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
 GLY-338   ASN-339  15.1 16.6 -26.2 6.1 93.0 91.1 19.8
 ASN-339   LEU-340  11.7 13.4 24.2 -20.3 107.8 120.3 -4.4
 LEU-340   MET-341  10.9 12.7 18.2 -11.1 44.5 47.7 26.5
 MET-341   GLY-342  11.7 13.1 -14.9 30.4 134.0 132.2 101.8
 GLY-342   LYS-343  8.7 9.9 13.9 -25.1 30.1 28.7 -88.5
 LYS-343   ARG-344  11.3 11.6 14.8 -9.3 71.1 71.0 -6.9
 ARG-344   VAL-345  10.9 10.6 -24.5 23.3 88.0 94.6 49.0

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
 ALA-1396   LEU-1397  18.5 18.6 -79.2 86.1 62.4 50.9 -30.9
 LEU-1397   MET-1398  16.4 15.9 -4.3 3.7 30.7 29.0 15.5
 MET-1398   ARG-1399  14.6 14.7 29.0 -54.4 137.3 143.1 95.2

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
 ASP-1419   ASP-1420  14.4 14.5 -1.9 -11.6 76.1 72.5 18.2
 ASP-1420   CYS-1421  11.4 11.7 5.8 -4.0 55.9 59.6 5.0
 CYS-1421   ARG-1422  9.4 9.5 -3.8 6.2 102.2 103.2 9.8
 ARG-1422   GLY-1423  8.6 9.1 5.6 16.8 10.7 12.9 163.7
 GLY-1423   VAL-1424  9.5 10.2 32.0 -52.0 56.2 57.3 -139.1
 VAL-1424   SER-1425  7.1 7.9 36.4 -17.5 77.1 75.0 -11.8
 SER-1425   GLU-1426  9.2 10.1 -28.3 24.3 41.7 40.5 10.6
 GLU-1426   ASN-1427  10.5 10.9 -6.0 -3.2 75.5 83.2 8.6
 ASN-1427   VAL-1428  7.2 7.3 -9.6 -3.6 137.2 138.3 -107.3
 VAL-1428   ILE-1429  7.8 7.8 7.6 3.4 104.4 101.1 40.5

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
 GLN-1432   MET-1433  4.9 4.9 -6.9 6.5 119.6 123.3 10.8
 MET-1433   ALA-1434  1.4 1.6 6.6 8.8 126.2 126.8 -61.4
 ALA-1434   PRO-1435  3.8 4.2 -4.0 -7.0 63.9 53.8 85.4

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