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

Taylor

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

 

Hydrophobicity

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

 

Helix Propensity

E M A Z L
K F Q I W
V D X H R
B T S C Y
N G P

 

Strand propensity

V I Y F W
L T C Q M
X R N H A
S G Z K B
P D E

 

Turn propensity

N G P B D
S C Y K X
Q W T R H
Z E A F M
L V I

 

Buried index

C I V L F
M G A W X
S H T P Y
N B D Q Z
E R K

 

Nucleotide Colours

A C G T

 

Blosum62

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.