
#######################################################
#                                                     #
#                        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   23 (  188),  selected   23 , name T0383TS009_2_1
# Molecule2: number of CA atoms  125 ( 1020),  selected  125 , name T0383.pdb
# PARAMETERS: T0383TS009_2_1.T0383.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       3           -
LGA    -       -      M       4           -
LGA    -       -      N       5           -
LGA    -       -      L       6           -
LGA    -       -      K       7           -
LGA    -       -      R       8           -
LGA    -       -      E       9           -
LGA    -       -      Q      10           -
LGA    -       -      E      11           -
LGA    -       -      F      12           -
LGA    -       -      V      13           -
LGA    -       -      S      14           -
LGA    -       -      Q      15           -
LGA    -       -      Y      16           -
LGA    -       -      H      17           -
LGA    -       -      F      18           -
LGA    -       -      D      19           -
LGA    -       -      A      20           -
LGA    -       -      R      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      E      24           -
LGA    -       -      W      25           -
LGA    -       -      E      26           -
LGA    -       -      N      27           -
LGA    -       -      E      28           -
LGA    -       -      N      29           -
LGA    -       -      G      30           -
LGA    -       -      A      31           -
LGA    -       -      P      32           -
LGA    -       -      E      33           -
LGA    -       -      T      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      D      37           -
LGA    -       -      V      38           -
LGA    -       -      N      39           -
LGA    -       -      F      40           -
LGA    -       -      Q      41           -
LGA    -       -      L      42           -
LGA    -       -      L      43           -
LGA    -       -      Q      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      Q      47           -
LGA    -       -      E      48           -
LGA    -       -      N      49           -
LGA    -       -      Q      50           -
LGA    -       -      V      51           -
LGA    -       -      T      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      I      55           -
LGA    -       -      V      56           -
LGA    -       -      I      57           -
LGA    -       -      L      58           -
LGA    -       -      S      59           -
LGA    -       -      F      60           -
LGA    -       -      M      61           -
LGA    -       -      I      62           -
LGA    -       -      V      63           -
LGA    -       -      F      64           -
LGA    -       -      D      65           -
LGA    -       -      K      66           -
LGA    -       -      F      67           -
LGA    -       -      V      68           -
LGA    -       -      I      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      T      72           -
LGA    -       -      I      73           -
LGA    -       -      S      74           -
LGA    -       -      Q      75           -
LGA    -       -      V      76           -
LGA    -       -      N      77           -
LGA    -       -      H      78           -
LGA    -       -      I      79           -
LGA    -       -      D      80           -
LGA    -       -      G      81           -
LGA    -       -      R      82           -
LGA    -       -      I      83           -
LGA    -       -      V      84           -
LGA    -       -      N      85           -
LGA    -       -      E      86           -
LGA    L      42      P      87          4.286
LGA    L      43      S      88          2.388
LGA    Q      44      E      89          3.553
LGA    H      45      L      90          2.661
LGA    -       -      N      91           -
LGA    -       -      Q      92           -
LGA    -       -      E      93           -
LGA    -       -      E      94           -
LGA    D      46      V      95          1.235
LGA    Q      47      E      96          2.743
LGA    -       -      T      97           -
LGA    E      48      L      98          1.429
LGA    N      49      A      99          2.199
LGA    Q      50      R     100          3.183
LGA    -       -      P     101           -
LGA    V      51      C     102          2.218
LGA    T      52      L     103          1.411
LGA    S      53      N     104          2.014
LGA    L      54      M     105          2.034
LGA    -       -      L     106           -
LGA    I      55      N     107          0.544
LGA    V      56      R     108          0.539
LGA    I      57      L     109          1.089
LGA    L      58      T     110          0.782
LGA    S      59      Y     111          4.675
LGA    F      60      E     112          2.945
LGA    -       -      V     113           -
LGA    -       -      T     114           -
LGA    M      61      E     115          3.868
LGA    I      62      I     116          3.293
LGA    -       -      A     117           -
LGA    -       -      L     118           -
LGA    -       -      D     119           -
LGA    -       -      L     120           -
LGA    V      63      P     121          2.407
LGA    F      64      G     122          1.626
LGA    -       -      I     123           -
LGA    -       -      N     124           -
LGA    -       -      L     125           -
LGA    -       -      E     126           -
LGA    -       -      F     127           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  125    5.0     23    2.57     4.35     13.271     0.861

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.096804 * X  +   0.188893 * Y  +  -0.977215 * Z  + -50.533566
  Y_new =   0.442599 * X  +  -0.887577 * Y  +  -0.127721 * Z  + -26.643808
  Z_new =  -0.891479 * X  +  -0.420150 * Y  +  -0.169525 * Z  + -15.943996 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.954305    1.187288  [ DEG:  -111.9734     68.0266 ]
  Theta =   1.100600    2.040993  [ DEG:    63.0597    116.9403 ]
  Phi   =   1.355469   -1.786124  [ DEG:    77.6627   -102.3373 ]
 
# 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: T0383TS009_2_1                                
REMARK     2: T0383.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0383TS009_2_1.T0383.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  125   5.0   23   2.57    4.35  13.271
REMARK  ---------------------------------------------------------- 
MOLECULE T0383TS009_2_1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0383                                                                    
PARENT N/A                                                                      
ATOM    348  N   LEU    42       6.127  41.741  16.342  1.00  0.00              
ATOM    349  CA  LEU    42       5.116  42.791  16.281  1.00  0.00              
ATOM    350  C   LEU    42       5.096  43.611  17.566  1.00  0.00              
ATOM    351  O   LEU    42       5.207  44.836  17.534  1.00  0.00              
ATOM    352  CB  LEU    42       5.363  43.703  15.078  1.00  0.00              
ATOM    353  CG  LEU    42       4.506  43.438  13.839  1.00  0.00              
ATOM    354  CD1 LEU    42       4.060  44.746  13.203  1.00  0.00              
ATOM    355  CD2 LEU    42       3.306  42.571  14.191  1.00  0.00              
ATOM    356  N   LEU    43       4.954  42.926  18.696  1.00  0.00              
ATOM    357  CA  LEU    43       4.919  43.590  19.995  1.00  0.00              
ATOM    358  C   LEU    43       6.184  44.408  20.231  1.00  0.00              
ATOM    359  O   LEU    43       6.327  45.513  19.708  1.00  0.00              
ATOM    360  CB  LEU    43       3.685  44.488  20.104  1.00  0.00              
ATOM    361  CG  LEU    43       2.681  44.130  21.202  1.00  0.00              
ATOM    362  CD1 LEU    43       2.306  45.361  22.011  1.00  0.00              
ATOM    363  CD2 LEU    43       3.237  43.038  22.103  1.00  0.00              
ATOM    364  N   GLN    44       7.100  43.857  21.020  1.00  0.00              
ATOM    365  CA  GLN    44       8.355  44.534  21.326  1.00  0.00              
ATOM    366  C   GLN    44       9.240  44.641  20.089  1.00  0.00              
ATOM    367  O   GLN    44       9.108  45.575  19.299  1.00  0.00              
ATOM    368  CB  GLN    44       8.086  45.925  21.904  1.00  0.00              
ATOM    369  CG  GLN    44       8.134  45.987  23.422  1.00  0.00              
ATOM    370  CD  GLN    44       8.542  47.354  23.936  1.00  0.00              
ATOM    371  OE1 GLN    44       8.321  47.680  25.102  1.00  0.00              
ATOM    372  NE2 GLN    44       9.138  48.159  23.064  1.00  0.00              
ATOM    373  N   HIS    45      10.142  43.678  19.928  1.00  0.00              
ATOM    374  CA  HIS    45      11.050  43.663  18.787  1.00  0.00              
ATOM    375  C   HIS    45      10.568  42.694  17.712  1.00  0.00              
ATOM    376  O   HIS    45       9.434  42.219  17.755  1.00  0.00              
ATOM    377  CB  HIS    45      11.199  45.068  18.202  1.00  0.00              
ATOM    378  CG  HIS    45      12.610  45.434  17.860  1.00  0.00              
ATOM    379  ND1 HIS    45      13.583  44.492  17.611  1.00  0.00              
ATOM    380  CD2 HIS    45      13.211  46.640  17.727  1.00  0.00              
ATOM    381  CE1 HIS    45      14.723  45.102  17.338  1.00  0.00              
ATOM    382  NE2 HIS    45      14.525  46.404  17.402  1.00  0.00              
ATOM    383  N   ASP    46      11.438  42.407  16.749  1.00  0.00              
ATOM    384  CA  ASP    46      11.103  41.496  15.661  1.00  0.00              
ATOM    385  C   ASP    46      12.327  40.711  15.203  1.00  0.00              
ATOM    386  O   ASP    46      12.207  39.718  14.485  1.00  0.00              
ATOM    387  CB  ASP    46       9.991  40.537  16.089  1.00  0.00              
ATOM    388  CG  ASP    46       8.706  40.750  15.314  1.00  0.00              
ATOM    389  OD1 ASP    46       8.113  39.749  14.859  1.00  0.00              
ATOM    390  OD2 ASP    46       8.292  41.918  15.161  1.00  0.00              
ATOM    391  N   GLN    47      13.504  41.161  15.623  1.00  0.00              
ATOM    392  CA  GLN    47      14.752  40.501  15.257  1.00  0.00              
ATOM    393  C   GLN    47      14.524  39.027  14.939  1.00  0.00              
ATOM    394  O   GLN    47      14.728  38.588  13.808  1.00  0.00              
ATOM    395  CB  GLN    47      15.399  41.204  14.062  1.00  0.00              
ATOM    396  CG  GLN    47      16.918  41.150  14.059  1.00  0.00              
ATOM    397  CD  GLN    47      17.502  41.282  12.666  1.00  0.00              
ATOM    398  OE1 GLN    47      18.683  41.590  12.504  1.00  0.00              
ATOM    399  NE2 GLN    47      16.675  41.047  11.654  1.00  0.00              
ATOM    400  N   GLU    48      14.099  38.269  15.945  1.00  0.00              
ATOM    401  CA  GLU    48      13.843  36.844  15.773  1.00  0.00              
ATOM    402  C   GLU    48      13.290  36.545  14.384  1.00  0.00              
ATOM    403  O   GLU    48      13.377  35.418  13.900  1.00  0.00              
ATOM    404  CB  GLU    48      15.120  36.037  16.016  1.00  0.00              
ATOM    405  CG  GLU    48      15.112  35.236  17.308  1.00  0.00              
ATOM    406  CD  GLU    48      16.282  34.277  17.406  1.00  0.00              
ATOM    407  OE1 GLU    48      17.431  34.752  17.529  1.00  0.00              
ATOM    408  OE2 GLU    48      16.051  33.051  17.358  1.00  0.00              
ATOM    409  N   ASN    49      12.720  37.564  13.749  1.00  0.00              
ATOM    410  CA  ASN    49      12.152  37.414  12.414  1.00  0.00              
ATOM    411  C   ASN    49      13.217  36.995  11.406  1.00  0.00              
ATOM    412  O   ASN    49      13.087  35.964  10.745  1.00  0.00              
ATOM    413  CB  ASN    49      11.012  36.393  12.430  1.00  0.00              
ATOM    414  CG  ASN    49       9.862  36.791  11.525  1.00  0.00              
ATOM    415  OD1 ASN    49       8.949  36.002  11.283  1.00  0.00              
ATOM    416  ND2 ASN    49       9.904  38.018  11.021  1.00  0.00              
ATOM    417  N   GLN    50      14.267  37.801  11.293  1.00  0.00              
ATOM    418  CA  GLN    50      15.355  37.515  10.365  1.00  0.00              
ATOM    419  C   GLN    50      15.480  36.018  10.107  1.00  0.00              
ATOM    420  O   GLN    50      16.314  35.583   9.310  1.00  0.00              
ATOM    421  CB  GLN    50      15.144  38.262   9.046  1.00  0.00              
ATOM    422  CG  GLN    50      16.294  39.178   8.661  1.00  0.00              
ATOM    423  CD  GLN    50      16.178  39.692   7.239  1.00  0.00              
ATOM    424  OE1 GLN    50      17.085  40.352   6.732  1.00  0.00              
ATOM    425  NE2 GLN    50      15.057  39.391   6.592  1.00  0.00              
ATOM    426  N   VAL    51      14.648  35.233  10.783  1.00  0.00              
ATOM    427  CA  VAL    51      14.664  33.751  10.623  1.00  0.00              
ATOM    428  C   VAL    51      14.981  33.354   9.185  1.00  0.00              
ATOM    429  O   VAL    51      15.519  32.277   8.933  1.00  0.00              
ATOM    430  CB  VAL    51      15.691  33.094  11.565  1.00  0.00              
ATOM    431  CG1 VAL    51      15.048  32.755  12.901  1.00  0.00              
ATOM    432  CG2 VAL    51      16.894  34.004  11.759  1.00  0.00              
ATOM    433  N   THR    52      14.642  34.233   8.246  1.00  0.00              
ATOM    434  CA  THR    52      14.895  33.970   6.801  1.00  0.00              
ATOM    435  C   THR    52      16.366  33.656   6.546  1.00  0.00              
ATOM    436  O   THR    52      16.701  32.912   5.623  1.00  0.00              
ATOM    437  CB  THR    52      14.033  32.804   6.280  1.00  0.00              
ATOM    438  OG1 THR    52      13.627  31.978   7.378  1.00  0.00              
ATOM    439  CG2 THR    52      12.799  33.334   5.566  1.00  0.00              
ATOM    440  N   SER    53      17.239  34.226   7.370  1.00  0.00              
ATOM    441  CA  SER    53      18.674  34.008   7.235  1.00  0.00              
ATOM    442  C   SER    53      18.976  32.579   6.798  1.00  0.00              
ATOM    443  O   SER    53      19.913  32.337   6.037  1.00  0.00              
ATOM    444  CB  SER    53      19.276  35.002   6.239  1.00  0.00              
ATOM    445  OG  SER    53      20.410  35.649   6.788  1.00  0.00              
ATOM    446  N   LEU    54      18.176  31.635   7.283  1.00  0.00              
ATOM    447  CA  LEU    54      18.355  30.229   6.942  1.00  0.00              
ATOM    448  C   LEU    54      18.517  30.042   5.438  1.00  0.00              
ATOM    449  O   LEU    54      18.859  28.955   4.971  1.00  0.00              
ATOM    450  CB  LEU    54      19.566  29.650   7.678  1.00  0.00              
ATOM    451  CG  LEU    54      19.381  28.268   8.307  1.00  0.00              
ATOM    452  CD1 LEU    54      20.637  27.427   8.139  1.00  0.00              
ATOM    453  CD2 LEU    54      18.174  27.562   7.708  1.00  0.00              
ATOM    454  N   ILE    55      18.270  31.108   4.684  1.00  0.00              
ATOM    455  CA  ILE    55      18.390  31.062   3.199  1.00  0.00              
ATOM    456  C   ILE    55      18.642  29.640   2.709  1.00  0.00              
ATOM    457  O   ILE    55      17.960  29.153   1.807  1.00  0.00              
ATOM    458  CB  ILE    55      17.127  31.614   2.512  1.00  0.00              
ATOM    459  CG2 ILE    55      17.174  33.133   2.453  1.00  0.00              
ATOM    460  CG1 ILE    55      15.871  31.140   3.247  1.00  0.00              
ATOM    461  CD1 ILE    55      14.822  32.216   3.420  1.00  0.00              
ATOM    462  N   VAL    56      19.626  28.978   3.311  1.00  0.00              
ATOM    463  CA  VAL    56      19.977  27.580   2.929  1.00  0.00              
ATOM    464  C   VAL    56      18.737  26.790   2.523  1.00  0.00              
ATOM    465  O   VAL    56      18.612  26.358   1.377  1.00  0.00              
ATOM    466  CB  VAL    56      20.995  27.549   1.774  1.00  0.00              
ATOM    467  CG1 VAL    56      22.386  27.227   2.298  1.00  0.00              
ATOM    468  CG2 VAL    56      20.992  28.874   1.027  1.00  0.00              
ATOM    469  N   ILE    57      17.822  26.607   3.470  1.00  0.00              
ATOM    470  CA  ILE    57      16.563  25.853   3.206  1.00  0.00              
ATOM    471  C   ILE    57      16.187  25.907   1.729  1.00  0.00              
ATOM    472  O   ILE    57      15.577  24.977   1.200  1.00  0.00              
ATOM    473  CB  ILE    57      16.685  24.381   3.641  1.00  0.00              
ATOM    474  CG2 ILE    57      16.103  24.187   5.033  1.00  0.00              
ATOM    475  CG1 ILE    57      18.146  23.932   3.598  1.00  0.00              
ATOM    476  CD1 ILE    57      18.407  22.630   4.325  1.00  0.00              
ATOM    477  N   LEU    58      16.552  27.002   1.070  1.00  0.00              
ATOM    478  CA  LEU    58      16.254  27.179  -0.346  1.00  0.00              
ATOM    479  C   LEU    58      16.822  26.033  -1.177  1.00  0.00              
ATOM    480  O   LEU    58      16.837  26.093  -2.407  1.00  0.00              
ATOM    481  CB  LEU    58      14.743  27.290  -0.566  1.00  0.00              
ATOM    482  CG  LEU    58      14.276  28.396  -1.514  1.00  0.00              
ATOM    483  CD1 LEU    58      12.929  28.046  -2.127  1.00  0.00              
ATOM    484  CD2 LEU    58      15.314  28.650  -2.596  1.00  0.00              
ATOM    485  N   SER    59      17.287  24.990  -0.497  1.00  0.00              
ATOM    486  CA  SER    59      17.856  23.829  -1.171  1.00  0.00              
ATOM    487  C   SER    59      18.681  24.245  -2.384  1.00  0.00              
ATOM    488  O   SER    59      19.333  23.415  -3.018  1.00  0.00              
ATOM    489  CB  SER    59      18.718  23.016  -0.202  1.00  0.00              
ATOM    490  OG  SER    59      18.090  21.792   0.134  1.00  0.00              
ATOM    491  N   PHE    60      18.649  25.534  -2.702  1.00  0.00              
ATOM    492  CA  PHE    60      19.393  26.063  -3.839  1.00  0.00              
ATOM    493  C   PHE    60      20.690  25.292  -4.056  1.00  0.00              
ATOM    494  O   PHE    60      21.558  25.718  -4.816  1.00  0.00              
ATOM    495  CB  PHE    60      18.537  26.020  -5.107  1.00  0.00              
ATOM    496  CG  PHE    60      18.245  27.374  -5.688  1.00  0.00              
ATOM    497  CD1 PHE    60      18.556  28.526  -4.986  1.00  0.00              
ATOM    498  CD2 PHE    60      17.660  27.495  -6.936  1.00  0.00              
ATOM    499  CE1 PHE    60      18.287  29.772  -5.520  1.00  0.00              
ATOM    500  CE2 PHE    60      17.393  28.742  -7.471  1.00  0.00              
ATOM    501  CZ  PHE    60      17.703  29.877  -6.769  1.00  0.00              
ATOM    502  N   MET    61      20.814  24.152  -3.383  1.00  0.00              
ATOM    503  CA  MET    61      22.005  23.319  -3.500  1.00  0.00              
ATOM    504  C   MET    61      22.584  23.379  -4.909  1.00  0.00              
ATOM    505  O   MET    61      23.641  23.970  -5.132  1.00  0.00              
ATOM    506  CB  MET    61      23.062  23.746  -2.479  1.00  0.00              
ATOM    507  CG  MET    61      23.668  22.594  -1.694  1.00  0.00              
ATOM    508  SD  MET    61      24.783  23.152  -0.390  1.00  0.00              
ATOM    509  CE  MET    61      24.735  21.748   0.720  1.00  0.00              
ATOM    510  N   ILE    62      21.883  22.766  -5.859  1.00  0.00              
ATOM    511  CA  ILE    62      22.335  22.749  -7.279  1.00  0.00              
ATOM    512  C   ILE    62      22.331  24.152  -7.876  1.00  0.00              
ATOM    513  O   ILE    62      22.077  24.329  -9.067  1.00  0.00              
ATOM    514  CB  ILE    62      23.747  22.147  -7.414  1.00  0.00              
ATOM    515  CG2 ILE    62      23.680  20.628  -7.424  1.00  0.00              
ATOM    516  CG1 ILE    62      24.648  22.643  -6.281  1.00  0.00              
ATOM    517  CD1 ILE    62      25.973  21.916  -6.193  1.00  0.00              
ATOM    518  N   VAL    63      22.616  25.145  -7.041  1.00  0.00              
ATOM    519  CA  VAL    63      22.647  26.565  -7.495  1.00  0.00              
ATOM    520  C   VAL    63      22.076  27.497  -6.430  1.00  0.00              
ATOM    521  O   VAL    63      21.715  27.060  -5.338  1.00  0.00              
ATOM    522  CB  VAL    63      24.077  27.016  -7.845  1.00  0.00              
ATOM    523  CG1 VAL    63      24.415  26.647  -9.281  1.00  0.00              
ATOM    524  CG2 VAL    63      25.079  26.404  -6.879  1.00  0.00              
ATOM    525  N   PHE    64      21.998  28.783  -6.757  1.00  0.00              
ATOM    526  CA  PHE    64      21.472  29.778  -5.830  1.00  0.00              
ATOM    527  C   PHE    64      22.429  30.956  -5.685  1.00  0.00              
ATOM    528  O   PHE    64      23.367  30.914  -4.887  1.00  0.00              
ATOM    529  CB  PHE    64      20.100  30.269  -6.293  1.00  0.00              
ATOM    530  CG  PHE    64      18.989  29.958  -5.330  1.00  0.00              
ATOM    531  CD1 PHE    64      19.259  29.708  -3.996  1.00  0.00              
ATOM    532  CD2 PHE    64      17.673  29.917  -5.760  1.00  0.00              
ATOM    533  CE1 PHE    64      18.237  29.423  -3.111  1.00  0.00              
ATOM    534  CE2 PHE    64      16.651  29.631  -4.874  1.00  0.00              
ATOM    535  CZ  PHE    64      16.928  29.385  -3.555  1.00  0.00              
TER
END
