
#######################################################
#                                                     #
#                        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   16 (  145),  selected   16 , name T0386TS009_1_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386TS009_1_2-D1.T0386_D1.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    -       -      I      13           -
LGA    -       -      I      14           -
LGA    -       -      S      15           -
LGA    -       -      P      16           -
LGA    -       -      H      17           -
LGA    -       -      H      18           -
LGA    -       -      Y      19           -
LGA    -       -      V      20           -
LGA    -       -      Y      21           -
LGA    -       -      P      22           -
LGA    -       -      N      23           -
LGA    -       -      T      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      N      29           -
LGA    -       -      K      30           -
LGA    -       -      Y      31           -
LGA    -       -      G      32           -
LGA    -       -      I      33           -
LGA    -       -      K      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      N      37           -
LGA    -       -      A      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      C      43           -
LGA    -       -      S      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      T      47           -
LGA    -       -      A      48           -
LGA    -       -      K      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      I      52           -
LGA    -       -      N      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      S      58           -
LGA    -       -      L      59           -
LGA    -       -      P      60           -
LGA    -       -      E      61           -
LGA    -       -      Y      62           -
LGA    -       -      F      63           -
LGA    -       -      D      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      Y      67           -
LGA    -       -      L      68           -
LGA    -       -      C      69           -
LGA    -       -      H      70           -
LGA    -       -      I      71           -
LGA    -       -      H      72           -
LGA    -       -      Q      73           -
LGA    -       -      Q      74           -
LGA    -       -      L      75           -
LGA    -       -      F      76           -
LGA    -       -      K      77           -
LGA    -       -      N      78           -
LGA    -       -      T      79           -
LGA    -       -      F      80           -
LGA    -       -      E      81           -
LGA    -       -      W      82           -
LGA    -       -      A      83           -
LGA    -       -      G      84           -
LGA    -       -      Y      85           -
LGA    -       -      L      86           -
LGA    -       -      R      87           -
LGA    -       -      H      88           -
LGA    -       -      I      89           -
LGA    -       -      P      90           -
LGA    -       -      F      91           -
LGA    -       -      T      92           -
LGA    -       -      F      93           -
LGA    -       -      A      94           -
LGA    -       -      D      95           -
LGA    -       -      G      96           -
LGA    -       -      T      97           -
LGA    -       -      T      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      M     101           -
LGA    -       -      P     102           -
LGA    -       -      E     103           -
LGA    -       -      M     104           -
LGA    -       -      K     105           -
LGA    -       -      R     106           -
LGA    -       -      T     107           -
LGA    -       -      G     108           -
LGA    -       -      W     109           -
LGA    -       -      K     110           -
LGA    -       -      N     111           -
LGA    -       -      A     112           -
LGA    -       -      F     113           -
LGA    -       -      A     114           -
LGA    -       -      I     115           -
LGA    -       -      G     116           -
LGA    -       -      D     117           -
LGA    -       -      E     118           -
LGA    Q      73      I     119          4.320
LGA    -       -      Q     120           -
LGA    -       -      E     121           -
LGA    -       -      G     122           -
LGA    Q      74      L     123          1.015
LGA    L      75      Q     124           #
LGA    F      76      R     125          2.711
LGA    K      77      L     126          1.729
LGA    -       -      D     127           -
LGA    -       -      Q     128           -
LGA    -       -      T     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      E     132           -
LGA    -       -      K     133           -
LGA    -       -      N     134           -
LGA    -       -      N     135           -
LGA    -       -      L     136           -
LGA    -       -      Q     137           -
LGA    -       -      G     138           -
LGA    -       -      L     139           -
LGA    -       -      T     140           -
LGA    -       -      R     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    -       -      F     144           -
LGA    -       -      N     145           -
LGA    -       -      S     146           -
LGA    -       -      E     147           -
LGA    -       -      A     148           -
LGA    N      78      I     149           #
LGA    -       -      E     150           -
LGA    T      79      L     151          2.918
LGA    -       -      F     152           -
LGA    -       -      N     153           -
LGA    F      80      S     154          1.934
LGA    E      81      L     155          1.254
LGA    -       -      N     156           -
LGA    W      82      Q     157          4.489
LGA    A      83      L     158          1.828
LGA    G      84      H     159          1.366
LGA    Y      85      P     160          0.971
LGA    L      86      F     161          2.999
LGA    R      87      R     162          2.995
LGA    -       -      E     163           -
LGA    -       -      G     164           -
LGA    H      88      N     165          1.992
LGA    -       -      G     166           -
LGA    -       -      R     167           -
LGA    -       -      T     168           -
LGA    -       -      Q     169           -
LGA    -       -      R     170           -
LGA    -       -      L     171           -
LGA    -       -      F     172           -
LGA    -       -      F     173           -
LGA    -       -      E     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      A     177           -
LGA    -       -      K     178           -
LGA    -       -      A     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      H     182           -
LGA    -       -      Q     183           -
LGA    -       -      L     184           -
LGA    -       -      N     185           -
LGA    -       -      F     186           -
LGA    -       -      S     187           -
LGA    -       -      L     188           -
LGA    -       -      I     189           -
LGA    -       -      T     190           -
LGA    -       -      K     191           -
LGA    -       -      E     192           -
LGA    -       -      R     193           -
LGA    -       -      M     194           -
LGA    -       -      M     195           -
LGA    -       -      V     196           -
LGA    -       -      A     197           -
LGA    -       -      S     198           -
LGA    -       -      V     199           -
LGA    -       -      A     200           -
LGA    -       -      V     201           -
LGA    -       -      A     202           -
LGA    -       -      E     203           -
LGA    -       -      N     204           -
LGA    -       -      G     205           -
LGA    -       -      D     206           -
LGA    -       -      L     207           -
LGA    -       -      E     208           -
LGA    -       -      P     209           -
LGA    -       -      M     210           -
LGA    -       -      Q     211           -
LGA    -       -      H     212           -
LGA    -       -      L     213           -
LGA    -       -      F     214           -
LGA    -       -      E     215           -
LGA    -       -      D     216           -
LGA    -       -      I     217           -
LGA    -       -      S     218           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16  206    5.0     14    2.56     7.14      4.914     0.525

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.753633 * X  +  -0.484545 * Y  +  -0.444132 * Z  +  58.145718
  Y_new =   0.460385 * X  +  -0.871393 * Y  +   0.169471 * Z  +  40.116459
  Z_new =  -0.469130 * X  +  -0.076753 * Y  +   0.879788 * Z  +  14.789314 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.087020    3.054573  [ DEG:    -4.9859    175.0141 ]
  Theta =   0.488305    2.653288  [ DEG:    27.9778    152.0222 ]
  Phi   =   2.593206   -0.548386  [ DEG:   148.5798    -31.4202 ]
 
# 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: T0386TS009_1_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS009_1_2-D1.T0386_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  206   5.0   14   2.56    7.14   4.914
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS009_1_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0386                                                                    
PARENT N/A                       
ATOM    586  N   GLN    73       8.740  52.429  47.553  1.00  0.00             
ATOM    587  CA  GLN    73       9.435  51.148  47.588  1.00  0.00             
ATOM    588  C   GLN    73       8.500  50.003  47.214  1.00  0.00             
ATOM    589  O   GLN    73       8.795  48.837  47.476  1.00  0.00             
ATOM    590  CB  GLN    73      10.644  51.168  46.649  1.00  0.00             
ATOM    591  CG  GLN    73      11.798  50.291  47.105  1.00  0.00             
ATOM    592  CD  GLN    73      12.918  50.226  46.086  1.00  0.00             
ATOM    593  OE1 GLN    73      14.053  49.882  46.417  1.00  0.00             
ATOM    594  NE2 GLN    73      12.602  50.557  44.840  1.00  0.00             
ATOM    595  N   GLN    74       7.371  50.344  46.600  1.00  0.00             
ATOM    596  CA  GLN    74       6.390  49.346  46.190  1.00  0.00             
ATOM    597  C   GLN    74       6.477  48.098  47.061  1.00  0.00             
ATOM    598  O   GLN    74       5.457  47.546  47.476  1.00  0.00             
ATOM    599  CB  GLN    74       4.977  49.929  46.246  1.00  0.00             
ATOM    600  CG  GLN    74       4.678  50.712  47.514  1.00  0.00             
ATOM    601  CD  GLN    74       4.354  52.167  47.237  1.00  0.00             
ATOM    602  OE1 GLN    74       3.287  52.657  47.608  1.00  0.00             
ATOM    603  NE2 GLN    74       5.276  52.863  46.583  1.00  0.00             
ATOM    604  N   LEU    75       7.701  47.656  47.333  1.00  0.00             
ATOM    605  CA  LEU    75       7.922  46.471  48.155  1.00  0.00             
ATOM    606  C   LEU    75       7.049  46.497  49.406  1.00  0.00             
ATOM    607  O   LEU    75       7.535  46.753  50.507  1.00  0.00             
ATOM    608  CB  LEU    75       7.650  45.201  47.348  1.00  0.00             
ATOM    609  CG  LEU    75       8.345  43.927  47.833  1.00  0.00             
ATOM    610  CD1 LEU    75       7.429  42.723  47.679  1.00  0.00             
ATOM    611  CD2 LEU    75       8.800  44.079  49.277  1.00  0.00             
ATOM    612  N   PHE    76       5.760  46.229  49.226  1.00  0.00             
ATOM    613  CA  PHE    76       4.818  46.220  50.339  1.00  0.00             
ATOM    614  C   PHE    76       4.201  47.598  50.549  1.00  0.00             
ATOM    615  O   PHE    76       3.364  47.785  51.433  1.00  0.00             
ATOM    616  CB  PHE    76       3.719  45.182  50.102  1.00  0.00             
ATOM    617  CG  PHE    76       2.685  45.135  51.190  1.00  0.00             
ATOM    618  CD1 PHE    76       1.749  46.147  51.319  1.00  0.00             
ATOM    619  CD2 PHE    76       2.647  44.080  52.084  1.00  0.00             
ATOM    620  CE1 PHE    76       0.797  46.104  52.320  1.00  0.00             
ATOM    621  CE2 PHE    76       1.695  44.037  53.085  1.00  0.00             
ATOM    622  CZ  PHE    76       0.773  45.043  53.205  1.00  0.00             
ATOM    623  N   LYS    77       4.618  48.560  49.733  1.00  0.00             
ATOM    624  CA  LYS    77       4.108  49.922  49.829  1.00  0.00             
ATOM    625  C   LYS    77       4.277  50.476  51.239  1.00  0.00             
ATOM    626  O   LYS    77       3.477  50.187  52.129  1.00  0.00             
ATOM    627  CB  LYS    77       4.812  50.830  48.818  1.00  0.00             
ATOM    628  CG  LYS    77       3.918  51.904  48.220  1.00  0.00             
ATOM    629  CD  LYS    77       3.950  51.866  46.701  1.00  0.00             
ATOM    630  CE  LYS    77       3.804  53.259  46.112  1.00  0.00             
ATOM    631  NZ  LYS    77       4.445  53.365  44.771  1.00  0.00             
ATOM    632  N   ASN    78       5.321  51.275  51.435  1.00  0.00             
ATOM    633  CA  ASN    78       5.596  51.870  52.737  1.00  0.00             
ATOM    634  C   ASN    78       6.434  50.938  53.605  1.00  0.00             
ATOM    635  O   ASN    78       7.128  51.381  54.520  1.00  0.00             
ATOM    636  CB  ASN    78       6.307  53.215  52.571  1.00  0.00             
ATOM    637  CG  ASN    78       5.914  54.218  53.638  1.00  0.00             
ATOM    638  OD1 ASN    78       6.625  55.192  53.881  1.00  0.00             
ATOM    639  ND2 ASN    78       4.775  53.981  54.279  1.00  0.00             
ATOM    640  N   THR    79       6.363  49.643  53.311  1.00  0.00             
ATOM    641  CA  THR    79       7.132  48.623  54.081  1.00  0.00             
ATOM    642  C   THR    79       8.631  48.889  54.005  1.00  0.00             
ATOM    643  O   THR    79       9.280  48.558  53.012  1.00  0.00             
ATOM    644  CB  THR    79       6.702  48.589  55.560  1.00  0.00             
ATOM    645  OG1 THR    79       6.897  49.881  56.147  1.00  0.00             
ATOM    646  CG2 THR    79       5.236  48.200  55.679  1.00  0.00             
ATOM    647  N   PHE    80       9.176  49.487  55.059  1.00  0.00             
ATOM    648  CA  PHE    80      10.600  49.798  55.113  1.00  0.00             
ATOM    649  C   PHE    80      11.055  50.518  53.848  1.00  0.00             
ATOM    650  O   PHE    80      12.165  50.296  53.361  1.00  0.00             
ATOM    651  CB  PHE    80      10.916  50.648  56.345  1.00  0.00             
ATOM    652  CG  PHE    80      12.160  50.224  57.071  1.00  0.00             
ATOM    653  CD1 PHE    80      13.356  50.068  56.393  1.00  0.00             
ATOM    654  CD2 PHE    80      12.135  49.981  58.433  1.00  0.00             
ATOM    655  CE1 PHE    80      14.501  49.677  57.061  1.00  0.00             
ATOM    656  CE2 PHE    80      13.280  49.589  59.102  1.00  0.00             
ATOM    657  CZ  PHE    80      14.459  49.437  58.421  1.00  0.00             
ATOM    658  N   GLU    81      10.193  51.379  53.320  1.00  0.00             
ATOM    659  CA  GLU    81      10.505  52.133  52.112  1.00  0.00             
ATOM    660  C   GLU    81      11.371  51.314  51.160  1.00  0.00             
ATOM    661  O   GLU    81      12.333  51.824  50.587  1.00  0.00             
ATOM    662  CB  GLU    81       9.220  52.572  51.407  1.00  0.00             
ATOM    663  CG  GLU    81       8.399  53.586  52.187  1.00  0.00             
ATOM    664  CD  GLU    81       7.406  54.328  51.314  1.00  0.00             
ATOM    665  OE1 GLU    81       7.181  53.890  50.167  1.00  0.00             
ATOM    666  OE2 GLU    81       6.853  55.347  51.779  1.00  0.00             
ATOM    667  N   TRP    82      11.021  50.042  50.995  1.00  0.00             
ATOM    668  CA  TRP    82      11.766  49.151  50.114  1.00  0.00             
ATOM    669  C   TRP    82      12.493  49.933  49.025  1.00  0.00             
ATOM    670  O   TRP    82      11.871  50.450  48.098  1.00  0.00             
ATOM    671  CB  TRP    82      12.764  48.313  50.916  1.00  0.00             
ATOM    672  CG  TRP    82      12.452  46.848  50.917  1.00  0.00             
ATOM    673  CD1 TRP    82      13.197  45.853  51.481  1.00  0.00             
ATOM    674  CD2 TRP    82      11.310  46.213  50.328  1.00  0.00             
ATOM    675  NE1 TRP    82      12.592  44.636  51.279  1.00  0.00             
ATOM    676  CE2 TRP    82      11.431  44.831  50.573  1.00  0.00             
ATOM    677  CE3 TRP    82      10.201  46.679  49.618  1.00  0.00             
ATOM    678  CZ2 TRP    82      10.482  43.909  50.133  1.00  0.00             
ATOM    679  CZ3 TRP    82       9.262  45.764  49.182  1.00  0.00             
ATOM    680  CH2 TRP    82       9.406  44.391  49.440  1.00  0.00             
ATOM    681  N   ALA    83      13.814  50.016  49.146  1.00  0.00             
ATOM    682  CA  ALA    83      14.628  50.735  48.174  1.00  0.00             
ATOM    683  C   ALA    83      14.784  52.202  48.560  1.00  0.00             
ATOM    684  O   ALA    83      14.884  53.074  47.697  1.00  0.00             
ATOM    685  CB  ALA    83      15.995  50.081  48.039  1.00  0.00             
ATOM    686  N   GLY    84      14.801  52.466  49.863  1.00  0.00             
ATOM    687  CA  GLY    84      14.944  53.830  50.338  1.00  0.00             
ATOM    688  C   GLY    84      14.279  54.836  49.420  1.00  0.00             
ATOM    689  O   GLY    84      14.816  55.916  49.173  1.00  0.00             
ATOM    690  N   TYR    85      13.103  54.485  48.910  1.00  0.00             
ATOM    691  CA  TYR    85      12.362  55.365  48.014  1.00  0.00             
ATOM    692  C   TYR    85      13.301  56.300  47.259  1.00  0.00             
ATOM    693  O   TYR    85      12.873  57.317  46.713  1.00  0.00             
ATOM    694  CB  TYR    85      11.529  54.546  47.026  1.00  0.00             
ATOM    695  CG  TYR    85      12.190  53.260  46.587  1.00  0.00             
ATOM    696  CD1 TYR    85      11.429  52.148  46.249  1.00  0.00             
ATOM    697  CD2 TYR    85      13.574  53.160  46.510  1.00  0.00             
ATOM    698  CE1 TYR    85      12.024  50.968  45.846  1.00  0.00             
ATOM    699  CE2 TYR    85      14.187  51.989  46.109  1.00  0.00             
ATOM    700  CZ  TYR    85      13.398  50.889  45.776  1.00  0.00             
ATOM    701  OH  TYR    85      13.998  49.716  45.375  1.00  0.00             
ATOM    702  N   LEU    86      14.582  55.948  47.231  1.00  0.00             
ATOM    703  CA  LEU    86      15.584  56.753  46.543  1.00  0.00             
ATOM    704  C   LEU    86      15.187  58.226  46.523  1.00  0.00             
ATOM    705  O   LEU    86      14.532  58.690  45.590  1.00  0.00             
ATOM    706  CB  LEU    86      16.953  56.586  47.205  1.00  0.00             
ATOM    707  CG  LEU    86      18.025  57.604  46.811  1.00  0.00             
ATOM    708  CD1 LEU    86      19.410  56.979  46.874  1.00  0.00             
ATOM    709  CD2 LEU    86      17.949  58.836  47.699  1.00  0.00             
ATOM    710  N   ARG    87      15.591  58.956  47.558  1.00  0.00             
ATOM    711  CA  ARG    87      15.279  60.377  47.661  1.00  0.00             
ATOM    712  C   ARG    87      13.990  60.604  48.444  1.00  0.00             
ATOM    713  O   ARG    87      13.114  61.353  48.013  1.00  0.00             
ATOM    714  CB  ARG    87      16.435  61.133  48.320  1.00  0.00             
ATOM    715  CG  ARG    87      16.019  61.995  49.500  1.00  0.00             
ATOM    716  CD  ARG    87      14.520  62.250  49.497  1.00  0.00             
ATOM    717  NE  ARG    87      13.946  62.119  48.162  1.00  0.00             
ATOM    718  CZ  ARG    87      12.692  62.435  47.853  1.00  0.00             
ATOM    719  NH1 ARG    87      11.878  62.904  48.789  1.00  0.00             
ATOM    720  NH2 ARG    87      12.257  62.282  46.610  1.00  0.00             
ATOM    721  N   HIS    88      13.881  59.950  49.596  1.00  0.00             
ATOM    722  CA  HIS    88      12.700  60.078  50.441  1.00  0.00             
ATOM    723  C   HIS    88      11.768  58.883  50.273  1.00  0.00             
ATOM    724  O   HIS    88      10.622  58.909  50.721  1.00  0.00             
ATOM    725  CB  HIS    88      13.104  60.226  51.909  1.00  0.00             
ATOM    726  CG  HIS    88      12.286  61.226  52.664  1.00  0.00             
ATOM    727  ND1 HIS    88      11.397  62.079  52.047  1.00  0.00             
ATOM    728  CD2 HIS    88      12.219  61.508  53.986  1.00  0.00             
ATOM    729  CE1 HIS    88      10.820  62.843  52.956  1.00  0.00             
ATOM    730  NE2 HIS    88      11.300  62.518  54.141  1.00  0.00             
TER
END
