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Protein Properties Coloring Schemes

  • Updated

How do I color protein sequences based on amino acid properties?

SnapGene allows amino acid color highlighting based on color schemes as detailed below. These color schemes are available for protein sequences (see Show or Hide or Set Protein Colors), or a multiple alignment of protein sequences (3 or more protein sequences). These color schemes are not currently available for pairwise protein alignments.

Physicochemical Properties (Zappo)

Residues are coloured according to their physicochemical properties as follows:

Category  Color  Residues 
Aliphatic/hydrophobic         I, L, V, A, M
Aromatic         F, W, Y
Positive         K, R, H
Negative         D, E
Hydrophilic         S, T, N, Q
Conformationally special         P, G
Cysteine         C

Properties + Conservation (Clustal X)

Residues are colored according to their properties and conservation using the default Clustal X coloring scheme, as follows:

Category  Color  Residues 
Hydrophobic  A, I, L, M, F, W, V, C 
Positive charge  K, R
Negative charge  E, D
Polar  N, Q, S, T
Glycine  G
Proline  P
Aromatic  H, Y
Unconserved  WHITE any / gap

Chemical Properties (DNASTAR)

Amino acids are colored according to their side-chain chemistry, as follows:

Category  Color  Residues 
Aromatic  F, W, Y 
Acidic (Negatively charged) D, E
Basic (Positively charged) R, H, K
Non-Polar (Aliphatic) A, G, I, L, M, P, V
Polar (Neutral) C, N, Q, S, T

Transmembrane Tendency (Zhao and London)

Residues are coloured according to their "transmembrane tendency", as defined by Zhao and London, 2006:

Residue  Color 
Lys (K)   Most Hydrophilic
Asp (D) 
Glu (E) 
Arg (R) 
Gln (Q) 
Asn (N) 
Pro (P) 
His (H) 
Ser (S) 
Thr (T) 
Cys (C) 
Gly (G)   Neutral
Ala (A) 
Tyr (Y) 
Met (M) 
Val (V) 
Trp (W) 
Leu (L) 
Ile (I) 
Phe (F)   Least Hydrophilic

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