
#######################################################
#                                                     #
#                        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   40 (  160),  selected   40 , name T0289TS383_1-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS383_1-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          1.882
LGA    M     225      M     225          1.915
LGA    E     226      E     226          1.874
LGA    K     227      K     227          1.108
LGA    V     228      V     228          1.167
LGA    D     229      D     229          1.046
LGA    R     232      Y     230          1.696
LGA    N     233      P     231          3.946
LGA    E     234      R     232          3.145
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    -       -      V     238           -
LGA    -       -      A     239           -
LGA    -       -      A     240           -
LGA    -       -      V     241           -
LGA    -       -      I     242           -
LGA    D     237      H     243          2.637
LGA    -       -      P     244           -
LGA    V     238      N     245          2.847
LGA    A     239      L     246          4.291
LGA    A     240      Q     247          2.743
LGA    V     241      D     248          2.104
LGA    I     242      Q     249          1.671
LGA    H     243      D     250          3.072
LGA    D     250      -       -           -
LGA    W     251      W     251          1.375
LGA    K     252      K     252          1.127
LGA    P     253      P     253          0.293
LGA    L     254      L     254          0.773
LGA    H     255      H     255          1.999
LGA    P     256      P     256          3.802
LGA    G     257      G     257          2.450
LGA    P     259      D     258          2.894
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    V     260      P     270          3.834
LGA    F     261      L     271          3.653
LGA    V     262      G     272           #
LGA    L     271      G     273          2.228
LGA    G     272      D     274          2.567
LGA    D     274      C     275          2.184
LGA    C     275      T     276          2.680
LGA    T     276      -       -           -
LGA    V     277      V     277          0.968
LGA    Y     278      Y     278          0.878
LGA    P     279      P     279          0.608
LGA    V     280      V     280          0.609
LGA    F     281      F     281          0.805
LGA    V     282      V     282          0.530
LGA    N     283      N     283          0.866
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      A     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      E     289           -
LGA    -       -      K     290           -
LGA    -       -      K     291           -
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    -       -      F     294           -
LGA    -       -      A     295           -
LGA    -       -      K     296           -
LGA    -       -      T     297           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40   74    5.0     37    2.28    54.05     34.208     1.553

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.398768 * X  +   0.697896 * Y  +  -0.594916 * Z  + 102.586189
  Y_new =   0.095499 * X  +   0.676802 * Y  +   0.729945 * Z  + -61.920822
  Z_new =   0.912066 * X  +   0.234265 * Y  +  -0.336536 * Z  +   3.094169 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.533484   -0.608109  [ DEG:   145.1579    -34.8421 ]
  Theta =  -1.148294   -1.993299  [ DEG:   -65.7924   -114.2076 ]
  Phi   =   2.906535   -0.235058  [ DEG:   166.5322    -13.4678 ]
 
# 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: T0289TS383_1-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS383_1-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40   74   5.0   37   2.28   54.05  34.208
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS383_1-D2
PFRMAT TS
TARGET T0289
MODEL 1
PARENT 1yw4A
ATOM    833  N   ILE   224      25.794  28.282  20.463  1.00  0.00
ATOM    834  CA  ILE   224      25.258  29.112  21.529  1.00  0.00
ATOM    835  C   ILE   224      25.039  28.243  22.761  1.00  0.00
ATOM    836  O   ILE   224      24.587  27.104  22.652  1.00  0.00
ATOM    837  N   MET   225      25.375  28.776  23.928  1.00  0.00
ATOM    838  CA  MET   225      25.184  28.052  25.177  1.00  0.00
ATOM    839  C   MET   225      23.914  28.599  25.825  1.00  0.00
ATOM    840  O   MET   225      23.040  27.840  26.235  1.00  0.00
ATOM    841  N   GLU   226      23.825  29.924  25.903  1.00  0.00
ATOM    842  CA  GLU   226      22.667  30.607  26.477  1.00  0.00
ATOM    843  C   GLU   226      22.733  32.102  26.157  1.00  0.00
ATOM    844  O   GLU   226      23.813  32.643  25.909  1.00  0.00
ATOM    845  N   LYS   227      21.580  32.766  26.165  1.00  0.00
ATOM    846  CA  LYS   227      21.535  34.195  25.876  1.00  0.00
ATOM    847  C   LYS   227      21.532  35.012  27.160  1.00  0.00
ATOM    848  O   LYS   227      21.035  34.567  28.197  1.00  0.00
ATOM    849  N   VAL   228      22.098  36.212  27.084  1.00  0.00
ATOM    850  CA  VAL   228      22.150  37.110  28.231  1.00  0.00
ATOM    851  C   VAL   228      20.880  37.944  28.248  1.00  0.00
ATOM    852  O   VAL   228      20.857  39.055  27.723  1.00  0.00
ATOM    853  N   ASP   229      19.823  37.399  28.844  1.00  0.00
ATOM    854  CA  ASP   229      18.543  38.094  28.925  1.00  0.00
ATOM    855  C   ASP   229      18.682  39.363  29.764  1.00  0.00
ATOM    856  O   ASP   229      19.133  39.315  30.907  1.00  0.00
ATOM    857  N   ARG   232      18.299  40.499  29.195  1.00  0.00
ATOM    858  CA  ARG   232      18.392  41.760  29.917  1.00  0.00
ATOM    859  C   ARG   232      17.050  42.280  30.430  1.00  0.00
ATOM    860  O   ARG   232      16.036  42.242  29.731  1.00  0.00
ATOM    861  N   ASN   233      17.068  42.758  31.669  1.00  0.00
ATOM    862  CA  ASN   233      15.892  43.316  32.321  1.00  0.00
ATOM    863  C   ASN   233      16.332  44.373  33.334  1.00  0.00
ATOM    864  O   ASN   233      17.361  44.221  33.997  1.00  0.00
ATOM    865  N   GLU   234      15.551  45.445  33.433  1.00  0.00
ATOM    866  CA  GLU   234      15.828  46.559  34.340  1.00  0.00
ATOM    867  C   GLU   234      17.143  47.240  33.974  1.00  0.00
ATOM    868  O   GLU   234      17.248  47.900  32.940  1.00  0.00
ATOM    869  N   ASP   237      29.755  43.801  32.043  1.00  0.00
ATOM    870  CA  ASP   237      31.140  43.847  32.500  1.00  0.00
ATOM    871  C   ASP   237      32.218  43.696  31.426  1.00  0.00
ATOM    872  O   ASP   237      33.252  43.067  31.654  1.00  0.00
ATOM    873  N   VAL   238      31.971  44.277  30.257  1.00  0.00
ATOM    874  CA  VAL   238      32.928  44.238  29.158  1.00  0.00
ATOM    875  C   VAL   238      32.920  45.581  28.447  1.00  0.00
ATOM    876  O   VAL   238      31.876  46.228  28.339  1.00  0.00
ATOM    877  N   ALA   239      34.089  45.997  27.969  1.00  0.00
ATOM    878  CA  ALA   239      34.226  47.263  27.254  1.00  0.00
ATOM    879  C   ALA   239      33.217  47.322  26.111  1.00  0.00
ATOM    880  O   ALA   239      32.914  46.307  25.485  1.00  0.00
ATOM    881  N   ALA   240      32.707  48.519  25.838  1.00  0.00
ATOM    882  CA  ALA   240      31.720  48.704  24.779  1.00  0.00
ATOM    883  C   ALA   240      32.235  48.217  23.430  1.00  0.00
ATOM    884  O   ALA   240      31.453  47.873  22.546  1.00  0.00
ATOM    885  N   VAL   241      33.555  48.190  23.278  1.00  0.00
ATOM    886  CA  VAL   241      34.175  47.751  22.034  1.00  0.00
ATOM    887  C   VAL   241      34.718  46.326  22.112  1.00  0.00
ATOM    888  O   VAL   241      35.550  45.936  21.293  1.00  0.00
ATOM    889  N   ILE   242      34.266  45.550  23.093  1.00  0.00
ATOM    890  CA  ILE   242      34.741  44.172  23.235  1.00  0.00
ATOM    891  C   ILE   242      34.572  43.401  21.923  1.00  0.00
ATOM    892  O   ILE   242      33.515  43.454  21.294  1.00  0.00
ATOM    893  N   HIS   243      35.618  42.690  21.510  1.00  0.00
ATOM    894  CA  HIS   243      35.579  41.921  20.266  1.00  0.00
ATOM    895  C   HIS   243      34.730  40.661  20.382  1.00  0.00
ATOM    896  O   HIS   243      34.575  40.101  21.468  1.00  0.00
ATOM    897  N   ASP   250      34.181  40.217  19.253  1.00  0.00
ATOM    898  CA  ASP   250      33.378  39.004  19.246  1.00  0.00
ATOM    899  C   ASP   250      34.292  37.816  19.519  1.00  0.00
ATOM    900  O   ASP   250      35.470  37.824  19.145  1.00  0.00
ATOM    901  N   TRP   251      33.727  36.800  20.162  1.00  0.00
ATOM    902  CA  TRP   251      34.432  35.571  20.517  1.00  0.00
ATOM    903  C   TRP   251      35.461  35.790  21.615  1.00  0.00
ATOM    904  O   TRP   251      36.376  34.986  21.788  1.00  0.00
ATOM    905  N   LYS   252      35.315  36.883  22.359  1.00  0.00
ATOM    906  CA  LYS   252      36.236  37.155  23.457  1.00  0.00
ATOM    907  C   LYS   252      36.040  36.073  24.516  1.00  0.00
ATOM    908  O   LYS   252      34.919  35.840  24.967  1.00  0.00
ATOM    909  N   PRO   253      37.135  35.421  24.903  1.00  0.00
ATOM    910  CA  PRO   253      37.117  34.353  25.900  1.00  0.00
ATOM    911  C   PRO   253      36.745  34.854  27.297  1.00  0.00
ATOM    912  O   PRO   253      37.282  35.858  27.770  1.00  0.00
ATOM    913  N   LEU   254      35.826  34.149  27.953  1.00  0.00
ATOM    914  CA  LEU   254      35.390  34.512  29.299  1.00  0.00
ATOM    915  C   LEU   254      36.044  33.578  30.321  1.00  0.00
ATOM    916  O   LEU   254      35.706  32.405  30.406  1.00  0.00
ATOM    917  N   HIS   255      36.985  34.095  31.122  1.00  0.00
ATOM    918  CA  HIS   255      37.664  33.262  32.122  1.00  0.00
ATOM    919  C   HIS   255      36.750  32.687  33.194  1.00  0.00
ATOM    920  O   HIS   255      35.676  33.222  33.465  1.00  0.00
ATOM    921  N   PRO   256      37.177  31.581  33.796  1.00  0.00
ATOM    922  CA  PRO   256      36.393  30.946  34.846  1.00  0.00
ATOM    923  C   PRO   256      36.324  31.895  36.036  1.00  0.00
ATOM    924  O   PRO   256      37.349  32.251  36.617  1.00  0.00
ATOM    925  N   GLY   257      35.108  32.303  36.385  1.00  0.00
ATOM    926  CA  GLY   257      34.905  33.226  37.488  1.00  0.00
ATOM    927  C   GLY   257      33.789  34.212  37.185  1.00  0.00
ATOM    928  O   GLY   257      32.696  34.122  37.755  1.00  0.00
ATOM    929  N   PRO   259      34.055  35.156  36.285  1.00  0.00
ATOM    930  CA  PRO   259      33.051  36.152  35.909  1.00  0.00
ATOM    931  C   PRO   259      31.915  35.479  35.150  1.00  0.00
ATOM    932  O   PRO   259      32.147  34.749  34.188  1.00  0.00
ATOM    933  N   VAL   260      30.684  35.713  35.586  1.00  0.00
ATOM    934  CA  VAL   260      29.532  35.126  34.908  1.00  0.00
ATOM    935  C   VAL   260      28.326  36.048  35.072  1.00  0.00
ATOM    936  O   VAL   260      28.468  37.192  35.510  1.00  0.00
ATOM    937  N   PHE   261      27.142  35.571  34.718  1.00  0.00
ATOM    938  CA  PHE   261      25.959  36.409  34.843  1.00  0.00
ATOM    939  C   PHE   261      25.168  36.078  36.107  1.00  0.00
ATOM    940  O   PHE   261      25.032  34.909  36.477  1.00  0.00
ATOM    941  N   VAL   262      24.668  37.114  36.773  1.00  0.00
ATOM    942  CA  VAL   262      23.883  36.950  37.995  1.00  0.00
ATOM    943  C   VAL   262      23.023  38.192  38.232  1.00  0.00
ATOM    944  O   VAL   262      21.870  38.084  38.658  1.00  0.00
ATOM    945  N   LEU   271      27.959  26.583  33.080  1.00  0.00
ATOM    946  CA  LEU   271      28.079  27.858  33.778  1.00  0.00
ATOM    947  C   LEU   271      29.359  28.598  33.392  1.00  0.00
ATOM    948  O   LEU   271      29.316  29.601  32.676  1.00  0.00
ATOM    949  N   GLY   272      30.496  28.100  33.869  1.00  0.00
ATOM    950  CA  GLY   272      31.785  28.719  33.576  1.00  0.00
ATOM    951  C   GLY   272      32.909  27.685  33.604  1.00  0.00
ATOM    952  O   GLY   272      32.872  26.737  34.386  1.00  0.00
ATOM    953  N   ASP   274      33.901  27.872  32.741  1.00  0.00
ATOM    954  CA  ASP   274      35.016  26.944  32.689  1.00  0.00
ATOM    955  C   ASP   274      36.169  27.455  31.844  1.00  0.00
ATOM    956  O   ASP   274      37.046  26.691  31.443  1.00  0.00
ATOM    957  N   CYS   275      36.172  28.756  31.574  1.00  0.00
ATOM    958  CA  CYS   275      37.232  29.331  30.768  1.00  0.00
ATOM    959  C   CYS   275      37.158  28.901  29.315  1.00  0.00
ATOM    960  O   CYS   275      38.111  29.084  28.552  1.00  0.00
ATOM    961  N   THR   276      36.027  28.326  28.928  1.00  0.00
ATOM    962  CA  THR   276      35.831  27.874  27.555  1.00  0.00
ATOM    963  C   THR   276      34.822  28.736  26.796  1.00  0.00
ATOM    964  O   THR   276      34.839  28.789  25.567  1.00  0.00
ATOM    965  N   VAL   277      33.946  29.413  27.534  1.00  0.00
ATOM    966  CA  VAL   277      32.933  30.245  26.908  1.00  0.00
ATOM    967  C   VAL   277      33.489  31.551  26.331  1.00  0.00
ATOM    968  O   VAL   277      34.546  32.026  26.738  1.00  0.00
ATOM    969  N   TYR   278      32.772  32.112  25.364  1.00  0.00
ATOM    970  CA  TYR   278      33.172  33.361  24.729  1.00  0.00
ATOM    971  C   TYR   278      31.909  34.181  24.489  1.00  0.00
ATOM    972  O   TYR   278      30.820  33.630  24.339  1.00  0.00
ATOM    973  N   PRO   279      32.058  35.497  24.458  1.00  0.00
ATOM    974  CA  PRO   279      30.924  36.381  24.238  1.00  0.00
ATOM    975  C   PRO   279      30.802  36.623  22.733  1.00  0.00
ATOM    976  O   PRO   279      31.807  36.719  22.024  1.00  0.00
ATOM    977  N   VAL   280      29.576  36.707  22.240  1.00  0.00
ATOM    978  CA  VAL   280      29.370  36.935  20.818  1.00  0.00
ATOM    979  C   VAL   280      28.214  37.906  20.605  1.00  0.00
ATOM    980  O   VAL   280      27.178  37.796  21.256  1.00  0.00
ATOM    981  N   PHE   281      28.416  38.867  19.709  1.00  0.00
ATOM    982  CA  PHE   281      27.406  39.874  19.384  1.00  0.00
ATOM    983  C   PHE   281      26.823  40.609  20.595  1.00  0.00
ATOM    984  O   PHE   281      25.609  40.712  20.743  1.00  0.00
ATOM    985  N   VAL   282      27.685  41.140  21.475  1.00  0.00
ATOM    986  CA  VAL   282      27.194  41.861  22.655  1.00  0.00
ATOM    987  C   VAL   282      26.469  43.159  22.278  1.00  0.00
ATOM    988  O   VAL   282      26.933  43.905  21.417  1.00  0.00
ATOM    989  N   ASN   283      25.338  43.425  22.923  1.00  0.00
ATOM    990  CA  ASN   283      24.571  44.637  22.645  1.00  0.00
ATOM    991  C   ASN   283      23.755  45.023  23.875  1.00  0.00
ATOM    992  O   ASN   283      22.548  44.778  23.936  1.00  0.00
TER
END
