
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   51 (  204),  selected   51 , name T0316TS383_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS383_3-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220           -
LGA    V     225      R     221           -
LGA    D     226      M     222           -
LGA    G     227      M     223           -
LGA    R     228      T     224           -
LGA    D     229      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    M     230      M     237           #
LGA    -       -      Y     238           -
LGA    G     231      Y     239          3.286
LGA    E     232      T     240          2.994
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    Y     238      Q     243          3.328
LGA    Y     239      R     244          2.886
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    T     240      I     249          2.969
LGA    I     241      G     250          3.473
LGA    G     242      G     251          5.052
LGA    Q     243      -       -           -
LGA    R     244      D     256          3.404
LGA    G     245      -       -           -
LGA    G     246      -       -           -
LGA    L     247      -       -           -
LGA    G     248      -       -           -
LGA    I     249      -       -           -
LGA    G     250      -       -           -
LGA    G     251      -       -           -
LGA    D     256      -       -           -
LGA    N     257      -       -           -
LGA    A     258      -       -           -
LGA    P     259      -       -           -
LGA    W     260      -       -           -
LGA    F     261      N     257          2.620
LGA    V     262      A     258          1.605
LGA    V     263      P     259          1.144
LGA    G     264      W     260          1.040
LGA    K     265      F     261          0.994
LGA    D     266      V     262          1.532
LGA    L     267      V     263          2.747
LGA    S     268      G     264          2.057
LGA    K     269      K     265          3.025
LGA    N     270      D     266          2.945
LGA    I     271      L     267          3.262
LGA    L     272      S     268          4.664
LGA    Y     273      K     269          2.025
LGA    V     274      N     270          4.674
LGA    G     275      I     271          4.290
LGA    Q     276      L     272           #
LGA    G     277      Y     273          4.295
LGA    F     278      V     274           #
LGA    Y     279      G     275           -
LGA    H     280      Q     276           -
LGA    D     281      -       -           -
LGA    S     282      -       -           -
LGA    L     283      G     277           #
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   51   60    5.0     24    3.14     8.33     26.052     0.740

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.025230 * X  +   0.766012 * Y  +   0.642330 * Z  + -51.715370
  Y_new =   0.810219 * X  +  -0.360709 * Y  +   0.461989 * Z  + -89.511269
  Z_new =   0.585584 * X  +   0.532084 * Y  +  -0.611537 * Z  + -83.536598 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.425558   -0.716035  [ DEG:   138.9742    -41.0258 ]
  Theta =  -0.625600   -2.515993  [ DEG:   -35.8442   -144.1558 ]
  Phi   =   1.601925   -1.539667  [ DEG:    91.7836    -88.2164 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0316TS383_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS383_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   51   60   5.0   24   3.14    8.33  26.052
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS383_3-D2
PFRMAT TS
TARGET T0316
MODEL 3
PARENT 1gpmA
ATOM    693  N   GLY   220      23.716  17.717  -5.270  1.00  0.00
ATOM    694  CA  GLY   220      24.840  17.115  -4.538  1.00  0.00
ATOM    695  C   GLY   220      25.855  16.533  -5.530  1.00  0.00
ATOM    696  O   GLY   220      26.554  15.556  -5.247  1.00  0.00
ATOM    697  N   VAL   225      25.938  17.160  -6.701  1.00  0.00
ATOM    698  CA  VAL   225      26.844  16.723  -7.751  1.00  0.00
ATOM    699  C   VAL   225      28.054  17.634  -7.958  1.00  0.00
ATOM    700  O   VAL   225      29.001  17.267  -8.653  1.00  0.00
ATOM    701  N   ASP   226      28.046  18.801  -7.327  1.00  0.00
ATOM    702  CA  ASP   226      29.149  19.737  -7.480  1.00  0.00
ATOM    703  C   ASP   226      30.515  19.134  -7.144  1.00  0.00
ATOM    704  O   ASP   226      31.492  19.302  -7.898  1.00  0.00
ATOM    705  N   GLY   227      30.593  18.445  -6.012  1.00  0.00
ATOM    706  CA  GLY   227      31.849  17.835  -5.602  1.00  0.00
ATOM    707  C   GLY   227      32.049  16.465  -6.248  1.00  0.00
ATOM    708  O   GLY   227      33.016  15.760  -5.959  1.00  0.00
ATOM    709  N   ARG   228      31.161  16.104  -7.164  1.00  0.00
ATOM    710  CA  ARG   228      31.289  14.822  -7.846  1.00  0.00
ATOM    711  C   ARG   228      32.074  14.982  -9.148  1.00  0.00
ATOM    712  O   ARG   228      32.322  14.002  -9.850  1.00  0.00
ATOM    713  N   ASP   229      32.451  16.220  -9.470  1.00  0.00
ATOM    714  CA  ASP   229      33.211  16.530 -10.683  1.00  0.00
ATOM    715  C   ASP   229      34.373  17.466 -10.345  1.00  0.00
ATOM    716  O   ASP   229      34.278  18.255  -9.398  1.00  0.00
ATOM    717  N   MET   230      35.463  17.359 -11.109  1.00  0.00
ATOM    718  CA  MET   230      36.664  18.186 -10.920  1.00  0.00
ATOM    719  C   MET   230      36.413  19.608 -11.393  1.00  0.00
ATOM    720  O   MET   230      36.932  20.569 -10.825  1.00  0.00
ATOM    721  N   GLY   231      35.656  19.732 -12.479  1.00  0.00
ATOM    722  CA  GLY   231      35.303  21.034 -13.009  1.00  0.00
ATOM    723  C   GLY   231      33.991  20.943 -13.775  1.00  0.00
ATOM    724  O   GLY   231      33.625  19.881 -14.275  1.00  0.00
ATOM    725  N   GLU   232      33.266  22.051 -13.807  1.00  0.00
ATOM    726  CA  GLU   232      31.977  22.128 -14.476  1.00  0.00
ATOM    727  C   GLU   232      31.738  23.586 -14.828  1.00  0.00
ATOM    728  O   GLU   232      31.851  24.457 -13.967  1.00  0.00
ATOM    729  N   TYR   238      31.476  23.847 -16.103  1.00  0.00
ATOM    730  CA  TYR   238      31.237  25.194 -16.587  1.00  0.00
ATOM    731  C   TYR   238      30.461  25.143 -17.899  1.00  0.00
ATOM    732  O   TYR   238      30.169  24.066 -18.430  1.00  0.00
ATOM    733  N   TYR   239      30.140  26.320 -18.413  1.00  0.00
ATOM    734  CA  TYR   239      29.395  26.445 -19.650  1.00  0.00
ATOM    735  C   TYR   239      30.239  27.174 -20.676  1.00  0.00
ATOM    736  O   TYR   239      31.059  28.020 -20.324  1.00  0.00
ATOM    737  N   THR   240      30.103  26.779 -21.930  1.00  0.00
ATOM    738  CA  THR   240      30.826  27.412 -23.022  1.00  0.00
ATOM    739  C   THR   240      29.784  28.017 -23.965  1.00  0.00
ATOM    740  O   THR   240      28.767  27.400 -24.247  1.00  0.00
ATOM    741  N   ILE   241      30.013  29.232 -24.432  1.00  0.00
ATOM    742  CA  ILE   241      29.067  29.863 -25.335  1.00  0.00
ATOM    743  C   ILE   241      29.482  29.620 -26.788  1.00  0.00
ATOM    744  O   ILE   241      30.622  29.908 -27.172  1.00  0.00
ATOM    745  N   GLY   242      28.571  29.070 -27.590  1.00  0.00
ATOM    746  CA  GLY   242      28.874  28.821 -29.002  1.00  0.00
ATOM    747  C   GLY   242      28.125  29.839 -29.840  1.00  0.00
ATOM    748  O   GLY   242      26.905  29.967 -29.732  1.00  0.00
ATOM    749  N   GLN   243      28.848  30.576 -30.697  1.00  0.00
ATOM    750  CA  GLN   243      28.223  31.587 -31.555  1.00  0.00
ATOM    751  C   GLN   243      27.577  30.949 -32.795  1.00  0.00
ATOM    752  O   GLN   243      27.925  31.286 -33.930  1.00  0.00
ATOM    753  N   ARG   244      26.670  30.001 -32.578  1.00  0.00
ATOM    754  CA  ARG   244      25.990  29.329 -33.683  1.00  0.00
ATOM    755  C   ARG   244      24.490  29.470 -33.494  1.00  0.00
ATOM    756  O   ARG   244      23.997  29.489 -32.367  1.00  0.00
ATOM    757  N   GLY   245      23.768  29.555 -34.606  1.00  0.00
ATOM    758  CA  GLY   245      22.324  29.739 -34.570  1.00  0.00
ATOM    759  C   GLY   245      21.485  28.477 -34.557  1.00  0.00
ATOM    760  O   GLY   245      21.807  27.485 -35.203  1.00  0.00
ATOM    761  N   GLY   246      20.437  28.518 -33.746  1.00  0.00
ATOM    762  CA  GLY   246      19.498  27.420 -33.588  1.00  0.00
ATOM    763  C   GLY   246      18.122  28.071 -33.542  1.00  0.00
ATOM    764  O   GLY   246      17.952  29.097 -32.874  1.00  0.00
ATOM    765  N   LEU   247      17.151  27.498 -34.256  1.00  0.00
ATOM    766  CA  LEU   247      15.796  28.049 -34.285  1.00  0.00
ATOM    767  C   LEU   247      15.355  28.541 -32.910  1.00  0.00
ATOM    768  O   LEU   247      15.286  27.769 -31.958  1.00  0.00
ATOM    769  N   GLY   248      15.082  29.840 -32.837  1.00  0.00
ATOM    770  CA  GLY   248      14.664  30.493 -31.610  1.00  0.00
ATOM    771  C   GLY   248      13.482  29.905 -30.865  1.00  0.00
ATOM    772  O   GLY   248      12.687  29.127 -31.406  1.00  0.00
ATOM    773  N   ILE   249      13.365  30.286 -29.600  1.00  0.00
ATOM    774  CA  ILE   249      12.288  29.803 -28.760  1.00  0.00
ATOM    775  C   ILE   249      11.054  30.686 -28.928  1.00  0.00
ATOM    776  O   ILE   249      11.150  31.919 -28.887  1.00  0.00
ATOM    777  N   GLY   250       9.900  30.055 -29.152  1.00  0.00
ATOM    778  CA  GLY   250       8.645  30.785 -29.313  1.00  0.00
ATOM    779  C   GLY   250       8.379  31.564 -28.028  1.00  0.00
ATOM    780  O   GLY   250       7.998  30.997 -27.000  1.00  0.00
ATOM    781  N   GLY   251       8.612  32.866 -28.103  1.00  0.00
ATOM    782  CA  GLY   251       8.429  33.740 -26.961  1.00  0.00
ATOM    783  C   GLY   251       9.498  34.806 -27.054  1.00  0.00
ATOM    784  O   GLY   251       9.200  36.000 -27.052  1.00  0.00
ATOM    785  N   ASP   256      10.742  34.365 -27.225  1.00  0.00
ATOM    786  CA  ASP   256      11.881  35.269 -27.344  1.00  0.00
ATOM    787  C   ASP   256      11.711  36.233 -28.514  1.00  0.00
ATOM    788  O   ASP   256      12.260  37.338 -28.517  1.00  0.00
ATOM    789  N   ASN   257      10.941  35.808 -29.511  1.00  0.00
ATOM    790  CA  ASN   257      10.684  36.650 -30.663  1.00  0.00
ATOM    791  C   ASN   257      11.750  36.659 -31.744  1.00  0.00
ATOM    792  O   ASN   257      11.591  37.350 -32.754  1.00  0.00
ATOM    793  N   ALA   258      12.845  35.935 -31.535  1.00  0.00
ATOM    794  CA  ALA   258      13.902  35.880 -32.537  1.00  0.00
ATOM    795  C   ALA   258      13.691  34.623 -33.366  1.00  0.00
ATOM    796  O   ALA   258      13.179  33.626 -32.859  1.00  0.00
ATOM    797  N   PRO   259      14.066  34.673 -34.640  1.00  0.00
ATOM    798  CA  PRO   259      13.918  33.507 -35.505  1.00  0.00
ATOM    799  C   PRO   259      14.974  32.488 -35.087  1.00  0.00
ATOM    800  O   PRO   259      14.759  31.287 -35.162  1.00  0.00
ATOM    801  N   TRP   260      16.120  32.992 -34.645  1.00  0.00
ATOM    802  CA  TRP   260      17.234  32.158 -34.217  1.00  0.00
ATOM    803  C   TRP   260      17.856  32.683 -32.923  1.00  0.00
ATOM    804  O   TRP   260      17.928  33.895 -32.699  1.00  0.00
ATOM    805  N   PHE   261      21.003  31.482 -29.653  1.00  0.00
ATOM    806  CA  PHE   261      22.336  30.895 -29.509  1.00  0.00
ATOM    807  C   PHE   261      22.364  29.546 -28.792  1.00  0.00
ATOM    808  O   PHE   261      21.356  29.073 -28.249  1.00  0.00
ATOM    809  N   VAL   262      23.549  28.954 -28.762  1.00  0.00
ATOM    810  CA  VAL   262      23.760  27.652 -28.145  1.00  0.00
ATOM    811  C   VAL   262      24.876  27.691 -27.093  1.00  0.00
ATOM    812  O   VAL   262      25.817  28.489 -27.188  1.00  0.00
ATOM    813  N   VAL   263      24.741  26.862 -26.066  1.00  0.00
ATOM    814  CA  VAL   263      25.775  26.756 -25.044  1.00  0.00
ATOM    815  C   VAL   263      26.055  25.282 -24.824  1.00  0.00
ATOM    816  O   VAL   263      25.204  24.428 -25.108  1.00  0.00
ATOM    817  N   GLY   264      27.277  24.977 -24.408  1.00  0.00
ATOM    818  CA  GLY   264      27.649  23.598 -24.133  1.00  0.00
ATOM    819  C   GLY   264      28.017  23.467 -22.679  1.00  0.00
ATOM    820  O   GLY   264      28.674  24.342 -22.113  1.00  0.00
ATOM    821  N   LYS   265      27.478  22.432 -22.050  1.00  0.00
ATOM    822  CA  LYS   265      27.784  22.137 -20.664  1.00  0.00
ATOM    823  C   LYS   265      29.069  21.316 -20.714  1.00  0.00
ATOM    824  O   LYS   265      29.291  20.545 -21.656  1.00  0.00
ATOM    825  N   ASP   266      29.919  21.478 -19.712  1.00  0.00
ATOM    826  CA  ASP   266      31.186  20.754 -19.681  1.00  0.00
ATOM    827  C   ASP   266      31.465  20.339 -18.250  1.00  0.00
ATOM    828  O   ASP   266      31.364  21.151 -17.334  1.00  0.00
ATOM    829  N   LEU   267      31.708  19.050 -18.053  1.00  0.00
ATOM    830  CA  LEU   267      32.010  18.519 -16.731  1.00  0.00
ATOM    831  C   LEU   267      32.972  17.344 -16.878  1.00  0.00
ATOM    832  O   LEU   267      32.772  16.475 -17.736  1.00  0.00
ATOM    833  N   SER   268      34.044  17.350 -16.090  1.00  0.00
ATOM    834  CA  SER   268      35.044  16.288 -16.150  1.00  0.00
ATOM    835  C   SER   268      35.541  15.826 -14.793  1.00  0.00
ATOM    836  O   SER   268      35.475  16.558 -13.799  1.00  0.00
ATOM    837  N   LYS   269      36.083  14.612 -14.790  1.00  0.00
ATOM    838  CA  LYS   269      36.693  14.003 -13.620  1.00  0.00
ATOM    839  C   LYS   269      38.159  13.898 -14.014  1.00  0.00
ATOM    840  O   LYS   269      38.534  13.098 -14.873  1.00  0.00
ATOM    841  N   ASN   270      38.958  14.816 -13.496  1.00  0.00
ATOM    842  CA  ASN   270      40.378  14.838 -13.788  1.00  0.00
ATOM    843  C   ASN   270      41.090  13.702 -13.071  1.00  0.00
ATOM    844  O   ASN   270      41.039  13.602 -11.847  1.00  0.00
ATOM    845  N   ILE   271      44.467  12.865 -13.935  1.00  0.00
ATOM    846  CA  ILE   271      45.782  13.459 -13.749  1.00  0.00
ATOM    847  C   ILE   271      45.865  14.671 -14.663  1.00  0.00
ATOM    848  O   ILE   271      44.941  14.950 -15.430  1.00  0.00
ATOM    849  N   LEU   272      46.992  15.362 -14.623  1.00  0.00
ATOM    850  CA  LEU   272      47.177  16.572 -15.415  1.00  0.00
ATOM    851  C   LEU   272      47.310  16.356 -16.925  1.00  0.00
ATOM    852  O   LEU   272      47.702  17.261 -17.663  1.00  0.00
ATOM    853  N   TYR   273      46.899  15.180 -17.383  1.00  0.00
ATOM    854  CA  TYR   273      46.942  14.832 -18.794  1.00  0.00
ATOM    855  C   TYR   273      45.749  13.944 -19.159  1.00  0.00
ATOM    856  O   TYR   273      45.490  13.691 -20.337  1.00  0.00
ATOM    857  N   VAL   274      44.975  13.551 -18.153  1.00  0.00
ATOM    858  CA  VAL   274      43.816  12.700 -18.376  1.00  0.00
ATOM    859  C   VAL   274      42.621  13.113 -17.522  1.00  0.00
ATOM    860  O   VAL   274      42.741  13.297 -16.310  1.00  0.00
ATOM    861  N   GLY   275      41.472  13.283 -18.172  1.00  0.00
ATOM    862  CA  GLY   275      40.226  13.664 -17.504  1.00  0.00
ATOM    863  C   GLY   275      39.072  13.062 -18.292  1.00  0.00
ATOM    864  O   GLY   275      39.079  13.092 -19.515  1.00  0.00
ATOM    865  N   GLN   276      38.096  12.493 -17.605  1.00  0.00
ATOM    866  CA  GLN   276      36.968  11.877 -18.293  1.00  0.00
ATOM    867  C   GLN   276      35.725  12.753 -18.242  1.00  0.00
ATOM    868  O   GLN   276      35.507  13.452 -17.255  1.00  0.00
ATOM    869  N   GLY   277      34.924  12.751 -19.305  1.00  0.00
ATOM    870  CA  GLY   277      33.699  13.544 -19.264  1.00  0.00
ATOM    871  C   GLY   277      32.734  12.838 -18.314  1.00  0.00
ATOM    872  O   GLY   277      32.575  11.619 -18.369  1.00  0.00
ATOM    873  N   PHE   278      32.198  13.602 -17.368  1.00  0.00
ATOM    874  CA  PHE   278      31.269  13.106 -16.355  1.00  0.00
ATOM    875  C   PHE   278      29.971  12.516 -16.912  1.00  0.00
ATOM    876  O   PHE   278      29.280  13.135 -17.726  1.00  0.00
ATOM    877  N   TYR   279      23.609  12.204 -14.763  1.00  0.00
ATOM    878  CA  TYR   279      22.273  11.607 -14.861  1.00  0.00
ATOM    879  C   TYR   279      21.386  12.335 -15.858  1.00  0.00
ATOM    880  O   TYR   279      21.188  13.543 -15.750  1.00  0.00
ATOM    881  N   HIS   280      20.811  11.582 -16.791  1.00  0.00
ATOM    882  CA  HIS   280      19.957  12.142 -17.838  1.00  0.00
ATOM    883  C   HIS   280      18.859  13.082 -17.333  1.00  0.00
ATOM    884  O   HIS   280      18.608  14.121 -17.940  1.00  0.00
ATOM    885  N   ASP   281      18.200  12.728 -16.236  1.00  0.00
ATOM    886  CA  ASP   281      17.131  13.573 -15.705  1.00  0.00
ATOM    887  C   ASP   281      17.696  14.919 -15.278  1.00  0.00
ATOM    888  O   ASP   281      17.088  15.966 -15.499  1.00  0.00
ATOM    889  N   SER   282      18.868  14.882 -14.662  1.00  0.00
ATOM    890  CA  SER   282      19.543  16.089 -14.222  1.00  0.00
ATOM    891  C   SER   282      19.851  16.951 -15.448  1.00  0.00
ATOM    892  O   SER   282      19.555  18.156 -15.471  1.00  0.00
ATOM    893  N   LEU   283      20.416  16.309 -16.472  1.00  0.00
ATOM    894  CA  LEU   283      20.775  16.963 -17.728  1.00  0.00
ATOM    895  C   LEU   283      19.583  17.577 -18.455  1.00  0.00
ATOM    896  O   LEU   283      19.685  18.654 -19.037  1.00  0.00
TER
END
