
#######################################################
#                                                     #
#                        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   18 (  139),  selected   18 , name T0386TS009_2_1-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386TS009_2_1-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    I      33      T      65          0.888
LGA    K      34      A      66          4.107
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    N      35      L      86          3.423
LGA    L      36      R      87          5.797
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    N      37      A     114           #
LGA    -       -      I     115           -
LGA    -       -      G     116           -
LGA    -       -      D     117           -
LGA    -       -      E     118           -
LGA    A      38      I     119          2.366
LGA    F      39      Q     120          2.731
LGA    L      40      E     121           -
LGA    E      41      G     122          4.675
LGA    K      42      L     123          2.233
LGA    C      43      Q     124          2.510
LGA    S      44      R     125           #
LGA    -       -      L     126           -
LGA    H      45      D     127          1.881
LGA    D      46      Q     128          2.654
LGA    T      47      T     129          0.594
LGA    A      48      L     130          1.612
LGA    -       -      A     131           -
LGA    -       -      E     132           -
LGA    -       -      K     133           -
LGA    -       -      N     134           -
LGA    K      49      N     135          3.191
LGA    A      50      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    -       -      I     149           -
LGA    -       -      E     150           -
LGA    -       -      L     151           -
LGA    -       -      F     152           -
LGA    -       -      N     153           -
LGA    -       -      S     154           -
LGA    -       -      L     155           -
LGA    -       -      N     156           -
LGA    -       -      Q     157           -
LGA    -       -      L     158           -
LGA    -       -      H     159           -
LGA    -       -      P     160           -
LGA    -       -      F     161           -
LGA    -       -      R     162           -
LGA    -       -      E     163           -
LGA    -       -      G     164           -
LGA    -       -      N     165           -
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)   18  206    5.0     14    3.08     7.14      4.287     0.440

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.759221 * X  +  -0.570607 * Y  +   0.313035 * Z  + -19.853752
  Y_new =  -0.179136 * X  +  -0.279189 * Y  +  -0.943379 * Z  + 120.602753
  Z_new =   0.625695 * X  +  -0.772309 * Y  +   0.109750 * Z  +  46.952930 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.429635    1.711957  [ DEG:   -81.9121     98.0879 ]
  Theta =  -0.676022   -2.465571  [ DEG:   -38.7332   -141.2668 ]
  Phi   =  -2.909883    0.231709  [ DEG:  -166.7240     13.2760 ]
 
# 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_2_1-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS009_2_1-D1.T0386_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  206   5.0   14   3.08    7.14   4.287
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS009_2_1-D1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0386                                                                    
PARENT N/A                                                                       
ATOM    259  N   ILE    33       3.416  57.160  48.869  1.00  0.00             
ATOM    260  CA  ILE    33       3.573  56.438  47.574  1.00  0.00             
ATOM    261  C   ILE    33       3.704  57.415  46.410  1.00  0.00             
ATOM    262  O   ILE    33       2.976  58.405  46.333  1.00  0.00             
ATOM    263  CB  ILE    33       4.800  55.508  47.592  1.00  0.00             
ATOM    264  CG2 ILE    33       4.399  54.107  48.031  1.00  0.00             
ATOM    265  CG1 ILE    33       5.885  56.073  48.511  1.00  0.00             
ATOM    266  CD1 ILE    33       6.446  55.063  49.486  1.00  0.00             
ATOM    267  N   LYS    34       4.637  57.130  45.508  1.00  0.00             
ATOM    268  CA  LYS    34       4.866  57.982  44.347  1.00  0.00             
ATOM    269  C   LYS    34       6.262  57.768  43.772  1.00  0.00             
ATOM    270  O   LYS    34       7.084  58.684  43.756  1.00  0.00             
ATOM    271  CB  LYS    34       3.809  57.718  43.273  1.00  0.00             
ATOM    272  CG  LYS    34       3.045  58.958  42.838  1.00  0.00             
ATOM    273  CD  LYS    34       2.121  58.655  41.669  1.00  0.00             
ATOM    274  CE  LYS    34       1.223  59.841  41.352  1.00  0.00             
ATOM    275  NZ  LYS    34       0.046  59.443  40.532  1.00  0.00             
ATOM    276  N   ASN    35       6.524  56.553  43.302  1.00  0.00             
ATOM    277  CA  ASN    35       7.821  56.217  42.726  1.00  0.00             
ATOM    278  C   ASN    35       8.911  56.207  43.792  1.00  0.00             
ATOM    279  O   ASN    35       9.320  57.259  44.284  1.00  0.00             
ATOM    280  CB  ASN    35       7.759  54.859  42.024  1.00  0.00             
ATOM    281  CG  ASN    35       8.153  54.940  40.563  1.00  0.00             
ATOM    282  OD1 ASN    35       8.566  53.946  39.965  1.00  0.00             
ATOM    283  ND2 ASN    35       8.027  56.128  39.983  1.00  0.00             
ATOM    284  N   LEU    36       9.379  55.013  44.143  1.00  0.00             
ATOM    285  CA  LEU    36      10.423  54.865  45.149  1.00  0.00             
ATOM    286  C   LEU    36      10.160  53.657  46.042  1.00  0.00             
ATOM    287  O   LEU    36       9.410  53.742  47.015  1.00  0.00             
ATOM    288  CB  LEU    36      11.795  54.740  44.484  1.00  0.00             
ATOM    289  CG  LEU    36      12.974  55.353  45.243  1.00  0.00             
ATOM    290  CD1 LEU    36      14.290  55.000  44.567  1.00  0.00             
ATOM    291  CD2 LEU    36      12.973  54.899  46.694  1.00  0.00             
ATOM    292  N   ASN    37      10.782  52.532  45.704  1.00  0.00             
ATOM    293  CA  ASN    37      10.617  51.305  46.474  1.00  0.00             
ATOM    294  C   ASN    37       9.634  50.357  45.796  1.00  0.00             
ATOM    295  O   ASN    37       8.541  50.111  46.306  1.00  0.00             
ATOM    296  CB  ASN    37      11.967  50.611  46.672  1.00  0.00             
ATOM    297  CG  ASN    37      12.401  50.583  48.123  1.00  0.00             
ATOM    298  OD1 ASN    37      13.455  50.043  48.457  1.00  0.00             
ATOM    299  ND2 ASN    37      11.586  51.169  48.994  1.00  0.00             
ATOM    300  N   ALA    38      10.030  49.826  44.643  1.00  0.00             
ATOM    301  CA  ALA    38       9.186  48.905  43.893  1.00  0.00             
ATOM    302  C   ALA    38       7.828  49.527  43.586  1.00  0.00             
ATOM    303  O   ALA    38       6.787  48.905  43.799  1.00  0.00             
ATOM    304  CB  ALA    38       9.873  48.486  42.603  1.00  0.00             
ATOM    305  N   PHE    39       7.846  50.758  43.084  1.00  0.00             
ATOM    306  CA  PHE    39       6.616  51.466  42.748  1.00  0.00             
ATOM    307  C   PHE    39       5.993  52.108  43.983  1.00  0.00             
ATOM    308  O   PHE    39       4.955  51.661  44.469  1.00  0.00             
ATOM    309  CB  PHE    39       6.887  52.531  41.681  1.00  0.00             
ATOM    310  CG  PHE    39       6.038  52.383  40.451  1.00  0.00             
ATOM    311  CD1 PHE    39       5.176  51.310  40.310  1.00  0.00             
ATOM    312  CD2 PHE    39       6.100  53.320  39.434  1.00  0.00             
ATOM    313  CE1 PHE    39       4.395  51.175  39.178  1.00  0.00             
ATOM    314  CE2 PHE    39       5.319  53.186  38.302  1.00  0.00             
ATOM    315  CZ  PHE    39       4.470  52.119  38.171  1.00  0.00             
ATOM    316  N   LEU    40       6.635  53.158  44.485  1.00  0.00             
ATOM    317  CA  LEU    40       6.144  53.863  45.664  1.00  0.00             
ATOM    318  C   LEU    40       5.819  52.890  46.792  1.00  0.00             
ATOM    319  O   LEU    40       4.673  52.796  47.231  1.00  0.00             
ATOM    320  CB  LEU    40       7.172  54.893  46.138  1.00  0.00             
ATOM    321  CG  LEU    40       6.610  56.169  46.767  1.00  0.00             
ATOM    322  CD1 LEU    40       7.571  56.722  47.809  1.00  0.00             
ATOM    323  CD2 LEU    40       5.242  55.911  47.377  1.00  0.00             
ATOM    324  N   GLU    41       6.833  52.168  47.257  1.00  0.00             
ATOM    325  CA  GLU    41       6.656  51.201  48.333  1.00  0.00             
ATOM    326  C   GLU    41       5.794  50.027  47.884  1.00  0.00             
ATOM    327  O   GLU    41       4.603  49.965  48.191  1.00  0.00             
ATOM    328  CB  GLU    41       8.013  50.699  48.831  1.00  0.00             
ATOM    329  CG  GLU    41       8.054  50.391  50.318  1.00  0.00             
ATOM    330  CD  GLU    41       9.468  50.308  50.857  1.00  0.00             
ATOM    331  OE1 GLU    41      10.180  51.334  50.822  1.00  0.00             
ATOM    332  OE2 GLU    41       9.866  49.216  51.316  1.00  0.00             
ATOM    333  N   LYS    42       6.403  49.097  47.157  1.00  0.00             
ATOM    334  CA  LYS    42       5.693  47.923  46.663  1.00  0.00             
ATOM    335  C   LYS    42       4.784  48.279  45.492  1.00  0.00             
ATOM    336  O   LYS    42       3.609  47.913  45.472  1.00  0.00             
ATOM    337  CB  LYS    42       6.683  46.833  46.249  1.00  0.00             
ATOM    338  CG  LYS    42       6.168  45.417  46.449  1.00  0.00             
ATOM    339  CD  LYS    42       6.957  44.418  45.618  1.00  0.00             
ATOM    340  CE  LYS    42       6.314  43.042  45.651  1.00  0.00             
ATOM    341  NZ  LYS    42       6.937  42.114  44.666  1.00  0.00             
ATOM    342  N   CYS    43       5.337  48.994  44.518  1.00  0.00             
ATOM    343  CA  CYS    43       4.577  49.402  43.342  1.00  0.00             
ATOM    344  C   CYS    43       3.304  50.142  43.737  1.00  0.00             
ATOM    345  O   CYS    43       2.212  49.575  43.714  1.00  0.00             
ATOM    346  CB  CYS    43       5.434  50.279  42.428  1.00  0.00             
ATOM    347  SG  CYS    43       5.579  49.669  40.717  1.00  0.00             
ATOM    348  N   SER    44       3.452  51.412  44.098  1.00  0.00             
ATOM    349  CA  SER    44       2.315  52.233  44.497  1.00  0.00             
ATOM    350  C   SER    44       1.591  51.626  45.696  1.00  0.00             
ATOM    351  O   SER    44       0.396  51.339  45.631  1.00  0.00             
ATOM    352  CB  SER    44       2.770  53.657  44.824  1.00  0.00             
ATOM    353  OG  SER    44       1.763  54.601  44.502  1.00  0.00             
ATOM    354  N   HIS    45       2.324  51.434  46.788  1.00  0.00             
ATOM    355  CA  HIS    45       1.754  50.862  48.001  1.00  0.00             
ATOM    356  C   HIS    45       1.541  49.358  47.855  1.00  0.00             
ATOM    357  O   HIS    45       1.593  48.819  46.749  1.00  0.00             
ATOM    358  CB  HIS    45       2.653  51.152  49.204  1.00  0.00             
ATOM    359  CG  HIS    45       1.900  51.457  50.462  1.00  0.00             
ATOM    360  ND1 HIS    45       0.571  51.820  50.464  1.00  0.00             
ATOM    361  CD2 HIS    45       2.291  51.454  51.758  1.00  0.00             
ATOM    362  CE1 HIS    45       0.177  52.028  51.707  1.00  0.00             
ATOM    363  NE2 HIS    45       1.200  51.812  52.512  1.00  0.00             
ATOM    364  N   ASP    46       1.304  48.687  48.977  1.00  0.00             
ATOM    365  CA  ASP    46       1.085  47.246  48.976  1.00  0.00             
ATOM    366  C   ASP    46       0.925  46.711  50.396  1.00  0.00             
ATOM    367  O   ASP    46       1.903  46.329  51.039  1.00  0.00             
ATOM    368  CB  ASP    46      -0.147  46.893  48.140  1.00  0.00             
ATOM    369  CG  ASP    46       0.199  46.081  46.907  1.00  0.00             
ATOM    370  OD1 ASP    46      -0.265  44.926  46.807  1.00  0.00             
ATOM    371  OD2 ASP    46       0.935  46.601  46.042  1.00  0.00             
ATOM    372  N   THR    47      -0.312  46.688  50.879  1.00  0.00             
ATOM    373  CA  THR    47      -0.608  46.189  52.252  1.00  0.00             
ATOM    374  C   THR    47      -0.625  47.332  53.262  1.00  0.00             
ATOM    375  O   THR    47       0.424  47.855  53.639  1.00  0.00             
ATOM    376  CB  THR    47      -1.958  45.449  52.306  1.00  0.00             
ATOM    377  OG1 THR    47      -2.917  46.140  51.498  1.00  0.00             
ATOM    378  CG2 THR    47      -1.804  44.024  51.796  1.00  0.00             
ATOM    379  N   ALA    48      -1.822  47.713  53.696  1.00  0.00             
ATOM    380  CA  ALA    48      -1.977  48.794  54.662  1.00  0.00             
ATOM    381  C   ALA    48      -2.103  50.144  53.964  1.00  0.00             
ATOM    382  O   ALA    48      -1.208  50.561  53.230  1.00  0.00             
ATOM    383  CB  ALA    48      -3.190  48.545  55.546  1.00  0.00             
ATOM    384  N   LYS    49      -3.222  50.823  54.198  1.00  0.00             
ATOM    385  CA  LYS    49      -3.468  52.126  53.592  1.00  0.00             
ATOM    386  C   LYS    49      -3.862  51.987  52.126  1.00  0.00             
ATOM    387  O   LYS    49      -3.215  52.550  51.242  1.00  0.00             
ATOM    388  CB  LYS    49      -4.556  52.878  54.361  1.00  0.00             
ATOM    389  CG  LYS    49      -4.285  54.364  54.527  1.00  0.00             
ATOM    390  CD  LYS    49      -5.184  54.974  55.590  1.00  0.00             
ATOM    391  CE  LYS    49      -4.958  56.473  55.711  1.00  0.00             
ATOM    392  NZ  LYS    49      -6.093  57.152  56.393  1.00  0.00             
ATOM    393  N   ALA    50      -4.929  51.235  51.874  1.00  0.00             
ATOM    394  CA  ALA    50      -5.412  51.021  50.515  1.00  0.00             
ATOM    395  C   ALA    50      -4.253  50.906  49.529  1.00  0.00             
ATOM    396  O   ALA    50      -3.975  51.835  48.773  1.00  0.00             
ATOM    397  CB  ALA    50      -6.280  49.774  50.451  1.00  0.00             
TER
END
