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Backbone-independent rotamer library May 15, 2002
*********************************************
* *
* Roland L. Dunbrack, Jr., Ph. D. *
* *
* Associate Member *
* Institute for Cancer Research *
* Fox Chase Cancer Center *
* 7701 Burholme Avenue *
* Philadelphia PA 19111 *
* *
* Email: RL_Dunbrack@fccc.edu *
* URL: www.fccc.edu/research/labs/dunbrack *
* *
*********************************************
Rotamers are defined as follows:
r1 = chi1 rotamer = N- CA-CB- XG(1) dihedral
r2 = chi2 rotamer = CA-CB-XG(1)-XD(1) dihedral
r3 = chi3 rotamer = CB-XG-XD- XE(1) dihedral
r4 = chi4 rotamer = XG-XD-XE- XZ dihedral
Chi angle ranges for each rotamer type
=======================================
r1 rotamers of all residue types except Pro
r2 rotamers of Arg, Gln, Glu, Ile, Leu, Lys, Met
r3 rotamers of Arg, Lys, Met
r4 rotamers of Arg, Lys
r1,r2,r3,r4 Conformation chi range
----------- ------------ -----------------
1 g+ 0 <= chi < 120
2 t 120 <= chi < 240
3 g- -120 <= chi < 0
r2 rotamers of Asn, Asp
r3 rotamers of Gln, Glu
r2, r3 Conformation chi range
----------- ------------ -----------------
1 g+ 30 <= chi < 90
2 t -30 <= chi < 30
3 g- -90 <= chi < -30
r2 rotamers of Phe, Tyr, His
r2 Conformation chi range
----------- ------------ -----------------
1 g 30 <= chi < 150
2 t -30 <= chi < 30
r2 rotamers of Trp
r2 Conformation chi range
----------- ------------ -----------------
1 g+ -180 <= chi < -60
2 t -60 <= chi < 60
3 g- 60 <= chi < 180
r1 rotamers of Pro
r1 Conformation chi range
----------- ------------ -----------------
1 g+ (Cg-endo) 0 <= chi < 90
2 g- (Cg-exo) -90 <= chi < 0
This library contains both a traditional backbone-independent rotamer library
which contains values for p(r1,r2,r3,r4), and a conditional backbone-independent
rotamer library, which consists of values for p(r2,r3,r4 | r1).
The conditional library gives the probability that a sidechain will be
in an r2 or r2,r3 or r2,r3,r4 rotamer given that r1 is a particular
rotamer. These values are combined with the backbone-dependent r1
preferences to form a complete backbone-dependent rotamer library.
This rotamer library was derived from a Bayesian statistical analysis of
sidechains from 850 protein chains in the Protein Databank.
Details, Protein Science, 6, 1661-1681 (1997).
Res Rotamer n(r1) n(r1234) p(r1234) sig p(r234|r1) sig chi1 sig chi2 sig chi3 sig chi4 sig
1 2 3 4
ARG 1 1 1 1 568 2 0.04 0.02 0.41 0.22 55.4 19.8 79.7 16.1 62.4 15.0 82.3 11.9
ARG 1 1 1 2 568 5 0.07 0.03 0.83 0.31 59.2 23.2 85.4 16.6 68.2 15.4 -166.2 25.4
ARG 1 1 1 3 568 0 0.00 0.01 0.04 0.07 54.5 21.5 79.4 17.2 64.6 16.6 -103.2 12.5
ARG 1 1 2 1 568 3 0.05 0.02 0.56 0.26 54.5 19.0 86.6 13.0 178.2 13.1 85.5 12.6
ARG 1 1 2 2 568 9 0.13 0.04 1.49 0.42 53.9 18.9 87.8 13.9 -178.5 18.0 178.1 22.0
ARG 1 1 2 3 568 4 0.06 0.03 0.73 0.29 53.5 20.2 87.8 11.8 -176.0 17.5 -81.1 12.2
ARG 1 1 3 1 568 0 0.00 0.00 0.01 0.04 54.5 21.5 83.5 14.5 -78.4 20.8 102.9 14.2
ARG 1 1 3 2 568 2 0.03 0.02 0.29 0.18 50.0 23.4 82.4 13.6 -92.5 15.5 169.0 21.6
ARG 1 1 3 3 568 0 0.00 0.01 0.04 0.07 54.5 21.5 83.5 14.5 -77.1 19.2 -84.1 10.7
ARG 1 2 1 1 568 35 0.62 0.08 7.05 0.88 62.0 14.2 177.8 15.7 64.9 12.0 84.4 12.2
ARG 1 2 1 2 568 70 1.09 0.11 12.40 1.13 64.1 10.6 -175.8 15.2 68.0 15.3 -172.6 22.0
ARG 1 2 1 3 568 12 0.19 0.04 2.15 0.50 65.1 9.4 -178.6 11.3 61.1 13.6 -104.5 10.5
ARG 1 2 2 1 568 104 1.36 0.12 15.48 1.24 65.3 9.0 180.0 11.2 178.0 13.7 85.7 11.8
ARG 1 2 2 2 568 110 1.74 0.13 19.82 1.36 66.5 11.2 -177.6 13.9 -178.9 13.0 -177.2 21.2
ARG 1 2 2 3 568 94 1.34 0.12 15.19 1.23 66.4 9.1 -175.2 12.6 -177.5 11.9 -82.5 15.2
ARG 1 2 3 1 568 8 0.16 0.04 1.86 0.46 63.8 13.0 -171.9 17.8 -64.5 16.4 102.9 11.6
ARG 1 2 3 2 568 64 1.03 0.10 11.69 1.10 63.4 11.4 -176.5 14.2 -66.7 13.7 173.2 22.5
ARG 1 2 3 3 568 27 0.58 0.08 6.63 0.85 62.9 10.6 179.9 15.6 -69.2 13.0 -82.5 12.8
ARG 1 3 1 1 568 1 0.01 0.01 0.15 0.13 65.2 23.2 -85.1 20.9 84.2 18.8 84.5 13.8
LYS 2 3 2 2 2910 40 0.49 0.06 1.45 0.18 -165.2 19.3 -87.2 19.8 -177.2 19.8 -178.9 18.5
LYS 2 3 2 3 2910 11 0.13 0.03 0.39 0.09 -166.1 22.6 -83.0 20.9 -177.8 18.1 -67.3 18.4
LYS 2 3 3 1 2910 2 0.02 0.01 0.06 0.04 -160.1 20.9 -90.5 18.7 -80.9 23.3 68.3 26.6
LYS 2 3 3 2 2910 10 0.11 0.03 0.32 0.09 -166.8 19.3 -96.6 12.9 -69.4 15.3 178.4 14.6
LYS 2 3 3 3 2910 6 0.06 0.02 0.17 0.06 -168.0 17.8 -93.8 14.0 -76.0 17.4 -65.7 16.6
LYS 3 1 1 1 5105 5 0.06 0.02 0.10 0.04 -88.0 19.5 81.2 19.8 68.0 13.0 69.3 17.1
LYS 3 1 1 2 5105 14 0.16 0.04 0.27 0.06 -80.9 21.8 81.3 21.0 66.9 19.5 -179.6 24.1
LYS 3 1 1 3 5105 3 0.03 0.02 0.05 0.03 -86.8 20.3 86.0 19.6 84.3 20.7 -83.2 18.3
LYS 3 1 2 1 5105 33 0.33 0.05 0.56 0.09 -80.7 23.8 75.7 23.4 176.2 22.0 62.3 19.4
LYS 3 1 2 2 5105 56 0.74 0.08 1.26 0.13 -81.0 23.1 74.0 21.2 -178.3 18.4 177.9 18.5
LYS 3 1 2 3 5105 29 0.30 0.05 0.51 0.08 -87.6 17.8 74.5 25.3 178.0 24.9 -61.8 21.2
LYS 3 1 3 1 5105 2 0.02 0.01 0.03 0.02 -86.6 21.7 83.2 24.1 -85.6 20.2 68.2 26.5
LYS 3 1 3 2 5105 5 0.06 0.02 0.10 0.04 -82.6 18.5 71.2 28.5 -96.3 16.5 -172.0 20.3
LYS 3 1 3 3 5105 1 0.01 0.01 0.02 0.02 -85.8 22.3 78.0 23.9 -86.1 21.0 -66.3 16.9
LYS 3 2 1 1 5105 113 1.31 0.10 2.21 0.17 -70.1 12.8 178.9 16.4 73.0 18.8 72.3 18.0
LYS 3 2 1 2 5105 294 3.48 0.16 5.87 0.27 -68.5 11.2 176.2 15.7 69.4 16.1 177.3 15.9
LYS 3 2 1 3 5105 30 0.39 0.05 0.65 0.09 -70.3 15.4 174.9 19.8 84.2 17.2 -76.5 18.0
LYS 3 2 2 1 5105 445 5.29 0.20 8.92 0.33 -67.1 10.4 -178.4 14.6 177.7 16.7 66.5 17.3
LYS 3 2 2 2 5105 1994 22.79 0.37 38.46 0.56 -67.1 9.0 -179.4 11.6 -179.4 13.4 179.5 15.0
LYS 3 2 2 3 5105 458 5.44 0.20 9.18 0.33 -66.8 9.8 -178.0 12.9 -177.5 15.1 -65.9 16.9
LYS 3 2 3 1 5105 42 0.48 0.06 0.82 0.10 -66.8 13.1 -174.8 18.2 -76.5 23.6 78.2 24.3
LYS 3 2 3 2 5105 328 3.83 0.17 6.47 0.28 -67.6 10.3 -175.0 14.5 -72.6 15.3 -176.5 16.1
LYS 3 2 3 3 5105 121 1.39 0.10 2.35 0.17 -65.1 11.1 -174.8 14.1 -72.3 16.3 -65.7 14.5
LYS 3 3 1 1 5105 5 0.08 0.02 0.13 0.04 -64.8 10.7 -75.8 23.0 85.4 20.4 76.5 20.7
LYS 3 3 1 2 5105 28 0.32 0.05 0.54 0.08 -62.3 13.4 -76.6 19.6 91.0 18.1 -179.6 19.6
LYS 3 3 1 3 5105 4 0.04 0.02 0.07 0.03 -62.3 14.4 -83.2 20.5 88.3 19.6 -84.3 19.4
LYS 3 3 2 1 5105 154 1.79 0.12 3.02 0.20 -63.5 13.1 -67.5 15.3 -177.9 18.8 64.3 19.8
LYS 3 3 2 2 5105 592 6.96 0.22 11.75 0.37 -62.2 10.8 -66.1 12.4 -177.3 12.5 -177.9 14.8
LYS 3 3 2 3 5105 194 2.12 0.13 3.57 0.21 -60.1 10.5 -67.0 13.2 -174.3 18.3 -69.4 18.3
LYS 3 3 3 1 5105 13 0.15 0.03 0.26 0.06 -65.2 13.9 -68.9 18.8 -76.9 24.7 78.3 21.6
LYS 3 3 3 2 5105 107 1.25 0.10 2.12 0.16 -63.4 12.1 -66.5 17.6 -70.5 14.3 -179.8 14.1
LYS 3 3 3 3 5105 35 0.42 0.06 0.71 0.10 -60.5 11.4 -68.5 19.4 -73.1 16.7 -72.7 22.6
MET 1 1 1 0 221 11 0.38 0.09 5.26 1.22 60.8 12.7 78.3 8.1 73.3 14.2
MET 1 1 2 0 221 7 0.19 0.06 2.63 0.88 57.6 17.2 78.1 12.1 177.7 26.3
MET 1 1 3 0 221 0 0.02 0.02 0.25 0.27 59.4 15.4 77.8 12.6 -97.4 20.6
MET 1 2 1 0 221 75 2.53 0.23 35.00 2.62 64.4 8.4 -178.3 12.5 76.1 17.4
MET 1 2 2 0 221 43 1.44 0.18 19.89 2.19 64.9 7.3 -176.0 7.7 -175.0 19.5
MET 1 2 3 0 221 78 2.44 0.23 33.80 2.59 63.4 9.8 179.1 11.4 -71.8 14.7
MET 1 3 1 0 221 0 0.01 0.01 0.12 0.19 72.5 13.4 -70.1 14.6 99.6 10.6
MET 1 3 2 0 221 1 0.03 0.03 0.44 0.36 72.2 12.8 -70.4 14.7 174.3 23.8
MET 1 3 3 0 221 6 0.19 0.06 2.60 0.87 72.6 13.3 -72.0 15.5 -71.4 11.6
MET 2 1 1 0 904 212 6.90 0.37 23.35 1.15 -176.0 9.6 64.0 8.8 72.5 14.4
MET 2 1 2 0 904 51 1.72 0.19 5.82 0.64 -174.5 11.1 69.3 10.4 -166.1 22.4
MET 2 1 3 0 904 29 0.93 0.14 3.13 0.47 -172.4 12.9 76.6 14.3 -96.9 20.7
MET 2 2 1 0 904 207 7.02 0.38 23.75 1.16 -177.8 10.7 179.2 12.3 72.1 14.1
MET 2 2 2 0 904 107 3.73 0.28 12.64 0.90 -177.4 12.5 174.6 12.4 177.3 20.8
MET 2 2 3 0 904 236 7.22 0.38 24.45 1.17 -174.6 12.3 179.7 10.3 -71.6 16.9
MET 2 3 1 0 904 0 0.08 0.04 0.27 0.14 -178.7 9.5 -73.7 12.9 99.6 10.6
MET 2 3 2 0 904 10 0.31 0.08 1.04 0.28 -178.2 13.5 -78.4 12.2 173.0 21.9
MET 2 3 3 0 904 52 1.64 0.19 5.54 0.62 -178.8 7.3 -82.3 7.2 -73.4 11.7
MET 3 1 1 0 1935 17 0.57 0.11 0.89 0.17 -78.6 15.2 67.3 16.8 73.0 19.8
MET 3 1 2 0 1935 6 0.18 0.06 0.29 0.10 -78.9 13.8 69.3 13.8 -175.6 23.8
MET 3 1 3 0 1935 2 0.07 0.04 0.11 0.06 -77.7 13.5 70.6 14.5 -98.9 19.1
MET 3 2 1 0 1935 510 16.34 0.55 25.83 0.81 -67.4 9.4 178.0 11.6 70.4 14.2
MET 3 2 2 0 1935 293 9.31 0.43 14.72 0.66 -67.3 9.1 179.2 9.6 -177.6 19.6
MET 3 2 3 0 1935 343 11.81 0.48 18.67 0.72 -67.7 9.0 -176.3 11.9 -73.7 13.2
MET 3 3 1 0 1935 98 3.11 0.26 4.92 0.40 -65.8 8.2 -64.9 11.1 99.6 10.5
MET 3 3 2 0 1935 101 3.32 0.26 5.25 0.41 -62.7 8.2 -64.0 12.5 171.9 24.2
MET 3 3 3 0 1935 565 18.53 0.57 29.31 0.84 -65.8 10.3 -61.8 10.0 -69.4 13.4
PHE 1 1 0 0 749 743 11.06 0.31 99.20 0.27 63.0 10.0 90.4 9.6
PHE 1 2 0 0 749 6 0.09 0.03 0.80 0.27 62.0 12.3 -6.5 29.7
PHE 2 1 0 0 2257 2130 31.71 0.46 94.37 0.40 -178.8 10.4 78.1 13.6
PHE 2 2 0 0 2257 127 1.89 0.14 5.63 0.40 -174.2 9.5 21.2 24.3
PHE 3 1 0 0 3712 3163 47.08 0.50 85.21 0.48 -66.9 10.6 97.7 16.2
PHE 3 2 0 0 3712 549 8.17 0.27 14.79 0.48 -68.2 10.4 -15.3 22.0
PRO 1 1 0 0 2868 2868 50.72 0.54 100.00 0.00 27.0 8.8 -34.6 10.9
PRO 2 1 0 0 2787 2787 49.28 0.54 100.00 0.00 -25.1 8.1 36.3 9.5
SER 1 0 0 0 4931 4931 47.07 0.40 100.00 0.00 65.3 10.5
SER 2 0 0 0 2466 2466 23.54 0.34 100.00 0.00 179.0 11.6
SER 3 0 0 0 3078 3078 29.38 0.36 100.00 0.00 -63.9 10.5
THR 1 0 0 0 4907 4907 48.86 0.41 100.00 0.00 61.1 8.7
THR 2 0 0 0 754 754 7.51 0.21 100.00 0.00 -173.3 10.6
THR 3 0 0 0 4383 4383 43.64 0.40 100.00 0.00 -60.4 7.5
TRP 1 1 0 0 392 246 9.92 0.49 62.76 1.99 61.2 10.4 -89.9 9.8
TRP 1 2 0 0 392 14 0.56 0.12 3.57 0.76 66.0 8.2 -6.3 42.3
TRP 1 3 0 0 392 132 5.32 0.37 33.67 1.95 61.5 10.7 89.2 10.0
TRP 2 1 0 0 869 402 16.21 0.60 46.26 1.38 -177.3 12.5 -104.9 14.3
TRP 2 2 0 0 869 144 5.81 0.38 16.57 1.03 -175.1 12.4 17.3 30.8
TRP 2 3 0 0 869 323 13.02 0.55 37.17 1.34 -179.8 8.8 84.7 9.8
TRP 3 1 0 0 1219 132 5.32 0.37 10.83 0.73 -70.1 13.6 -92.2 14.1
TRP 3 2 0 0 1219 323 13.02 0.55 26.50 1.03 -68.6 9.3 -4.2 26.1
TRP 3 3 0 0 1219 764 30.81 0.76 62.67 1.13 -67.4 10.9 100.3 15.7
TYR 1 1 0 0 697 690 11.59 0.34 99.00 0.31 63.6 10.9 90.2 11.3
TYR 1 2 0 0 697 7 0.12 0.04 1.00 0.31 69.7 8.4 -9.5 16.5
TYR 2 1 0 0 2049 1934 32.48 0.50 94.39 0.42 -179.6 10.6 77.5 13.7
TYR 2 2 0 0 2049 115 1.93 0.15 5.61 0.42 -174.2 11.4 21.0 24.4
TYR 3 1 0 0 3208 2819 47.35 0.53 87.87 0.47 -65.8 10.9 97.8 16.3
TYR 3 2 0 0 3208 389 6.53 0.26 12.13 0.47 -67.2 10.4 -16.7 22.8
VAL 1 0 0 0 860 860 7.40 0.20 100.00 0.00 65.5 11.1
VAL 2 0 0 0 8585 8585 73.90 0.33 100.00 0.00 175.9 6.9
VAL 3 0 0 0 2172 2172 18.70 0.30 100.00 0.00 -61.7 8.4
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