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-344   VAL-345  20.9 20.7 82.1 -65.2 42.6 38.9 42.3
 VAL-345   ASP-346  20.5 19.4 86.5 -15.7 22.3 35.0 205.6
 ASP-346   PHE-347  20.3 20.4 35.8 -22.2 44.5 46.1 31.6
 PHE-347   SER-348  20.0 20.1 11.7 2.0 98.2 110.2 1.0

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
 THR-1382   SER-1383  19.4 18.9 -5.5 -3.6 57.9 65.1 14.6
 SER-1383   VAL-1384  20.4 19.8 -27.3 37.8 42.0 42.0 -19.6
 VAL-1384   THR-1385  19.4 19.2 84.0 -80.4 85.4 69.9 1.9
 THR-1385   ARG-1386  20.6 18.0 99.1 -92.3 58.1 67.4 45.3
 ARG-1386   HIS-1387  17.2 15.3 -122.5 8.0 164.1 139.9 -354.7
 HIS-1387   GLY-1388  15.5 15.2 55.1 -53.0 76.6 103.8 14.9
 GLY-1388   PHE-1389  12.0 14.9 115.6 36.1 104.2 140.1 564.8
 PHE-1389   ASN-1390  11.8 13.8 7.2 38.6 130.3 99.0 -1.7
 ASN-1390   ARG-1391  8.6 11.3 -71.6 117.0 67.0 137.7 -39.8
 ARG-1391   SER-1392  8.2 9.3 148.0 152.5 101.4 106.2 18.7
 SER-1392   ASN-1393  10.8 9.7 -148.7 136.5 53.4 74.1 -83.0
 ASN-1393   THR-1394  8.6 7.6 -83.0 78.8 50.1 32.7 7.2
 THR-1394   GLY-1395  5.9 6.4 -69.3 106.7 91.0 100.5 -0.8

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
 GLY-1431   GLN-1432  7.2 7.7 18.2 -4.0 59.1 56.9 44.7
 GLN-1432   MET-1433  3.6 4.2 -6.2 15.3 96.4 110.4 8.6
 MET-1433   ALA-1434  1.5 2.3 -14.2 -20.9 49.2 48.1 72.5
 ALA-1434   PRO-1435  3.0 3.6 1.6 3.6 69.6 70.8 17.9

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