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
 ARG-328   LEU-329  20.8 21.9 12.0 8.3 108.3 114.8 -41.1
 LEU-329   LYS-330  17.1 18.4 -5.4 -7.7 101.3 91.9 -15.6
 LYS-330   GLY-331  18.1 20.1 -141.7 -101.4 44.0 29.2 -326.7
 GLY-331   LYS-332  17.9 21.3 -129.8 165.8 61.0 48.6 1071.4
 LYS-332   GLU-333  20.3 18.3 -143.9 -176.8 86.4 104.1 -78.1
 GLU-333   GLY-334  22.4 15.8 -40.3 49.6 108.5 80.8 -43.1
 GLY-334   ARG-335  20.0 18.5 -137.5 -136.9 72.5 18.6 -273.4
 ARG-335   ILE-336  17.3 19.1 102.0 -77.0 108.3 124.7 -93.4
 VAL-345   ASP-346  18.4 20.1 -68.9 -5.1 33.7 16.2 214.3
 ASP-346   PHE-347  19.5 19.8 -16.0 8.0 50.7 52.1 25.8
 PHE-347   SER-348  19.3 19.0 -13.7 -13.7 110.6 102.5 -21.2

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
 THR-1382   SER-1383  17.5 17.9 1.9 -0.5 58.3 58.8 -4.4
 SER-1383   VAL-1384  18.5 18.8 -9.8 -3.7 146.4 144.7 -28.8
 VAL-1384   THR-1385  18.1 18.3 -60.7 31.9 72.5 88.5 -2.8
 THR-1385   ARG-1386  17.4 19.3 -96.0 100.9 87.2 60.2 0.2
 ARG-1386   HIS-1387  14.1 15.9 140.3 -36.5 136.4 166.4 -319.2
 HIS-1387   GLY-1388  13.8 14.2 -55.3 34.3 105.8 72.5 -8.1
 GLY-1388   PHE-1389  13.8 10.9 -135.2 -4.7 133.6 110.9 601.2
 PHE-1389   ASN-1390  12.2 11.3 -0.1 -59.3 98.7 128.5 -28.2
 ASN-1390   ARG-1391  9.5 8.0 101.6 -161.0 127.6 67.3 -42.3
 ARG-1391   SER-1392  7.9 7.4 -122.6 142.2 117.0 96.2 -86.7
 SER-1392   ASN-1393  8.9 9.6 26.4 22.0 84.6 46.9 18.7
 ASN-1393   THR-1394  6.3 7.4 67.5 -60.6 32.3 45.8 42.7
 THR-1394   GLY-1395  4.7 4.9 37.2 -84.3 92.2 96.4 3.6

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  3.2 4.5 56.7 -56.7 128.9 142.2 21.1
 LEU-1397   MET-1398  5.3 5.7 -2.3 6.7 81.4 65.9 9.6
 MET-1398   ARG-1399  6.2 6.4 -142.4 43.1 135.2 112.2 -141.5
 ARG-1399   CYS-1400  7.7 10.2 134.4 1.5 96.3 22.1 254.5
 CYS-1400   SER-1401  9.1 11.3 141.6 -2.4 117.6 58.5 12.1
 SER-1401   PHE-1402  11.2 12.5 124.8 -135.2 63.2 41.6 -39.8
 PHE-1402   GLU-1403  13.0 15.1 36.7 -117.0 17.5 106.7 -195.5
 GLU-1403   GLU-1404  15.1 17.5 39.0 0.4 48.5 63.5 -7.4
 GLU-1404   THR-1405  12.6 15.0 14.4 -22.5 113.4 107.9 34.2
 THR-1405   VAL-1406  11.8 12.0 50.7 -17.4 52.4 65.5 56.7
 VAL-1406   GLU-1407  13.0 12.7 41.5 -30.7 49.3 40.4 28.7

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  4.2 3.9 0.2 -29.9 101.4 93.7 0.2
 MET-1433   ALA-1434  1.5 1.0 -27.5 78.5 147.9 130.7 124.7
 ALA-1434   PRO-1435  2.7 2.4 -32.4 3.5 75.4 74.4 31.0
 PRO-1435   ILE-1436  5.9 5.2 -19.7 -9.7 76.7 88.3 23.2
 ILE-1436   GLY-1437  7.8 7.5 -26.9 77.6 35.5 18.5 -168.8
 GLY-1437   THR-1438  9.8 9.8 -54.3 10.5 56.6 43.1 97.8
 THR-1438   GLY-1439  6.6 7.8 8.1 3.6 62.2 74.6 1.5
 GLY-1439   ALA-1440  5.2 5.5 -26.6 26.1 130.6 131.9 -14.9
 ALA-1440   PHE-1441  8.5 8.6 67.1 -65.8 114.2 112.0 8.4
 PHE-1441   ASP-1442  9.8 9.6 20.8 -13.1 111.7 119.1 -9.6

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