
#######################################################
#                                                     #
#                        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   31 (  150),  selected   31 , name T0316TS102_2-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS102_2-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      -       -           -
LGA    R     221      -       -           -
LGA    M     222      G     220          2.183
LGA    M     223      R     221          2.745
LGA    Y     239      M     222          3.336
LGA    T     240      M     223          2.813
LGA    I     241      T     224          1.743
LGA    G     242      V     225          3.091
LGA    Q     243      D     226           -
LGA    R     244      G     227           -
LGA    G     251      R     228           -
LGA    Q     252      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     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    H     253      G     242           #
LGA    -       -      Q     243           -
LGA    G     254      R     244           #
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    G     255      A     258           #
LGA    K     265      P     259           #
LGA    D     266      W     260          2.737
LGA    L     267      -       -           -
LGA    S     268      -       -           -
LGA    K     269      F     261          2.514
LGA    N     270      V     262          2.265
LGA    I     271      V     263          3.522
LGA    L     272      G     264          1.912
LGA    Y     273      K     265          1.751
LGA    V     274      D     266          2.104
LGA    F     278      L     267          2.378
LGA    -       -      S     268           -
LGA    Y     279      K     269          3.035
LGA    H     280      N     270           -
LGA    D     281      I     271           -
LGA    S     282      L     272           -
LGA    L     283      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      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)   31   60    5.0     15    2.60     0.00     17.858     0.556

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.189859 * X  +  -0.981810 * Y  +   0.001369 * Z  +  52.118599
  Y_new =  -0.981555 * X  +   0.189841 * Y  +   0.022573 * Z  +  47.744965
  Z_new =  -0.022423 * X  +   0.002942 * Y  +  -0.999744 * Z  +   6.503609 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.138650   -0.002942  [ DEG:   179.8314     -0.1686 ]
  Theta =   0.022425    3.119168  [ DEG:     1.2848    178.7152 ]
  Phi   =  -1.761863    1.379730  [ DEG:  -100.9473     79.0527 ]
 
# 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: T0316TS102_2-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS102_2-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31   60   5.0   15   2.60    0.00  17.858
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS102_2-D2
PFRMAT TS
TARGET T0316
MODEL 2
PARENT 1b90_A
ATOM    675  N   GLY   220      49.285  25.802 -18.419  1.00  1.00
ATOM    676  CA  GLY   220      48.051  26.425 -17.993  1.00  1.00
ATOM    677  C   GLY   220      46.808  25.761 -18.561  1.00  1.00
ATOM    678  O   GLY   220      45.753  25.784 -17.925  1.00  1.00
ATOM    679  N   ARG   221      46.938  25.149 -19.744  1.00  1.00
ATOM    680  CA  ARG   221      45.850  24.470 -20.429  1.00  1.00
ATOM    681  C   ARG   221      45.212  23.280 -19.746  1.00  1.00
ATOM    682  O   ARG   221      45.835  22.629 -18.901  1.00  1.00
ATOM    683  CB  ARG   221      46.368  24.039 -21.762  1.00  1.00
ATOM    684  N   MET   222      43.969  22.958 -20.112  1.00  1.00
ATOM    685  CA  MET   222      43.304  21.813 -19.498  1.00  1.00
ATOM    686  C   MET   222      42.572  21.003 -20.546  1.00  1.00
ATOM    687  O   MET   222      42.134  21.553 -21.551  1.00  1.00
ATOM    688  CB  MET   222      42.273  22.214 -18.427  1.00  1.00
ATOM    689  N   MET   223      42.424  19.689 -20.385  1.00  1.00
ATOM    690  CA  MET   223      41.733  18.960 -21.425  1.00  1.00
ATOM    691  C   MET   223      40.451  18.400 -20.897  1.00  1.00
ATOM    692  O   MET   223      40.355  17.910 -19.789  1.00  1.00
ATOM    693  CB  MET   223      42.630  17.851 -21.980  1.00  1.00
ATOM    694  N   TYR   239      39.470  18.586 -21.766  1.00  1.00
ATOM    695  CA  TYR   239      38.095  18.185 -21.583  1.00  1.00
ATOM    696  C   TYR   239      37.530  17.388 -22.748  1.00  1.00
ATOM    697  O   TYR   239      38.075  17.377 -23.849  1.00  1.00
ATOM    698  CB  TYR   239      37.215  19.430 -21.395  1.00  1.00
ATOM    699  N   THR   240      36.476  16.624 -22.534  1.00  1.00
ATOM    700  CA  THR   240      35.853  15.920 -23.635  1.00  1.00
ATOM    701  C   THR   240      34.391  16.244 -23.537  1.00  1.00
ATOM    702  O   THR   240      33.795  16.474 -22.486  1.00  1.00
ATOM    703  CB  THR   240      35.891  14.346 -23.664  1.00  1.00
ATOM    704  N   ILE   241      33.869  16.373 -24.738  1.00  1.00
ATOM    705  CA  ILE   241      32.467  16.622 -24.859  1.00  1.00
ATOM    706  C   ILE   241      32.033  15.729 -25.990  1.00  1.00
ATOM    707  O   ILE   241      32.798  15.366 -26.880  1.00  1.00
ATOM    708  CB  ILE   241      32.254  18.091 -25.132  1.00  1.00
ATOM    709  N   GLY   242      30.794  15.306 -25.872  1.00  1.00
ATOM    710  CA  GLY   242      30.225  14.424 -26.865  1.00  1.00
ATOM    711  C   GLY   242      28.784  14.755 -27.172  1.00  1.00
ATOM    712  O   GLY   242      28.210  15.709 -26.647  1.00  1.00
ATOM    713  N   GLN   243      28.227  13.886 -28.012  1.00  1.00
ATOM    714  CA  GLN   243      26.873  13.990 -28.505  1.00  1.00
ATOM    715  C   GLN   243      25.709  13.643 -27.600  1.00  1.00
ATOM    716  O   GLN   243      24.630  14.201 -27.757  1.00  1.00
ATOM    717  CB  GLN   243      26.799  13.160 -29.781  1.00  1.00
ATOM    718  N   ARG   244      25.850  12.688 -26.701  1.00  1.00
ATOM    719  CA  ARG   244      24.789  12.311 -25.789  1.00  1.00
ATOM    720  C   ARG   244      24.848  13.195 -24.564  1.00  1.00
ATOM    721  O   ARG   244      25.915  13.686 -24.201  1.00  1.00
ATOM    722  CB  ARG   244      24.955  10.861 -25.343  1.00  1.00
ATOM    723  N   GLY   251      23.727  13.329 -23.853  1.00  1.00
ATOM    724  CA  GLY   251      23.685  14.151 -22.654  1.00  1.00
ATOM    725  C   GLY   251      24.637  13.682 -21.559  1.00  1.00
ATOM    726  O   GLY   251      25.088  14.481 -20.727  1.00  1.00
ATOM    727  N   GLN   252      25.011  12.394 -21.574  1.00  1.00
ATOM    728  CA  GLN   252      25.938  11.874 -20.569  1.00  1.00
ATOM    729  C   GLN   252      27.353  12.344 -20.828  1.00  1.00
ATOM    730  O   GLN   252      28.221  12.229 -19.963  1.00  1.00
ATOM    731  CB  GLN   252      25.934  10.342 -20.502  1.00  1.00
ATOM    732  N   HIS   253      27.585  12.904 -22.026  1.00  1.00
ATOM    733  CA  HIS   253      28.890  13.432 -22.391  1.00  1.00
ATOM    734  C   HIS   253      28.797  14.952 -22.545  1.00  1.00
ATOM    735  O   HIS   253      29.723  15.605 -23.020  1.00  1.00
ATOM    736  CB  HIS   253      29.368  12.812 -23.703  1.00  1.00
ATOM    737  N   GLY   254      27.650  15.554 -22.203  1.00  1.00
ATOM    738  CA  GLY   254      27.476  17.001 -22.278  1.00  1.00
ATOM    739  C   GLY   254      26.762  17.614 -23.477  1.00  1.00
ATOM    740  O   GLY   254      26.738  18.839 -23.555  1.00  1.00
ATOM    741  N   GLY   255      26.184  16.866 -24.419  1.00  1.00
ATOM    742  CA  GLY   255      25.497  17.392 -25.587  1.00  1.00
ATOM    743  C   GLY   255      26.260  18.489 -26.332  1.00  1.00
ATOM    744  O   GLY   255      25.762  19.572 -26.670  1.00  1.00
ATOM    745  N   LYS   265      27.562  18.238 -26.461  1.00  1.00
ATOM    746  CA  LYS   265      28.499  19.105 -27.160  1.00  1.00
ATOM    747  C   LYS   265      28.869  20.439 -26.543  1.00  1.00
ATOM    748  O   LYS   265      29.621  21.243 -27.110  1.00  1.00
ATOM    749  CB  LYS   265      27.989  19.334 -28.608  1.00  1.00
ATOM    750  N   ASP   266      28.356  20.635 -25.338  1.00  1.00
ATOM    751  CA  ASP   266      28.609  21.834 -24.587  1.00  1.00
ATOM    752  C   ASP   266      30.047  21.850 -24.110  1.00  1.00
ATOM    753  O   ASP   266      30.609  20.814 -23.774  1.00  1.00
ATOM    754  CB  ASP   266      27.671  21.860 -23.418  1.00  1.00
ATOM    755  N   LEU   267      30.640  23.036 -24.022  1.00  1.00
ATOM    756  CA  LEU   267      32.009  23.179 -23.593  1.00  1.00
ATOM    757  C   LEU   267      32.188  24.055 -22.388  1.00  1.00
ATOM    758  O   LEU   267      33.314  24.072 -21.895  1.00  1.00
ATOM    759  CB  LEU   267      32.881  23.776 -24.683  1.00  1.00
ATOM    760  N   SER   268      31.202  24.829 -21.893  1.00  1.00
ATOM    761  CA  SER   268      31.468  25.669 -20.715  1.00  1.00
ATOM    762  C   SER   268      30.919  25.206 -19.396  1.00  1.00
ATOM    763  O   SER   268      31.559  25.406 -18.368  1.00  1.00
ATOM    764  CB  SER   268      30.952  27.112 -20.805  1.00  1.00
ATOM    765  N   LYS   269      29.721  24.635 -19.419  1.00  1.00
ATOM    766  CA  LYS   269      29.072  24.169 -18.225  1.00  1.00
ATOM    767  C   LYS   269      29.289  22.724 -17.912  1.00  1.00
ATOM    768  O   LYS   269      29.752  22.392 -16.829  1.00  1.00
ATOM    769  CB  LYS   269      27.582  24.393 -18.330  1.00  1.00
ATOM    770  N   ASN   270      28.978  21.893 -18.905  1.00  1.00
ATOM    771  CA  ASN   270      29.061  20.452 -18.769  1.00  1.00
ATOM    772  C   ASN   270      30.231  19.550 -19.250  1.00  1.00
ATOM    773  O   ASN   270      30.099  18.326 -19.109  1.00  1.00
ATOM    774  CB  ASN   270      27.762  19.950 -19.356  1.00  1.00
ATOM    775  N   ILE   271      31.402  19.945 -19.787  1.00  1.00
ATOM    776  CA  ILE   271      32.450  19.024 -20.217  1.00  1.00
ATOM    777  C   ILE   271      33.115  18.218 -19.117  1.00  1.00
ATOM    778  O   ILE   271      33.188  18.675 -17.974  1.00  1.00
ATOM    779  CB  ILE   271      33.387  19.916 -20.948  1.00  1.00
ATOM    780  N   LEU   272      33.559  17.003 -19.452  1.00  1.00
ATOM    781  CA  LEU   272      34.208  16.184 -18.455  1.00  1.00
ATOM    782  C   LEU   272      35.697  16.396 -18.599  1.00  1.00
ATOM    783  O   LEU   272      36.219  16.555 -19.684  1.00  1.00
ATOM    784  CB  LEU   272      33.918  14.709 -18.630  1.00  1.00
ATOM    785  N   TYR   273      36.381  16.375 -17.475  1.00  1.00
ATOM    786  CA  TYR   273      37.787  16.603 -17.400  1.00  1.00
ATOM    787  C   TYR   273      38.707  15.401 -17.376  1.00  1.00
ATOM    788  O   TYR   273      38.527  14.404 -16.680  1.00  1.00
ATOM    789  CB  TYR   273      37.914  17.491 -16.177  1.00  1.00
ATOM    790  N   VAL   274      39.772  15.593 -18.122  1.00  1.00
ATOM    791  CA  VAL   274      40.818  14.613 -18.275  1.00  1.00
ATOM    792  C   VAL   274      42.063  15.157 -17.574  1.00  1.00
ATOM    793  O   VAL   274      42.278  16.364 -17.486  1.00  1.00
ATOM    794  CB  VAL   274      41.038  14.409 -19.756  1.00  1.00
ATOM    795  N   PHE   278      42.890  14.278 -17.008  1.00  1.00
ATOM    796  CA  PHE   278      44.096  14.639 -16.280  1.00  1.00
ATOM    797  C   PHE   278      45.396  14.110 -16.893  1.00  1.00
ATOM    798  O   PHE   278      45.518  12.929 -17.236  1.00  1.00
ATOM    799  CB  PHE   278      44.002  14.121 -14.845  1.00  1.00
ATOM    800  N   TYR   279      46.405  14.988 -16.991  1.00  1.00
ATOM    801  CA  TYR   279      47.709  14.641 -17.540  1.00  1.00
ATOM    802  C   TYR   279      48.459  13.645 -16.723  1.00  1.00
ATOM    803  O   TYR   279      48.634  13.803 -15.520  1.00  1.00
ATOM    804  CB  TYR   279      48.598  15.846 -17.650  1.00  1.00
ATOM    805  N   HIS   280      48.921  12.675 -17.480  1.00  1.00
ATOM    806  CA  HIS   280      49.696  11.587 -16.957  1.00  1.00
ATOM    807  C   HIS   280      51.064  11.927 -17.492  1.00  1.00
ATOM    808  O   HIS   280      51.363  11.775 -18.682  1.00  1.00
ATOM    809  CB  HIS   280      49.221  10.278 -17.528  1.00  1.00
ATOM    810  N   ASP   281      51.878  12.301 -16.512  1.00  1.00
ATOM    811  CA  ASP   281      53.254  12.709 -16.693  1.00  1.00
ATOM    812  C   ASP   281      54.181  11.608 -17.145  1.00  1.00
ATOM    813  O   ASP   281      55.159  11.858 -17.855  1.00  1.00
ATOM    814  CB  ASP   281      53.764  13.270 -15.394  1.00  1.00
ATOM    815  N   SER   282      53.855  10.388 -16.711  1.00  1.00
ATOM    816  CA  SER   282      54.645   9.214 -17.033  1.00  1.00
ATOM    817  C   SER   282      54.525   8.786 -18.487  1.00  1.00
ATOM    818  O   SER   282      55.507   8.326 -19.073  1.00  1.00
ATOM    819  CB  SER   282      54.231   8.042 -16.116  1.00  1.00
ATOM    820  N   LEU   283      53.338   8.948 -19.086  1.00  1.00
ATOM    821  CA  LEU   283      53.147   8.557 -20.467  1.00  1.00
ATOM    822  C   LEU   283      52.816   9.734 -21.354  1.00  1.00
ATOM    823  O   LEU   283      52.502   9.545 -22.518  1.00  1.00
ATOM    824  CB  LEU   283      52.040   7.509 -20.572  1.00  1.00
TER
END
