingroup$ @David Thanks for the reply. My knowledge in chemistry is very limited and close to zero. $\endgroup$ Mar 12, 2018 at 22:52
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    $\begingroup$ @JohnnyJohnston — You might try The Biochemical Society's "Essential Chemistry for Biochemists" or The Royal Society of Chemistry's "Chemistry for Biologists". $\endgroup$
    – David
    Mar 12, 2018 at 23:31

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