Ramachandran Plots

MolProbity Ramachandran analysis
1R05, all models
General case
180
[2] B
A
[6]
[6] A
B 36 GLU
Psi
77 HIS
HIS
[6] B
A 39
39 SER
SER
[4] B
A 44 LYS
LYS
[1] B
A 85
85 SER
SER
[4] B
A 38
38 ALA
ALA
[1] B
A 37
37 LYS
LYS
[2]
AB
ARG
ARG
[5] B
A 5583
83
GLU
GLU
[2] B
A
[4] B
A 83
83 GLU
GLU
Isoleucine and valine
180
Psi
44 LYS
LYS
[3] B
A 34
34 GLN
GLN
A 10
10 ALA
ALA
[3] B
[3] B
A 36
36 GLU
GLU
[5] B
A 34
34 GLN
GLN
0
0
[6] B
A 37
37 LYS
LYS
[6] B
A 17
17 ASP
ASP
[3] B
A 12
12 GLU
GLU
[4]
[5]
A
A
72
72
ASN
ASN
[1]
[1]
[2]
[4]
B
[3]
[5]
B
72
72
ASN
ASN
[3] A
A 72
72ASN
ASN
[5]
AB
44
LEU
[3]
A
20
20
LYS
LYS
[1] B
B
A 44
20
20LEU
LYS
LYS
[5] B
A
[3] B
A
55 ARG
ARG
77 HIS
HIS
[4] B
54ARG
MET
[4]
AB
56
56
ARG
[5] B
A 99 ASN
ASN
AB
61
LEU
[1]
B
61
LEU
[2]
B
71
GLN
[3]
[4]
A
B
AB
71
71
5571
GLN
ARG
ARG
GLN
[5]
A
A18
B
71
71
71
GLN
GLN
GLN
GLN
A
71
GLN
B
A
18
HIS
HIS
[3]
[3][2]
B
A[6]
39
39
SER
SER
[3]
B
A
11
11
LEU
LEU
[1]
B
A
71
71
GLN
GLN
[2]
[1] B
A 34
ALA
ALA
AB
3466 GLN
GLN
[3] [6]
B
A B
A
82
82 LEU
38
38
LEU
ALA
ALA [3] B
A 13
13 ARG
ARG
[6] B
A 40
40 ARG
ARG
[3][1]
B
A
51
51
ILE
ILE
[3]
A
19
19
ILE
ILE
[5]B
B
A19
19
19
ILE
ILE
AB
19
ILE
ILE
[2] B
A 36
36 GLU
GLU
[6] B
A 12
ALA
ALA
[1]
AB
1266 GLU
GLU
[1] B
A 13
13 ARG
ARG
[5] B
A 38
38 ALA
ALA
-180
-180
0
Phi
[5] B
A 39
39 SER
SER
-180
180
Pre-proline
180
-180
0
Psi
0
0
180
Glycine
180
Psi
Phi
[6] B
A 86
86 GLY
GLY
[3] B
A 86
86 GLY
GLY
A
86
GLY
[1] B
[4] 86
B
A GLY
84
84 GLY
GLY
[2] B
A 84
84 GLY
GLY
-180
-180
-180
0
Phi
180
Trans proline
180
Psi
Psi
0
0
There
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
were 123 outliers (phi, psi):
A 6 ALA (53.0, -88.6)
A 12 GLU (-66.4, -157.7)
A 13 ARG (38.0, -152.2)
A 19 ILE (-53.9, -79.5)
A 20 LYS (-27.9, -42.7)
A 37 LYS (-47.5, 90.3)
A 61 LEU (-59.3, -77.9)
A 71 GLN (-58.2, -86.0)
A 72 ASN (-40.6, -27.2)
A 85 SER (64.0, 109.8)
A 86 GLY (-160.7, -36.9)
B 6 ALA (53.1, -88.5)
B 12 GLU (-66.3, -157.7)
B 13 ARG (38.0, -152.0)
B 19 ILE (-53.9, -79.5)
B 20 LYS (-28.0, -42.9)
B 37 LYS (-47.4, 90.3)
B 61 LEU (-59.1, -78.1)
B 71 GLN (-58.2, -86.0)
B 72 ASN (-39.9, -27.8)
B 85 SER (64.0, 109.6)
B 86 GLY (-160.6, -37.0)
A 4 LYS (42.8, 78.9)
A 5 ARG (-64.0, 83.7)
A 7 HIS (56.6, 168.9)
A 18 HIS (-63.4, -83.1)
A 34 GLN (49.3, -89.0)
A 36 GLU (-68.7, -139.5)
A 71 GLN (-61.1, -80.1)
A 72 ASN (-39.2, -27.8)
A 84 GLY (-137.1, -49.6)
B 4 LYS (42.8, 78.9)
B 5 ARG (-63.9, 83.7)
B 7 HIS (56.6, 168.9)
B 18 HIS (-63.3, -83.1)
B 34 GLN (49.2, -89.0)
B 36 GLU (-68.7, -139.5)
B 71 GLN (-61.2, -79.9)
B 72 ASN (-39.5, -27.6)
B 84 GLY (-137.2, -49.6)
A 5 ARG (-177.0, -72.7)
A 10 ALA (175.5, 56.1)
A 11 LEU (-60.4, -85.3)
A 12 GLU (175.7, -41.5)
A 13 ARG (43.8, -95.6)
A 19 ILE (-47.7, -77.5)
A 20 LYS (-28.9, -40.7)
A 34 GLN (79.3, 70.8)
A 36 GLU (35.2, 34.8)
A 39 SER (-73.9, -84.4)
A 51 ILE (-62.4, -75.3)
A 71 GLN (-56.7, -81.3)
A 72 ASN (-36.2, -31.5)
A 82 LEU (-46.0, -93.5)
A 86 GLY (41.2, 90.7)
B 5 ARG (-177.1, -72.7)
B 10 ALA (175.4, 55.8)
B 11 LEU (-60.3, -85.2)
B 12 GLU (175.6, -41.5)
B
B
B
B
B
B
B
B
B
B
B
A
A
A
A
A
A
A
B
B
B
B
B
B
B
B
A
A
A
A
A
A
A
A
A
A
B
B
B
B
B
B
B
B
B
B
A
A
A
A
A
A
A
A
A
B
B
B
B
B
B
B
B
B
Phi
180
Phi
180
-180
-180
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[3]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
0
Cis proline
180
-180
63.4% (647/1020) of all residues were in favored (98%) regions.
87.9% (897/1020) of all residues were in allowed (>99.8%) regions.
-180
0
Phi
180
-180
0
13 ARG (43.7, -95.5)
19 ILE (-47.5, -77.9)
20 LYS (-28.6, -40.8)
34 GLN (79.4, 70.7)
36 GLU (35.1, 34.8)
39 SER (-74.1, -84.4)
51 ILE (-62.4, -75.3)
71 GLN (-56.9, -80.9)
72 ASN (-37.7, -30.0)
82 LEU (-45.9, -93.6)
86 GLY (41.3, 90.5)
4 LYS (60.9, 115.3)
5 ARG (-55.9, -80.5)
38 ALA (44.5, 99.0)
56 ARG (-51.5, -73.2)
72 ASN (-39.1, -26.6)
83 GLU (-66.0, 64.6)
84 GLY (-141.4, -39.5)
4 LYS (61.0, 115.2)
5 ARG (-55.9, -80.5)
38 ALA (45.0, 98.8)
54 MET (-45.8, -72.8)
56 ARG (-51.3, -73.2)
72 ASN (-38.8, -27.1)
83 GLU (-66.1, 64.5)
84 GLY (-141.3, -39.4)
7 HIS (177.9, -58.1)
9 ASN (60.5, -73.5)
19 ILE (-43.9, -78.8)
34 GLN (43.4, 18.4)
38 ALA (39.8, -168.2)
39 SER (158.8, -162.9)
44 LEU (-31.6, -38.4)
71 GLN (-47.6, -82.1)
72 ASN (-38.6, -26.8)
83 GLU (-59.0, 80.3)
7 HIS (177.8, -58.2)
9 ASN (60.6, -73.5)
19 ILE (-43.7, -78.9)
34 GLN (43.3, 18.4)
38 ALA (39.8, -168.2)
39 SER (158.8, -162.9)
44 LEU (-31.6, -38.3)
71 GLN (-47.3, -81.9)
72 ASN (-36.7, -29.3)
83 GLU (-58.9, 80.3)
6 ALA (-62.8, -155.5)
17 ASP (178.8, -30.3)
36 GLU (-35.4, 159.7)
37 LYS (171.8, -16.4)
38 ALA (-32.1, -93.6)
39 SER (163.8, 160.5)
40 ARG (41.9, -102.1)
71 GLN (-50.5, -81.4)
86 GLY (-44.5, 99.6)
6 ALA (-62.7, -155.6)
17 ASP (178.9, -30.3)
36 GLU (-33.5, 159.0)
37 LYS (171.9, -16.3)
38 ALA (-32.4, -93.3)
39 SER (163.8, 160.6)
40 ARG (41.7, -101.9)
71 GLN (-50.2, -81.5)
86 GLY (-44.5, 99.6)
http://kinemage.biochem.duke.edu
Lovell, Davis, et al. Proteins 50:437 (2003)
MolProbity Ramachandran analysis
1R05, model 1
General case
180
Isoleucine and valine
180
[1] B
A 85
85 SER
SER
Psi
Psi
[1] B
A 37
37 LYS
LYS
0
0
[1]
[1] A
B 72 ASN
[1] B
A 20
20 LYS
LYS
A 61
61 LEU
LEU
[1] B
[1] B
A 71
71 GLN
GLN
[1] B
A 12
12 GLU
GLU
[1] B
A
[1] B
A 19
19 ILE
ILE
66 ALA
ALA
[1] B
A 13
13 ARG
ARG
-180
-180
-180
0
Phi
180
Pre-proline
180
-180
0
Psi
0
0
180
Phi
180
Phi
180
Glycine
180
Psi
Phi
A 86
86 GLY
GLY
[1] B
-180
-180
-180
0
Phi
180
Trans proline
180
-180
Cis proline
180
Psi
Psi
0
0
-180
0
-180
-180
0
Phi
180
-180
0
67.1% (114/170) of all residues were in favored (98%) regions.
87.1% (148/170) of all residues were in allowed (>99.8%) regions.
There
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
[1]
were 22 outliers (phi, psi):
A 6 ALA (53.0, -88.6)
A 12 GLU (-66.4, -157.7)
A 13 ARG (38.0, -152.2)
A 19 ILE (-53.9, -79.5)
A 20 LYS (-27.9, -42.7)
A 37 LYS (-47.5, 90.3)
A 61 LEU (-59.3, -77.9)
A 71 GLN (-58.2, -86.0)
A 72 ASN (-40.6, -27.2)
A 85 SER (64.0, 109.8)
A 86 GLY (-160.7, -36.9)
B 6 ALA (53.1, -88.5)
B 12 GLU (-66.3, -157.7)
B 13 ARG (38.0, -152.0)
B 19 ILE (-53.9, -79.5)
B 20 LYS (-28.0, -42.9)
B 37 LYS (-47.4, 90.3)
B 61 LEU (-59.1, -78.1)
B 71 GLN (-58.2, -86.0)
B 72 ASN (-39.9, -27.8)
B 85 SER (64.0, 109.6)
B 86 GLY (-160.6, -37.0)
http://kinemage.biochem.duke.edu
Lovell, Davis, et al. Proteins 50:437 (2003)
MolProbity Ramachandran analysis
1R05, model 2
General case
180
[2] B
A
Psi
[2] B
A
55 ARG
ARG
[2] B
A
Isoleucine and valine
180
77 HIS
HIS
Psi
44 LYS
LYS
0
0
[2] B
A 72
72 ASN
ASN
[2] B
B
71
GLN
A 18
71 HIS
GLN
[2]
A
18
HIS
[2] B
A 34
34 GLN
GLN
[2] B
A 36
36 GLU
GLU
-180
-180
-180
0
Phi
180
Pre-proline
180
-180
0
Psi
0
0
180
Phi
180
Phi
180
Glycine
180
Psi
Phi
[2] B
A 84
84 GLY
GLY
-180
-180
-180
0
Phi
180
Trans proline
180
-180
Cis proline
180
Psi
Psi
0
0
-180
0
-180
-180
0
Phi
180
-180
0
61.2% (104/170) of all residues were in favored (98%) regions.
89.4% (152/170) of all residues were in allowed (>99.8%) regions.
There were 18 outliers (phi, psi):
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
[2]
A
A
A
A
A
A
A
A
A
B
B
B
B
B
B
B
B
B
4 LYS (42.8, 78.9)
5 ARG (-64.0, 83.7)
7 HIS (56.6, 168.9)
18 HIS (-63.4, -83.1)
34 GLN (49.3, -89.0)
36 GLU (-68.7, -139.5)
71 GLN (-61.1, -80.1)
72 ASN (-39.2, -27.8)
84 GLY (-137.1, -49.6)
4 LYS (42.8, 78.9)
5 ARG (-63.9, 83.7)
7 HIS (56.6, 168.9)
18 HIS (-63.3, -83.1)
34 GLN (49.2, -89.0)
36 GLU (-68.7, -139.5)
71 GLN (-61.2, -79.9)
72 ASN (-39.5, -27.6)
84 GLY (-137.2, -49.6)
http://kinemage.biochem.duke.edu
Lovell, Davis, et al. Proteins 50:437 (2003)
MolProbity Ramachandran analysis
1R05, model 3
General case
180
Isoleucine and valine
180
Psi
Psi
[3] B
A 34
34 GLN
GLN
A 10
10 ALA
ALA
[3] B
[3] B
A 36
36 GLU
GLU
0
0
[3]
[3] B
A 72
72 ASN
ASN
[3] B
A 20
20 LYS
LYS
[3] B
A
55 ARG
ARG
[3]
B
71
GLN
A SER
71LEU
GLN
[3]
[3] [3]
B
A B
39
39
SER
A
11
11
LEU
[3] B
A 82
82 LEU
LEU
[3] B
A 12
12 GLU
GLU
[3] [3]
B
A B
51
51 ILE
ILE
A
19
19 ILE
ILE
[3] B
A 13
13 ARG
ARG
-180
-180
-180
0
Phi
180
Pre-proline
180
-180
Psi
0
0
-180
Phi
180
Glycine
180
Psi
0
[3] B
A 86
86 GLY
GLY
-180
-180
0
Phi
180
Trans proline
180
-180
Psi
0
0
-180
Phi
180
Phi
180
Cis proline
180
Psi
0
-180
-180
0
Phi
180
-180
0
63.5% (108/170) of all residues were in favored (98%) regions.
82.4% (140/170) of all residues were in allowed (>99.8%) regions.
There were 30 outliers (phi, psi):
[3] A 5 ARG (-177.0, -72.7)
[3] A 10 ALA (175.5, 56.1)
[3] A 11 LEU (-60.4, -85.3)
[3] A 12 GLU (175.7, -41.5)
[3] A 13 ARG (43.8, -95.6)
[3] A 19 ILE (-47.7, -77.5)
[3] A 20 LYS (-28.9, -40.7)
[3] A 34 GLN (79.3, 70.8)
[3] A 36 GLU (35.2, 34.8)
[3] A 39 SER (-73.9, -84.4)
[3] A 51 ILE (-62.4, -75.3)
[3]
[3]
[3]
[3]
[3]
A 71 GLN (-56.7, -81.3)
A 72 ASN (-36.2, -31.5)
A 82 LEU (-46.0, -93.5)
A 86 GLY (41.2, 90.7)
B 5 ARG (-177.1, -72.7)
[3]
[3]
[3]
[3]
[3]
B
B
B
B
B
10 ALA (175.4, 55.8)
11 LEU (-60.3, -85.2)
12 GLU (175.6, -41.5)
13 ARG (43.7, -95.5)
19 ILE (-47.5, -77.9)
[3] B 20 LYS (-28.6, -40.8)
[3] B 34 GLN (79.4, 70.7)
[3] B 36 GLU (35.1, 34.8)
[3] B 39 SER (-74.1, -84.4)
[3] B 51 ILE (-62.4, -75.3)
[3] B 71 GLN (-56.9, -80.9)
[3] B 72 ASN (-37.7, -30.0)
[3] B 82 LEU (-45.9, -93.6)
[3] B 86 GLY (41.3, 90.5)
http://kinemage.biochem.duke.edu
Lovell, Davis, et al. Proteins 50:437 (2003)
MolProbity Ramachandran analysis
1R05, model 4
General case
180
[4] B
A
44 LYS
LYS
[4] B
A 38
38 ALA
ALA
Psi
Isoleucine and valine
180
Psi
[4] B
A 83
83 GLU
GLU
0
0
[4]
[4] A
B 72 ASN
[4] B
54ARG
MET
[4]
AB 56
56
ARG
[4] B
A 55 ARG
ARG
-180
-180
-180
0
Phi
180
Pre-proline
180
-180
0
Psi
0
0
180
Phi
180
Phi
180
Glycine
180
Psi
Phi
[4] B
A 84
84 GLY
GLY
-180
-180
-180
0
Phi
180
Trans proline
180
-180
Cis proline
180
Psi
Psi
0
0
-180
0
-180
-180
0
Phi
180
-180
0
62.9% (107/170) of all residues were in favored (98%) regions.
91.2% (155/170) of all residues were in allowed (>99.8%) regions.
There
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
[4]
were 15 outliers (phi, psi):
A 4 LYS (60.9, 115.3)
A 5 ARG (-55.9, -80.5)
A 38 ALA (44.5, 99.0)
A 56 ARG (-51.5, -73.2)
A 72 ASN (-39.1, -26.6)
A 83 GLU (-66.0, 64.6)
A 84 GLY (-141.4, -39.5)
B 4 LYS (61.0, 115.2)
B 5 ARG (-55.9, -80.5)
B 38 ALA (45.0, 98.8)
B 54 MET (-45.8, -72.8)
B 56 ARG (-51.3, -73.2)
B 72 ASN (-38.8, -27.1)
B 83 GLU (-66.1, 64.5)
B 84 GLY (-141.3, -39.4)
http://kinemage.biochem.duke.edu
Lovell, Davis, et al. Proteins 50:437 (2003)
MolProbity Ramachandran analysis
1R05, model 5
General case
180
Psi
Isoleucine and valine
180
Psi
[5] B
A 83
83 GLU
GLU
[5] B
A 34
34 GLN
GLN
0
0
[5]
[5] A
B 72
72 ASN
ASN
[5] B
A 44
44 LEU
LEU
[5] B
A
[5] B
A
[5] B
A 71
71 GLN
GLN
[5] B
A 38
38 ALA
ALA
-180
-180
0
Phi
[5] B
A 19
19 ILE
ILE
[5] B
A 39
39 SER
SER
-180
180
Pre-proline
180
77 HIS
HIS
99 ASN
ASN
-180
Psi
0
0
-180
Phi
180
Phi
180
Phi
180
Glycine
180
Psi
0
-180
-180
0
Phi
180
Trans proline
180
-180
Cis proline
180
Psi
Psi
0
0
-180
0
-180
-180
0
Phi
180
-180
0
62.9% (107/170) of all residues were in favored (98%) regions.
88.2% (150/170) of all residues were in allowed (>99.8%) regions.
There
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
[5]
were 20 outliers (phi, psi):
A 7 HIS (177.9, -58.1)
A 9 ASN (60.5, -73.5)
A 19 ILE (-43.9, -78.8)
A 34 GLN (43.4, 18.4)
A 38 ALA (39.8, -168.2)
A 39 SER (158.8, -162.9)
A 44 LEU (-31.6, -38.4)
A 71 GLN (-47.6, -82.1)
A 72 ASN (-38.6, -26.8)
A 83 GLU (-59.0, 80.3)
B 7 HIS (177.8, -58.2)
B 9 ASN (60.6, -73.5)
B 19 ILE (-43.7, -78.9)
B 34 GLN (43.3, 18.4)
B 38 ALA (39.8, -168.2)
B 39 SER (158.8, -162.9)
B 44 LEU (-31.6, -38.3)
B 71 GLN (-47.3, -81.9)
B 72 ASN (-36.7, -29.3)
B 83 GLU (-58.9, 80.3)
http://kinemage.biochem.duke.edu
Lovell, Davis, et al. Proteins 50:437 (2003)
MolProbity Ramachandran analysis
1R05, model 6
General case
180
Isoleucine and valine
180
[6] B
A 39
39 SER
SER
[6]
[6] A
B 36 GLU
Psi
Psi
0
0
[6] B
A 37
37 LYS
LYS
[6] B
A 17
17 ASP
ASP
[6] B
A 71
71 GLN
GLN
[6] B
A 38
38 ALA
ALA
[6] B
A
[6] B
A 40
40 ARG
ARG
66 ALA
ALA
-180
-180
-180
0
Phi
180
Pre-proline
180
-180
Psi
0
0
-180
Phi
180
Phi
180
Phi
180
Glycine
180
Psi
0
[6] B
A 86
86 GLY
GLY
-180
-180
0
Phi
180
Trans proline
180
-180
Cis proline
180
Psi
Psi
0
0
-180
0
-180
-180
0
Phi
180
-180
0
62.9% (107/170) of all residues were in favored (98%) regions.
89.4% (152/170) of all residues were in allowed (>99.8%) regions.
There were 18 outliers (phi, psi):
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
[6]
A
A
A
A
A
A
A
A
A
B
B
B
B
B
B
B
B
B
6 ALA (-62.8, -155.5)
17 ASP (178.8, -30.3)
36 GLU (-35.4, 159.7)
37 LYS (171.8, -16.4)
38 ALA (-32.1, -93.6)
39 SER (163.8, 160.5)
40 ARG (41.9, -102.1)
71 GLN (-50.5, -81.4)
86 GLY (-44.5, 99.6)
6 ALA (-62.7, -155.6)
17 ASP (178.9, -30.3)
36 GLU (-33.5, 159.0)
37 LYS (171.9, -16.3)
38 ALA (-32.4, -93.3)
39 SER (163.8, 160.6)
40 ARG (41.7, -101.9)
71 GLN (-50.2, -81.5)
86 GLY (-44.5, 99.6)
http://kinemage.biochem.duke.edu
Lovell, Davis, et al. Proteins 50:437 (2003)