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  18.2 18.2 66.4 -55.0 45.6 60.9 9.1  VAL-345   ASP-346  16.8 16.0 57.2 7.9 34.0 23.9 157.1  ASP-346   PHE-347  15.6 16.2 40.1 -17.5 45.4 47.9 60.2  PHE-347   SER-348  14.3 14.5 18.6 -19.4 87.4 96.3 11.7 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-1381   THR-1382  26.3 25.4 -12.2 10.9 91.4 87.6 2.0  THR-1382   SER-1383  23.4 22.2 -20.8 15.6 39.3 44.6 20.3  SER-1383   VAL-1384  24.4 23.5 -18.2 40.2 56.6 48.4 -30.4  VAL-1384   THR-1385  22.4 22.1 76.3 -79.0 104.9 80.8 12.6  THR-1385   ARG-1386  24.3 22.0 80.6 -69.5 44.4 53.0 64.4  ARG-1386   HIS-1387  21.6 20.1 -136.1 13.5 166.3 157.4 -353.5  HIS-1387   GLY-1388  21.2 20.8 58.0 -49.9 63.3 87.4 10.6  GLY-1388   PHE-1389  18.3 19.3 105.4 43.6 120.3 119.2 426.5  PHE-1389   ASN-1390  18.7 17.1 3.6 36.4 108.1 92.6 25.0  ASN-1390   ARG-1391  14.9 15.2 -69.9 119.7 82.5 155.8 37.3  ARG-1391   SER-1392  13.2 13.9 149.9 155.5 111.2 86.2 -11.6  SER-1392   ASN-1393  14.5 12.7 -156.7 138.8 71.6 91.2 -69.1  ASN-1393   THR-1394  11.3 9.4 -67.9 76.4 52.9 35.7 -25.3  THR-1394   GLY-1395  8.9 8.4 -53.2 86.6 120.8 102.9 28.2 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 4.1 -4.1 13.2 105.9 118.0 26.4  MET-1433   ALA-1434  1.0 1.0 -18.6 -8.1 33.1 45.4 62.8  ALA-1434   PRO-1435  2.1 2.1 -13.0 9.0 103.1 101.0 9.6 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