PDB Chemical Component LYS
The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.
Bond Distances for LYS
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N |
CA |
1.456 |
1.469 |
| N |
H |
1.019 |
1.009 |
| N |
H2 |
1.020 |
1.008 |
| CA |
C |
1.535 |
1.507 |
| CA |
CB |
1.525 |
1.530 |
| CA |
HA |
1.114 |
1.089 |
| C |
O |
1.254 |
1.208 |
| C |
OXT |
1.264 |
1.343 |
| CB |
CG |
1.515 |
1.531 |
| CB |
HB2 |
1.115 |
1.089 |
| CB |
HB3 |
1.115 |
1.090 |
| CG |
CD |
1.531 |
1.531 |
| CG |
HG2 |
1.115 |
1.089 |
| CG |
HG3 |
1.116 |
1.090 |
| CD |
CE |
1.538 |
1.529 |
| CD |
HD2 |
1.115 |
1.090 |
| CD |
HD3 |
1.115 |
1.090 |
| CE |
NZ |
1.480 |
1.469 |
| CE |
HE2 |
1.115 |
1.090 |
| CE |
HE3 |
1.115 |
1.090 |
| NZ |
HZ1 |
1.021 |
1.009 |
| NZ |
HZ2 |
1.019 |
1.008 |
| NZ |
HZ3 |
1.020 |
1.009 |
| OXT |
HXT |
0.950 |
0.967 |
Bond Angles for LYS
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
N |
H |
112.0 |
106.7 |
| CA |
N |
H2 |
111.3 |
106.7 |
| N |
CA |
C |
112.0 |
109.5 |
| N |
CA |
CB |
111.4 |
109.5 |
| N |
CA |
HA |
106.7 |
109.5 |
| H |
N |
H2 |
111.2 |
106.7 |
| C |
CA |
CB |
110.4 |
109.5 |
| C |
CA |
HA |
107.8 |
109.5 |
| CA |
C |
O |
120.4 |
120.0 |
| CA |
C |
OXT |
115.5 |
120.0 |
| CB |
CA |
HA |
108.3 |
109.5 |
| CA |
CB |
CG |
114.8 |
109.4 |
| CA |
CB |
HB2 |
110.3 |
109.5 |
| CA |
CB |
HB3 |
110.3 |
109.5 |
| O |
C |
OXT |
121.5 |
120.0 |
| C |
OXT |
HXT |
115.4 |
120.0 |
| CG |
CB |
HB2 |
110.2 |
109.5 |
| CG |
CB |
HB3 |
110.2 |
109.4 |
| CB |
CG |
CD |
110.7 |
109.4 |
| CB |
CG |
HG2 |
111.8 |
109.5 |
| CB |
CG |
HG3 |
111.8 |
109.5 |
| HB2 |
CB |
HB3 |
100.0 |
109.5 |
| CD |
CG |
HG2 |
111.7 |
109.5 |
| CD |
CG |
HG3 |
111.7 |
109.4 |
| CG |
CD |
CE |
110.2 |
109.5 |
| CG |
CD |
HD2 |
112.0 |
109.5 |
| CG |
CD |
HD3 |
112.0 |
109.4 |
| HG2 |
CG |
HG3 |
98.6 |
109.5 |
| CE |
CD |
HD2 |
111.9 |
109.5 |
| CE |
CD |
HD3 |
111.9 |
109.5 |
| CD |
CE |
NZ |
106.5 |
109.5 |
| CD |
CE |
HE2 |
113.3 |
109.5 |
| CD |
CE |
HE3 |
113.4 |
109.5 |
| HD2 |
CD |
HD3 |
98.5 |
109.5 |
| NZ |
CE |
HE2 |
113.3 |
109.4 |
| NZ |
CE |
HE3 |
113.3 |
109.5 |
| CE |
NZ |
HZ1 |
106.5 |
109.4 |
| CE |
NZ |
HZ2 |
113.3 |
109.5 |
| CE |
NZ |
HZ3 |
113.4 |
109.5 |
| HE2 |
CE |
HE3 |
97.2 |
109.4 |
| HZ1 |
NZ |
HZ2 |
113.3 |
109.5 |
| HZ1 |
NZ |
HZ3 |
113.3 |
109.5 |
| HZ2 |
NZ |
HZ3 |
97.1 |
109.5 |
Torsion Angles for LYS
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| H |
N |
CA |
H2 |
125.2 |
246.2 |
| C |
CA |
N |
CB |
124.3 |
120.0 |
| C |
CA |
N |
HA |
242.3 |
240.0 |
| N |
CA |
C |
O |
359.5 |
340.0 |
| N |
CA |
C |
OXT |
161.3 |
160.0 |
| CB |
CA |
N |
HA |
118.1 |
120.0 |
| N |
CA |
CB |
CG |
62.5 |
295.0 |
| N |
CA |
CB |
HB2 |
187.8 |
55.0 |
| N |
CA |
CB |
HB3 |
297.3 |
175.0 |
| CA |
N |
H |
H2 |
234.7 |
113.8 |
| H |
N |
CA |
C |
180.0 |
60.0 |
| H |
N |
CA |
CB |
55.7 |
300.0 |
| H |
N |
CA |
HA |
297.6 |
180.0 |
| CA |
N |
H2 |
H |
125.7 |
246.2 |
| H2 |
N |
CA |
C |
54.7 |
173.8 |
| H2 |
N |
CA |
CB |
290.5 |
53.8 |
| H2 |
N |
CA |
HA |
172.4 |
293.8 |
| C |
CA |
N |
H |
180.0 |
60.0 |
| C |
CA |
N |
H2 |
54.7 |
173.8 |
| N |
CA |
C |
CB |
235.2 |
240.0 |
| N |
CA |
C |
HA |
117.0 |
120.0 |
| CB |
CA |
C |
HA |
241.8 |
239.9 |
| C |
CA |
CB |
CG |
297.4 |
175.0 |
| C |
CA |
CB |
HB2 |
62.7 |
295.0 |
| C |
CA |
CB |
HB3 |
172.2 |
55.1 |
| O |
C |
CA |
OXT |
198.2 |
180.0 |
| CA |
C |
OXT |
HXT |
180.0 |
180.0 |
| CB |
CA |
N |
H |
55.7 |
300.0 |
| CB |
CA |
N |
H2 |
290.5 |
53.8 |
| N |
CA |
CB |
C |
125.1 |
120.0 |
| N |
CA |
CB |
HA |
242.9 |
240.0 |
| C |
CA |
CB |
HA |
117.8 |
120.0 |
| CB |
CA |
C |
O |
124.3 |
100.0 |
| CB |
CA |
C |
OXT |
286.1 |
280.0 |
| CG |
CB |
CA |
HB2 |
234.7 |
240.0 |
| CG |
CB |
CA |
HB3 |
125.2 |
119.9 |
| CA |
CB |
CG |
CD |
127.4 |
180.0 |
| CA |
CB |
CG |
HG2 |
252.6 |
300.0 |
| CA |
CB |
CG |
HG3 |
2.1 |
60.1 |
| HB2 |
CB |
CA |
HB3 |
250.5 |
240.0 |
| HA |
CA |
N |
H |
297.6 |
180.0 |
| HA |
CA |
N |
H2 |
172.4 |
293.8 |
| N |
CA |
HA |
C |
239.6 |
240.0 |
| N |
CA |
HA |
CB |
120.1 |
120.0 |
| C |
CA |
HA |
CB |
240.5 |
240.0 |
| HA |
CA |
C |
O |
242.4 |
220.0 |
| HA |
CA |
C |
OXT |
44.2 |
40.1 |
| HA |
CA |
CB |
CG |
179.6 |
55.0 |
| HA |
CA |
CB |
HB2 |
304.9 |
175.0 |
| HA |
CA |
CB |
HB3 |
54.4 |
295.0 |
| O |
C |
CA |
CB |
124.3 |
100.0 |
| O |
C |
CA |
HA |
242.4 |
220.0 |
| CA |
C |
O |
OXT |
160.7 |
180.0 |
| O |
C |
OXT |
HXT |
341.5 |
0.1 |
| OXT |
C |
CA |
CB |
286.1 |
280.0 |
| OXT |
C |
CA |
HA |
44.2 |
40.1 |
| CA |
C |
OXT |
O |
198.4 |
180.0 |
| CG |
CB |
CA |
HA |
179.6 |
55.0 |
| CA |
CB |
CG |
HB2 |
125.3 |
120.0 |
| CA |
CB |
CG |
HB3 |
234.7 |
240.0 |
| HB2 |
CB |
CG |
HB3 |
109.4 |
120.0 |
| CD |
CG |
CB |
HG2 |
234.8 |
240.0 |
| CD |
CG |
CB |
HG3 |
125.3 |
119.9 |
| CB |
CG |
CD |
CE |
200.8 |
180.0 |
| CB |
CG |
CD |
HD2 |
326.0 |
300.0 |
| CB |
CG |
CD |
HD3 |
75.5 |
60.0 |
| HG2 |
CG |
CB |
HG3 |
250.5 |
239.9 |
| HB2 |
CB |
CA |
HA |
304.9 |
175.0 |
| CA |
CB |
HB2 |
CG |
232.2 |
240.0 |
| CA |
CB |
HB2 |
HB3 |
116.1 |
120.0 |
| CG |
CB |
HB2 |
HB3 |
244.0 |
240.0 |
| HB2 |
CB |
CG |
CD |
2.1 |
60.0 |
| HB2 |
CB |
CG |
HG2 |
127.4 |
180.0 |
| HB2 |
CB |
CG |
HG3 |
236.8 |
300.0 |
| HB3 |
CB |
CA |
HA |
54.4 |
295.0 |
| CA |
CB |
HB3 |
CG |
127.8 |
119.9 |
| CA |
CB |
HB3 |
HB2 |
243.9 |
239.9 |
| CG |
CB |
HB3 |
HB2 |
116.0 |
120.0 |
| HB3 |
CB |
CG |
CD |
252.7 |
300.0 |
| HB3 |
CB |
CG |
HG2 |
17.9 |
59.9 |
| HB3 |
CB |
CG |
HG3 |
127.4 |
180.0 |
| CD |
CG |
CB |
HB2 |
2.1 |
60.0 |
| CD |
CG |
CB |
HB3 |
252.7 |
300.0 |
| CB |
CG |
CD |
HG2 |
125.3 |
120.0 |
| CB |
CG |
CD |
HG3 |
234.7 |
240.0 |
| HG2 |
CG |
CD |
HG3 |
109.4 |
120.0 |
| CE |
CD |
CG |
HD2 |
234.8 |
240.0 |
| CE |
CD |
CG |
HD3 |
125.2 |
120.0 |
| CG |
CD |
CE |
NZ |
324.2 |
180.0 |
| CG |
CD |
CE |
HE2 |
89.4 |
300.0 |
| CG |
CD |
CE |
HE3 |
198.9 |
60.0 |
| HD2 |
CD |
CG |
HD3 |
250.5 |
240.0 |
| HG2 |
CG |
CB |
HB2 |
127.4 |
180.0 |
| HG2 |
CG |
CB |
HB3 |
17.9 |
59.9 |
| CB |
CG |
HG2 |
CD |
235.3 |
240.0 |
| CB |
CG |
HG2 |
HG3 |
117.7 |
120.1 |
| CD |
CG |
HG2 |
HG3 |
242.4 |
240.0 |
| HG2 |
CG |
CD |
CE |
75.5 |
60.0 |
| HG2 |
CG |
CD |
HD2 |
200.7 |
180.1 |
| HG2 |
CG |
CD |
HD3 |
310.2 |
300.0 |
| HG3 |
CG |
CB |
HB2 |
236.8 |
300.0 |
| HG3 |
CG |
CB |
HB3 |
127.4 |
180.0 |
| CB |
CG |
HG3 |
CD |
124.7 |
119.9 |
| CB |
CG |
HG3 |
HG2 |
242.3 |
240.0 |
| CD |
CG |
HG3 |
HG2 |
117.6 |
120.0 |
| HG3 |
CG |
CD |
CE |
326.1 |
300.0 |
| HG3 |
CG |
CD |
HD2 |
91.3 |
60.0 |
| HG3 |
CG |
CD |
HD3 |
200.8 |
180.0 |
| CE |
CD |
CG |
HG2 |
75.5 |
60.0 |
| CE |
CD |
CG |
HG3 |
326.1 |
300.0 |
| CG |
CD |
CE |
HD2 |
125.3 |
120.0 |
| CG |
CD |
CE |
HD3 |
234.7 |
240.1 |
| HD2 |
CD |
CE |
HD3 |
109.5 |
120.0 |
| NZ |
CE |
CD |
HE2 |
234.8 |
240.0 |
| NZ |
CE |
CD |
HE3 |
125.2 |
120.0 |
| CD |
CE |
NZ |
HZ1 |
180.0 |
300.0 |
| CD |
CE |
NZ |
HZ2 |
305.3 |
60.0 |
| CD |
CE |
NZ |
HZ3 |
54.8 |
180.0 |
| HE2 |
CE |
CD |
HE3 |
250.5 |
240.0 |
| HD2 |
CD |
CG |
HG2 |
200.7 |
180.1 |
| HD2 |
CD |
CG |
HG3 |
91.3 |
60.0 |
| CG |
CD |
HD2 |
CE |
235.7 |
240.0 |
| CG |
CD |
HD2 |
HD3 |
117.9 |
120.0 |
| CE |
CD |
HD2 |
HD3 |
242.2 |
240.0 |
| HD2 |
CD |
CE |
NZ |
198.9 |
60.0 |
| HD2 |
CD |
CE |
HE2 |
324.1 |
180.0 |
| HD2 |
CD |
CE |
HE3 |
73.7 |
300.0 |
| HD3 |
CD |
CG |
HG2 |
310.2 |
300.0 |
| HD3 |
CD |
CG |
HG3 |
200.8 |
180.0 |
| CG |
CD |
HD3 |
CE |
124.3 |
120.0 |
| CG |
CD |
HD3 |
HD2 |
242.1 |
240.0 |
| CE |
CD |
HD3 |
HD2 |
117.8 |
120.0 |
| HD3 |
CD |
CE |
NZ |
89.4 |
300.0 |
| HD3 |
CD |
CE |
HE2 |
214.7 |
60.0 |
| HD3 |
CD |
CE |
HE3 |
324.2 |
180.0 |
| NZ |
CE |
CD |
HD2 |
198.9 |
60.0 |
| NZ |
CE |
CD |
HD3 |
89.4 |
300.0 |
| CD |
CE |
NZ |
HE2 |
125.3 |
120.1 |
| CD |
CE |
NZ |
HE3 |
234.7 |
239.9 |
| HE2 |
CE |
NZ |
HE3 |
109.4 |
119.9 |
| HZ1 |
NZ |
CE |
HZ2 |
234.7 |
240.0 |
| HZ1 |
NZ |
CE |
HZ3 |
125.3 |
120.0 |
| HZ2 |
NZ |
CE |
HZ3 |
250.5 |
239.9 |
| HE2 |
CE |
CD |
HD2 |
324.1 |
180.0 |
| HE2 |
CE |
CD |
HD3 |
214.7 |
60.0 |
| CD |
CE |
HE2 |
NZ |
238.5 |
240.0 |
| CD |
CE |
HE2 |
HE3 |
119.3 |
120.0 |
| NZ |
CE |
HE2 |
HE3 |
240.8 |
240.1 |
| HE2 |
CE |
NZ |
HZ1 |
54.7 |
179.9 |
| HE2 |
CE |
NZ |
HZ2 |
180.0 |
299.9 |
| HE2 |
CE |
NZ |
HZ3 |
289.5 |
60.0 |
| HE3 |
CE |
CD |
HD2 |
73.7 |
300.0 |
| HE3 |
CE |
CD |
HD3 |
324.2 |
180.0 |
| CD |
CE |
HE3 |
NZ |
121.5 |
120.1 |
| CD |
CE |
HE3 |
HE2 |
240.7 |
239.9 |
| NZ |
CE |
HE3 |
HE2 |
119.2 |
119.9 |
| HE3 |
CE |
NZ |
HZ1 |
305.3 |
60.1 |
| HE3 |
CE |
NZ |
HZ2 |
70.6 |
180.0 |
| HE3 |
CE |
NZ |
HZ3 |
180.0 |
300.1 |
| HZ1 |
NZ |
CE |
HE2 |
54.7 |
179.9 |
| HZ1 |
NZ |
CE |
HE3 |
305.3 |
60.1 |
| CE |
NZ |
HZ1 |
HZ2 |
125.3 |
119.9 |
| CE |
NZ |
HZ1 |
HZ3 |
234.7 |
240.0 |
| HZ2 |
NZ |
HZ1 |
HZ3 |
109.4 |
120.1 |
| HZ2 |
NZ |
CE |
HE2 |
180.0 |
299.9 |
| HZ2 |
NZ |
CE |
HE3 |
70.6 |
180.0 |
| CE |
NZ |
HZ2 |
HZ1 |
238.5 |
240.1 |
| CE |
NZ |
HZ2 |
HZ3 |
119.3 |
120.1 |
| HZ1 |
NZ |
HZ2 |
HZ3 |
240.8 |
240.0 |
| HZ3 |
NZ |
CE |
HE2 |
289.5 |
60.0 |
| HZ3 |
NZ |
CE |
HE3 |
180.0 |
300.1 |
| CE |
NZ |
HZ3 |
HZ1 |
121.6 |
119.9 |
| CE |
NZ |
HZ3 |
HZ2 |
240.8 |
239.9 |
| HZ1 |
NZ |
HZ3 |
HZ2 |
119.2 |
120.0 |