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This file is a Amino-acid similarity file for use with BOX.
This file is used in colouring residues that are "similar"
to a single consensus residue.
Similarities contained in this file are not automatically
set-forming. This means:
The line
I LVM means that I is similar to L,V and M and also that
L,V,M are similar to I.
It does not imply that L is similar to V or to M.
For achieving this, more lines (the next ones) are necessary.
Although is seems weird, this feature has been chosen DELIBERATELY
because I think it could be helpful in some cases.
This table was taken from ClustalX v1.3b:
WEAK groups:
These are all the positively scoring groups that occur in
the Gonnet Pam250 matrix
..
F YW
Y WF
W FY
C SA
S AC
A CS
A TV
T VA
V AT
S AG
A GS
G SA
S TNK
T NKS
N KST
K STN
S TPA
T PAS
P AST
A STP
S GND
G NDS
N DSG
D SGN
S NDEQK
N DEQKS
D EQKSN
E QKSND
Q KSNDE
K SNDEQ
N DEQHK
D EQHKN
E QHKND
Q HKNDE
H KNDEQ
K NDEQH
N EQHRK
E QHRKN
Q HRKNE
H RKNEQ
R KNEQH
K NEQHR
F VLIM
V LIMF
L IMFV
I MFVL
M FVLI
H FY
F YH
Y HF
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