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
 ASN-339   LEU-340  8.5 9.9 20.8 -25.5 106.8 118.0 22.7
 LEU-340   MET-341  6.0 7.7 42.5 -33.9 43.7 49.5 32.0
 MET-341   GLY-342  5.9 7.2 1.3 0.3 45.7 46.9 19.3
 GLY-342   LYS-343  4.5 5.0 57.8 -60.3 31.2 25.8 -8.8
 LYS-343   ARG-344  7.3 7.5 2.8 2.1 71.4 71.1 12.9

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
 ALA-1396   LEU-1397  12.1 12.2 -21.0 27.4 62.9 63.6 -58.8
 LEU-1397   MET-1398  10.3 10.2 1.3 -2.7 150.3 154.0 17.3
 MET-1398   ARG-1399  8.2 8.4 19.3 -34.6 136.7 136.0 93.8

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
 LEU-1418   ASP-1419  9.9 10.1 9.6 2.9 39.9 38.9 69.6
 ASP-1419   ASP-1420  7.9 7.9 -13.4 6.9 76.8 74.5 5.6
 ASP-1420   CYS-1421  4.8 5.0 -6.9 9.9 124.2 120.9 -12.2
 CYS-1421   ARG-1422  2.9 2.9 1.3 -0.5 76.9 71.4 24.2
 ARG-1422   GLY-1423  2.7 3.1 -16.5 25.9 169.8 173.5 62.7
 GLY-1423   VAL-1424  3.1 3.6 36.4 -44.3 56.6 60.3 -66.1
 VAL-1424   SER-1425  0.7 1.2 13.6 4.6 78.2 79.9 20.8
 SER-1425   GLU-1426  3.4 4.1 -19.6 13.5 40.6 37.1 13.3
 GLU-1426   ASN-1427  5.0 5.2 -1.1 -3.5 75.4 79.3 0.4
 ASN-1427   VAL-1428  4.0 3.7 -1.7 -11.5 136.6 136.3 -71.0
 VAL-1428   ILE-1429  5.6 5.5 11.6 -4.2 105.4 102.4 0.3
 ILE-1429   LEU-1430  8.6 8.4 -15.5 14.3 39.3 41.9 13.9

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
 GLN-1432   MET-1433  7.1 7.1 2.2 -2.1 59.4 59.7 4.3
 MET-1433   ALA-1434  5.9 5.9 -4.3 12.7 54.1 57.3 5.7
 ALA-1434   PRO-1435  3.2 3.3 -14.6 5.5 64.9 60.0 32.0

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