Dna-Directed RNA Polymerase II Largest Subunit

(All numbering and residues are taken from first PDB file)

Bending Residue Dihedral Analysis

Residue
i
Residue
i+1
Distance of hinge axis to residue i in conformer 1
(A)
Distance of hinge axis to residue i in conformer 2
(A)
Change in psi (i)
(deg)
Change in phi (i+1)
(deg)
Angle of psi(i) axis to hinge axis conformer 1
(deg)
Angle of psi(i) axis to hinge axis conformer 2
(deg)
Percentage Progress
 SER-1071   ILE-1072  10.0 10.5 44.1 -138.6 99.6 84.8 -224.3
 ILE-1072   GLY-1073  7.1 7.1 66.7 16.5 29.0 29.1 191.3
 GLY-1073   GLU-1074  8.0 8.2 -53.9 47.2 99.4 90.4 4.2
 GLU-1074   PRO-1075  11.6 11.7 17.0 -16.5 91.6 97.7 43.0
 PRO-1075   ALA-1076  12.8 11.2 21.2 -30.2 47.3 50.3 -25.0
 ALA-1076   THR-1077  10.8 8.5 18.9 -4.2 34.1 41.2 30.1

Downloading Image

Graph shows rotational transition at bending residues and can be used to identify hinge bending residues.
Probably only informative for interdomain rotations greater than 20 degrees


Residue
i
Residue
i+1
Distance of hinge axis to residue i in conformer 1
(A)
Distance of hinge axis to residue i in conformer 2
(A)
Change in psi (i)
(deg)
Change in phi (i+1)
(deg)
Angle of psi(i) axis to hinge axis conformer 1
(deg)
Angle of psi(i) axis to hinge axis conformer 2
(deg)
Percentage Progress
 PHE-1084   HIS-1085  21.7 19.6 -61.7 -89.6 124.6 108.6 353.0
 HIS-1085   PHE-1086  24.4 22.2 -152.3 96.3 94.4 104.0 -287.6
 PHE-1086   ALA-1087  26.1 23.4 -5.6 112.3 68.2 42.5 437.0
 ALA-1087   GLY-1088  27.1 24.8 -113.1 -139.3 106.6 105.6 121.3
 GLY-1088   VAL-1089  26.4 28.6 -156.4 -77.9 162.1 137.4 -356.6
 VAL-1089   ALA-1090  25.1 28.3 118.9 92.9 129.1 110.4 324.9
 ALA-1090   SER-1091  22.6 27.2 -146.3 155.3 130.5 124.8 -49.9

Downloading Image

Graph shows rotational transition at bending residues and can be used to identify hinge bending residues.
Probably only informative for interdomain rotations greater than 20 degrees


Residue
i
Residue
i+1
Distance of hinge axis to residue i in conformer 1
(A)
Distance of hinge axis to residue i in conformer 2
(A)
Change in psi (i)
(deg)
Change in phi (i+1)
(deg)
Angle of psi(i) axis to hinge axis conformer 1
(deg)
Angle of psi(i) axis to hinge axis conformer 2
(deg)
Percentage Progress
 PRO-1099   ARG-1100  9.3 9.5 2.1 -2.8 50.2 50.2 9.1
 ARG-1100   LEU-1101  9.2 9.1 -24.9 20.9 103.4 98.1 -15.6
 LEU-1101   LYS-1102  5.6 5.5 -5.2 8.3 41.1 39.7 -10.4

Downloading Image

Graph shows rotational transition at bending residues and can be used to identify hinge bending residues.
Probably only informative for interdomain rotations greater than 20 degrees