Native Redesign Same Fraction designed correctly ln[(#same/#native)/(#design/#total)]
-----------------------------------------------------------------------------------------------
VAL 306 271 154 0.50 2.14
ILE 206 268 106 0.51 2.17
LEU 332 458 185 0.56 1.71
MET 77 72 14 0.18 2.44
PHE 170 258 101 0.59 2.35
GLY 370 349 293 0.79 2.34
ALA 407 267 127 0.31 1.67
PRO 196 244 129 0.66 2.51
TRP 57 93 26 0.46 3.11
TYR 163 233 54 0.33 1.87
SER 275 177 60 0.22 1.73
THR 289 173 53 0.18 1.58
ASN 204 218 33 0.16 1.22
GLN 148 239 14 0.09 0.59
ASP 339 241 66 0.19 1.30
GLU 306 287 51 0.17 0.97
ARG 153 196 19 0.12 1.06
LYS 325 297 49 0.15 0.84
HIS 81 63 11 0.14 2.29
CYS 157 157 157 1.00 3.37
For total residue = 4561 ,the identity for all positions is 0.35.
The distribution of each residue in different enviroment states (*Nat:Native *Des:Redesign) :
% Buried % Boundary % Surface
(Nat Des change) (Nat Des change) (Nat Des change)
------------------------------------------------------------------------------
VAL 0.57 0.61 0.04 0.26 0.24 -0.02 0.17 0.15 -0.02
ILE 0.59 0.47 -0.12 0.28 0.29 0.01 0.13 0.23 0.11
LEU 0.55 0.34 -0.20 0.33 0.37 0.04 0.13 0.29 0.17
MET 0.52 0.47 -0.05 0.30 0.42 0.12 0.18 0.11 -0.07
PHE 0.66 0.58 -0.08 0.26 0.32 0.06 0.08 0.10 0.02
GLY 0.21 0.21 0.00 0.38 0.39 0.00 0.41 0.40 -0.01
ALA 0.37 0.61 0.24 0.29 0.30 0.01 0.34 0.09 -0.25
PRO 0.17 0.16 -0.02 0.24 0.29 0.05 0.58 0.55 -0.03
TRP 0.63 0.55 -0.08 0.23 0.29 0.06 0.14 0.16 0.02
TYR 0.63 0.35 -0.27 0.27 0.34 0.07 0.10 0.30 0.20
SER 0.18 0.25 0.07 0.30 0.32 0.02 0.52 0.43 -0.09
THR 0.22 0.20 -0.02 0.44 0.36 -0.08 0.34 0.44 0.10
ASN 0.18 0.07 -0.11 0.39 0.14 -0.25 0.43 0.79 0.36
GLN 0.15 0.06 -0.09 0.45 0.31 -0.14 0.40 0.63 0.23
ASP 0.14 0.17 0.03 0.28 0.32 0.03 0.58 0.52 -0.06
GLU 0.08 0.14 0.05 0.36 0.35 -0.01 0.56 0.51 -0.05
ARG 0.16 0.22 0.06 0.41 0.49 0.08 0.43 0.29 -0.15
LYS 0.13 0.17 0.05 0.40 0.44 0.04 0.47 0.39 -0.09
HIS 0.35 0.65 0.31 0.33 0.25 -0.08 0.32 0.10 -0.23
CYS 0.71 0.71 0.00 0.20 0.20 0.00 0.09 0.09 0.00
The probabilities for all residues in buried, boundary and surface states :
% Buried % Boundary % Surface
(Nat Des change) (Nat Des change) (Nat Des change)
------------------------------------------------------------------------------
VAL 0.12 0.11 -0.01 0.05 0.04 -0.01 0.03 0.03 -0.01
ILE 0.08 0.09 0.00 0.04 0.05 0.01 0.02 0.04 0.02
LEU 0.12 0.11 -0.02 0.07 0.11 0.04 0.03 0.08 0.06
MET 0.03 0.02 -0.00 0.02 0.02 0.00 0.01 0.01 -0.00
PHE 0.08 0.10 0.03 0.03 0.05 0.03 0.01 0.02 0.01
GLY 0.05 0.05 -0.00 0.10 0.09 -0.00 0.09 0.09 -0.01
ALA 0.10 0.11 0.01 0.08 0.05 -0.03 0.09 0.01 -0.07
PRO 0.02 0.03 0.00 0.03 0.05 0.02 0.07 0.08 0.01
TRP 0.02 0.03 0.01 0.01 0.02 0.01 0.01 0.01 0.00
TYR 0.07 0.06 -0.01 0.03 0.05 0.02 0.01 0.04 0.03
SER 0.03 0.03 -0.00 0.06 0.04 -0.02 0.09 0.05 -0.04
THR 0.04 0.02 -0.02 0.09 0.04 -0.04 0.06 0.05 -0.01
ASN 0.03 0.01 -0.01 0.05 0.02 -0.03 0.06 0.11 0.05
GLN 0.01 0.01 -0.00 0.04 0.05 0.00 0.04 0.09 0.06
ASP 0.03 0.03 -0.00 0.06 0.05 -0.01 0.12 0.08 -0.05
GLU 0.02 0.03 0.01 0.07 0.07 -0.01 0.11 0.09 -0.02
ARG 0.02 0.03 0.01 0.04 0.06 0.02 0.04 0.04 -0.01
LYS 0.03 0.03 0.01 0.09 0.09 0.00 0.10 0.07 -0.02
HIS 0.02 0.03 0.01 0.02 0.01 -0.01 0.02 0.00 -0.01
CYS 0.08 0.08 0.00 0.02 0.02 0.00 0.01 0.01 0.00
The fraction of redesigned correctly for the following groups are:
1. hydrophobic non-polar amino acids(VAL,ILE,LEU,MET,PHE,GLY,ALA,PRO,TRP,TYR) = 0.52
2. polar uncharged amino acid except CYS (SER,THR,ASN,GLN) = 0.17
3. negative charged amino acid(ASP,GLU) = 0.18
4. positive charged amino acid(ARG,LYS,HIS) = 0.14
The distribution of amino acid in each group are :
Native Redesign
hydrophobic non-polar 0.52 0.57
polar uncharged 0.21 0.18
negative charged 0.15 0.12
positive charged 0.13 0.13
Nat\Des VAL ILE LEU MET PHE GLY ALA PRO TRP TYR SER THR ASN GLN ASP GLU ARG LYS HIS CYS
VAL 154 42 13 2 7 1 10 4 3 9 7 16 1 3 3 8 11 11 1 0
ILE 29 106 19 3 4 1 3 4 4 3 3 8 0 2 4 4 1 6 2 0
LEU 11 14 185 7 15 4 15 2 3 8 3 3 5 5 6 12 14 16 4 0
MET 2 5 14 14 6 3 4 0 0 3 2 1 3 7 3 1 5 3 1 0
PHE 2 3 6 1 101 0 4 0 9 20 2 1 0 2 2 4 6 0 7 0
GLY 1 0 6 0 2 293 8 2 3 0 7 3 11 7 11 4 5 6 1 0
ALA 7 6 23 4 11 14 127 20 6 7 21 9 20 33 18 29 15 32 5 0
PRO 0 1 4 0 1 0 6 129 0 1 7 1 6 8 15 9 0 8 0 0
TRP 0 0 1 1 5 1 2 0 26 7 0 2 3 1 0 4 1 1 2 0
TYR 2 2 7 1 53 1 2 3 6 54 2 0 0 4 3 4 3 9 7 0
SER 2 1 18 3 2 3 27 15 2 16 60 9 21 22 27 16 10 16 5 0
THR 23 28 18 4 5 2 13 8 5 17 17 53 7 25 9 20 18 16 1 0
ASN 4 7 17 3 9 8 8 5 2 12 5 6 33 12 28 17 13 12 3 0
GLN 5 10 21 8 4 3 5 3 2 6 4 6 9 14 3 18 8 19 0 0
ASP 10 13 15 1 7 5 7 18 4 14 13 10 47 25 66 32 15 30 7 0
GLU 9 10 31 7 6 3 10 9 6 18 5 14 18 28 18 51 21 40 2 0
ARG 3 6 18 5 4 0 4 6 4 8 8 11 8 13 5 15 19 15 1 0
LYS 4 12 38 8 11 6 10 14 7 22 8 14 22 24 13 34 26 49 3 0
HIS 3 2 4 0 5 1 2 2 1 8 3 6 4 4 7 5 5 8 11 0
CYS 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 157
Nat\Des hydrophobic polar negatative positive
hydrophobic 1738 219 144 183
polar 354 303 138 121
negative 203 160 167 115
positive 218 125 79 137