rigid_group_atom_positions
The coordinates of the atoms in each amino acid in the local coordinate system of rigid group to which the atom belongs.
- 8 groups are
0 - backbone-group Main chain rigid group corresponding to torsion angle backbone between atoms \(N-C\alpha-C-C\beta\) in amino acid. CA is the origin point, C is on positive x-axis and N is on X-Y plane.
1 - pre-omega-group Rigid group corresponding to torsion angle pre-omega between atoms \(N_i-C\alpha_i-N_{i-1}-C\alpha_{i-1}\) in amino acid.
2 - phi-group Rigid group corresponding to torsion angle phi between atoms \(C_i-C\alpha_i-N_i-C_{i+1}\) in amino acid.
3 - psi-group Rigid group corresponding to torsion angle psi between atoms \(N_{i-1}-C_i-C\alpha_i-N_i\) in amino acid.
4 - chi1-group
5 - chi2-group
6 - chi3-group
7 - chi4-group
chi1,2,3,4-group correspond to torsion angles in the amino acids in chi_angle_atoms . Torsion angles are determined by the coordinates of four atoms [A, B, C, D]. Atom B and C constitute the axis of rotation, in x-axis. The third atom C is the origin point. Atom B is on the negative x-axis. The first atom A is on X-Y plane. So we can determine the coordinate of the fourth atom D.
pre-omega-group and backbone-group have the same coordinate system, and the coordinate transformation is the identity transformation.
The coordinate transformation matrix from phi-group to backbone-group, from psi-group to backbone-group, from chi1-group to backbone-group, from chi2-group to chi1-group, from chi3-group to chi2-group and from chi4-group to chi3-group need to be obtained by calculating using function _make_rigid_transformation_4x4 .
amino acid |
Atom |
group |
positions |
|---|---|---|---|
ALA
|
N
CA
C
CB
O
|
0
0
0
0
3
|
(-0.525, 1.363, 0.0)
(0.0, 0.0, 0.0)
(1.526, -0.0, -0.0)
(-0.529, -0.774, -1.205)
(0.627, 1.062, 0.0)
|
ARG
|
N
CA
C
CB
O
CG
CD
NE
NH1
NH2
CZ
|
0
0
0
0
3
4
5
6
7
7
7
|
(-0.524, 1.363, 0.0)
(0.0, 0.0, 0.0)
(1.525, -0.0, -0.0)
(-0.524, -0.778, -1.209)
(0.627, 1.062, 0.0)
(0.616, 1.39, -0.0)
(0.564, 1.414, 0.0)
(0.539, 1.357, -0.0)
(0.206, 2.301, 0.0)
(2.078, 0.978, -0.0)
(0.758, 1.093, -0.0)
|
ASN
|
N
CA
C
CB
O
CG
ND2
OD1
|
0
0
0
0
3
4
5
5
|
(-0.536, 1.357, 0.0)
(0.0, 0.0, 0.0)
(1.526, -0.0, -0.0)
(-0.531, -0.787, -1.2)
(0.625, 1.062, 0.0)
(0.584, 1.399, 0.0)
(0.593, -1.188, 0.001)
(0.633, 1.059, 0.0)
|
ASP
|
N
CA
C
CB
O
CG
OD1
OD2
|
0
0
0
0
3
4
5
5
|
(-0.525, 1.362, -0.0)
(0.0, 0.0, 0.0)
(1.527, 0.0, -0.0)
(-0.526, -0.778, -1.208)
(0.626, 1.062, -0.0)
(0.593, 1.398, -0.0)
(0.61, 1.091, 0.0)
(0.592, -1.101, -0.003)
|
CYS
|
N
CA
C
CB
O
SG
|
0
0
0
0
3
4
|
(-0.525, 1.362, -0.0)
(0.0, 0.0, 0.0)
(1.524, 0.0, -0.0)
(-0.519, -0.773, -1.212)
(0.625, 1.062, -0.0)
(0.728, 1.653, 0.0)
|
GLN
|
N
CA
C
CB
O
CG
CD
NE2
OE1
|
0
0
0
0
3
4
5
6
6
|
(-0.525, 1.362, -0.0)
(0.0, 0.0, 0.0)
(1.524, 0.0, -0.0)
(-0.519, -0.773, -1.212)
(0.625, 1.062, -0.0)
(0.584, 1.399, 0.0)
(0.587, 1.399, -0.000)
(0.593, -1.189, -0.001)
(0.634, 1.060, 0.000)
|
GLU
|
N
CA
C
CB
O
CG
CD
OE1
OE2
|
0
0
0
0
3
4
5
6
6
|
(-0.528, 1.361, 0.000)
(0.0, 0.0, 0.0)
(1.526, -0.000, -0.000)
(-0.526, -0.781, -1.207)
(0.626, 1.062, 0.000)
(0.615, 1.392, 0.000)
(0.589, -1.104, -0.001)
(0.607, 1.095, -0.000)
(0.589, -1.104, -0.001)
|
GLY
|
N
CA
C
O
|
0
0
0
3
|
(-0.528, 1.361, 0.000)
(0.0, 0.0, 0.0)
(1.526, -0.000, -0.000)
(0.626, 1.062, 0.000)
|
HIS
|
N
CA
C
CB
O
CG
CD2
ND1
CE1
NE2
|
0
0
0
0
3
4
5
6
5
5
|
(-0.527, 1.361, 0.000)
(0.0, 0.0, 0.0)
(1.526, -0.000, -0.000)
(-0.526, -0.781, -1.207)
(0.626, 1.062, 0.000)
(0.615, 1.392, 0.000)
(0.607, 1.095, -0.000)
(0.589, -1.104, -0.001)
(2.030, 0.851, 0.002)
(2.145, -0.466, 0.004)
|
ILE
|
N
CA
C
CB
O
CG1
CG2
CD1
|
0
0
0
0
3
4
3
5
|
(-0.493, 1.373, -0.000)
(0.0, 0.0, 0.0)
(1.526, -0.000, -0.000)
(-0.536, -0.793, -1.213)
(0.627, 1.062, -0.000)
(0.534, 1.437, -0.000)
(0.540, -0.785, -1.199)
(0.619, 1.391, 0.000)
|
LEU
|
N
CA
C
CB
O
CG
CD1
CD2
|
0
0
0
0
3
4
5
5
|
(-0.520, 1.363, 0.000)
(0.0, 0.0, 0.0)
(1.525, -0.000, -0.000)
(-0.522, -0.773, -1.214)
(0.625, 1.063, -0.000)
(0.678, 1.371, 0.000)
(0.530, 1.430, -0.000)
(0.535, -0.774, 1.200)
|
LYS
|
N
CA
C
CB
O
CG
CD
CE
NZ
|
0
0
0
0
3
4
5
6
7
|
(-0.526, 1.362, -0.000)
(0.0, 0.0, 0.0)
(1.526, 0.000, 0.000)
(-0.524, -0.778, -1.208)
(0.626, 1.062, -0.000)
(0.619, 1.390, 0.000)
(0.559, 1.417, 0.000)
(0.560, 1.416, 0.000)
(0.554, 1.387, 0.000)
|
MET
|
N
CA
C
CB
O
CG
SD
CE
|
0
0
0
0
3
4
5
6
|
(-0.521, 1.364, -0.000)
(0.0, 0.0, 0.0)
(1.525, 0.000, 0.000)
(-0.523, -0.776, -1.210)
(0.625, 1.062, -0.000)
(0.613, 1.391, -0.000)
(0.703, 1.695, 0.000)
(0.320, 1.786, -0.000)
|
PHE
|
N
CA
C
CB
O
CG
CD1
CD2
CE1
CE2
CZ
|
0
0
0
0
3
4
5
5
5
5
5
|
(-0.518, 1.363, 0.000)
(0.0, 0.0, 0.0)
(1.524, 0.000, -0.000)
(-0.525, -0.776, -1.212)
(0.626, 1.062, -0.000)
(0.607, 1.377, 0.000)
(0.709, 1.195, -0.000)
(0.706, -1.196, 0.000)
(2.102, 1.198, -0.000)
(2.098, -1.201, -0.000)
(2.794, -0.003, -0.001)
|
PRO
|
N
CA
C
CB
O
CG
CD
|
0
0
0
0
3
4
5
|
(-0.566, 1.351, -0.000)
(0.0, 0.0, 0.0)
(1.527, -0.000, 0.000)
(-0.546, -0.611, -1.293)
(0.621, 1.066, 0.000)
(0.382, 1.445, 0.0)
(0.477, 1.424, 0.0)
|
SER
|
N
CA
C
CB
O
CG
|
0
0
0
0
3
4
|
(-0.529, 1.360, -0.000)
(0.0, 0.0, 0.0)
(1.525, -0.000, -0.000)
(-0.518, -0.777, -1.211)
(0.626, 1.062, -0.000)
(0.503, 1.325, 0.000)
|
THR
|
N
CA
C
CB
O
CG2
OG1
|
0
0
0
0
3
4
4
|
(-0.517, 1.364, 0.000)
(0.0, 0.0, 0.0)
(1.526, 0.000, -0.000)
(-0.516, -0.793, -1.215)
(0.626, 1.062, 0.000)
(0.550, -0.718, -1.228)
(0.472, 1.353, 0.000)
|
TRP
|
N
CA
C
CB
O
CG
CD1
CD2
CE2
CE3
NE1
CH2
CZ2
CZ3
|
0
0
0
0
3
4
5
5
5
5
5
5
5
5
|
(-0.521, 1.363, 0.000)
(0.0, 0.0, 0.0)
(1.525, -0.000, 0.000)
(-0.523, -0.776, -1.212)
(0.627, 1.062, 0.000)
(0.609, 1.370, -0.000)
(0.824, 1.091, 0.000)
(0.854, -1.148, -0.005)
(2.186, -0.678, -0.007)
(0.622, -2.530, -0.007)
(2.140, 0.690, -0.004)
(3.028, -2.890, -0.013)
(3.283, -1.543, -0.011)
(1.715, -3.389, -0.011)
|
TYR
|
N
CA
C
CB
O
CG
CD1
CD2
CE1
CE2
OH
CZ
|
0
0
0
0
3
4
5
5
5
5
5
5
|
(-0.522, 1.362, 0.000)
(0.0, 0.0, 0.0)
(1.524, -0.000, -0.000)
(-0.522, -0.776, -1.213)
(0.627, 1.062, -0.000)
(0.607, 1.382, -0.000)
(0.716, 1.195, -0.000)
(0.713, -1.194, -0.001)
(2.107, 1.200, -0.002)
(2.104, -1.201, -0.003)
(4.168, -0.002, -0.005)
(2.791, -0.001, -0.003)
|
VAL
|
N
CA
C
CB
O
CG1
CG2
|
0
0
0
3
4
5
5
|
(-0.494, 1.373, -0.000)
(0.000, 0.000, 0.000)
(1.527, -0.000, -0.000)
(-0.533, -0.795, -1.213)
(0.627, 1.062, -0.000)
(0.540, 1.429, -0.000)
(0.533, -0.776, 1.203)
|