Zappo Colours
The residues are coloured according to their physico-chemical properties as
follows:
Aliphatic/hydrophobic | ILVAM |
Aromatic | FWY |
Positive | KRH |
Negative | DE |
Hydrophilic | STNQ |
conformationally special | PG |
Cysteine | C |
These colours were invented by Willie Taylor and an entertaining description of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)
A | V | I | L |
M | F | Y | W |
H | R | K | N |
Q | E | D | S |
T | G | P | C |
According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J. Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this table are coloured red and the most hydrophilic ones are coloured blue.
I | V | L | F | C |
M | A | G | X | T |
S | W | Y | P | H |
E | Z | Q | D | B |
N | K | R |
E | M | A | Z | L |
K | F | Q | I | W |
V | D | X | H | R |
B | T | S | C | Y |
N | G | P |
V | I | Y | F | W |
L | T | C | Q | M |
X | R | N | H | A |
S | G | Z | K | B |
P | D | E |
N | G | P | B | D |
S | C | Y | K | X |
Q | W | T | R | H |
Z | E | A | F | M |
L | V | I |
C | I | V | L | F |
M | G | A | W | X |
S | H | T | P | Y |
N | B | D | Q | Z |
E | R | K |
A | C | G | T |
Gaps are coloured white. If a residue matchs the consensus sequence residue at that position it is colored dark blue. If it does not match the consensus residue but the 2 residues have a positive Blosum62 score, it is colored light blue.
Colouring above a percentage identity threshold
Selecting this option causes the colour scheme to be applied to only those residues
that occur in that column more than a certain percentage of the time. For instance
selecting the threshold to be 100 will only colour those columns with 100 %
identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity
and User colour schemes.
This option depends on a consensus calculation having been performed. If no
consensus exists (e.g. after a copy or a clustalw alignment) then no residues
are coloured.
PID Colours
This depends on the applet having performed a consensus calculation on the alignment.
The PID option colours the residues (boxes and/or text) according to the percentage
of the residues in each column that agree with the consensus sequence. Only
the residues that agree with the consensus residue for each column are coloured.