
#######################################################
#                                                     #
#                        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 (  186),  selected   23 , name T0383TS009_1_1
# Molecule2: number of CA atoms  125 ( 1020),  selected  125 , name T0383.pdb
# PARAMETERS: T0383TS009_1_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    Q      41      V      38          4.348
LGA    L      42      N      39          3.141
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    -       -      P      87           -
LGA    -       -      S      88           -
LGA    -       -      E      89           -
LGA    L      43      L      90           #
LGA    Q      44      N      91           -
LGA    -       -      Q      92           -
LGA    -       -      E      93           -
LGA    -       -      E      94           -
LGA    -       -      V      95           -
LGA    -       -      E      96           -
LGA    -       -      T      97           -
LGA    H      45      L      98          0.979
LGA    D      46      A      99          0.807
LGA    Q      47      R     100          1.089
LGA    E      48      P     101          2.331
LGA    N      49      C     102          2.201
LGA    -       -      L     103           -
LGA    Q      50      N     104          2.814
LGA    V      51      M     105          1.849
LGA    T      52      L     106          1.735
LGA    S      53      N     107          1.619
LGA    -       -      R     108           -
LGA    L      54      L     109          1.841
LGA    I      55      T     110          2.168
LGA    -       -      Y     111           -
LGA    V      56      E     112          0.883
LGA    I      57      V     113          1.388
LGA    L      58      T     114          1.957
LGA    -       -      E     115           -
LGA    S      59      I     116          2.762
LGA    F      60      A     117          3.694
LGA    M      61      L     118          4.606
LGA    I      62      D     119          1.745
LGA    V      63      L     120          1.780
LGA    -       -      P     121           -
LGA    -       -      G     122           -
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     21    2.41     4.76     13.111     0.836

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.001827 * X  +   0.100801 * Y  +  -0.994905 * Z  + -54.538788
  Y_new =   0.576300 * X  +  -0.812969 * Y  +  -0.083426 * Z  + -24.856522
  Z_new =  -0.817236 * X  +  -0.573516 * Y  +  -0.056606 * Z  + -19.867777 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.669178    1.472415  [ DEG:   -95.6369     84.3631 ]
  Theta =   0.956599    2.184994  [ DEG:    54.8091    125.1909 ]
  Phi   =   1.573966   -1.567626  [ DEG:    90.1816    -89.8184 ]
 
# 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_1_1                                
REMARK     2: T0383.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0383TS009_1_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   21   2.41    4.76  13.111
REMARK  ---------------------------------------------------------- 
MOLECULE T0383TS009_1_1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0383                                                                    
PARENT N/A                                                                      
ATOM    339  N   GLN    41      11.006  35.701  13.099  1.00  0.00              
ATOM    340  CA  GLN    41       9.697  35.198  13.499  1.00  0.00              
ATOM    341  C   GLN    41       8.680  36.331  13.602  1.00  0.00              
ATOM    342  O   GLN    41       8.283  36.914  12.593  1.00  0.00              
ATOM    343  CB  GLN    41       9.205  34.137  12.512  1.00  0.00              
ATOM    344  CG  GLN    41       8.443  32.994  13.161  1.00  0.00              
ATOM    345  CD  GLN    41       7.654  32.176  12.156  1.00  0.00              
ATOM    346  OE1 GLN    41       6.682  31.509  12.511  1.00  0.00              
ATOM    347  NE2 GLN    41       8.073  32.225  10.896  1.00  0.00              
ATOM    348  N   LEU    42       8.264  36.636  14.827  1.00  0.00              
ATOM    349  CA  LEU    42       7.293  37.699  15.063  1.00  0.00              
ATOM    350  C   LEU    42       7.468  38.306  16.451  1.00  0.00              
ATOM    351  O   LEU    42       7.618  39.519  16.594  1.00  0.00              
ATOM    352  CB  LEU    42       7.418  38.786  13.994  1.00  0.00              
ATOM    353  CG  LEU    42       6.399  38.734  12.853  1.00  0.00              
ATOM    354  CD1 LEU    42       5.925  40.133  12.491  1.00  0.00              
ATOM    355  CD2 LEU    42       5.224  37.842  13.222  1.00  0.00              
ATOM    356  N   LEU    43       7.446  37.454  17.470  1.00  0.00              
ATOM    357  CA  LEU    43       7.602  37.904  18.849  1.00  0.00              
ATOM    358  C   LEU    43       8.917  38.654  19.039  1.00  0.00              
ATOM    359  O   LEU    43       9.032  39.825  18.679  1.00  0.00              
ATOM    360  CB  LEU    43       6.426  38.793  19.258  1.00  0.00              
ATOM    361  CG  LEU    43       5.558  38.282  20.410  1.00  0.00              
ATOM    362  CD1 LEU    43       5.336  39.376  21.442  1.00  0.00              
ATOM    363  CD2 LEU    43       6.185  37.053  21.050  1.00  0.00              
ATOM    364  N   GLN    44       9.905  37.970  19.606  1.00  0.00              
ATOM    365  CA  GLN    44      11.213  38.569  19.844  1.00  0.00              
ATOM    366  C   GLN    44      11.936  38.856  18.533  1.00  0.00              
ATOM    367  O   GLN    44      11.738  39.905  17.921  1.00  0.00              
ATOM    368  CB  GLN    44      11.072  39.856  20.660  1.00  0.00              
ATOM    369  CG  GLN    44      11.316  39.677  22.150  1.00  0.00              
ATOM    370  CD  GLN    44      11.836  40.938  22.810  1.00  0.00              
ATOM    371  OE1 GLN    44      11.778  41.079  24.032  1.00  0.00              
ATOM    372  NE2 GLN    44      12.345  41.861  22.003  1.00  0.00              
ATOM    373  N   HIS    45      12.774  37.916  18.107  1.00  0.00              
ATOM    374  CA  HIS    45      13.527  38.067  16.868  1.00  0.00              
ATOM    375  C   HIS    45      12.876  37.289  15.729  1.00  0.00              
ATOM    376  O   HIS    45      11.740  36.831  15.847  1.00  0.00              
ATOM    377  CB  HIS    45      13.652  39.544  16.492  1.00  0.00              
ATOM    378  CG  HIS    45      15.019  39.937  16.028  1.00  0.00              
ATOM    379  ND1 HIS    45      15.918  39.030  15.509  1.00  0.00              
ATOM    380  CD2 HIS    45      15.642  41.139  16.004  1.00  0.00              
ATOM    381  CE1 HIS    45      17.034  39.658  15.185  1.00  0.00              
ATOM    382  NE2 HIS    45      16.895  40.936  15.476  1.00  0.00              
ATOM    383  N   ASP    46      13.604  37.143  14.626  1.00  0.00              
ATOM    384  CA  ASP    46      13.100  36.421  13.465  1.00  0.00              
ATOM    385  C   ASP    46      14.225  35.698  12.734  1.00  0.00              
ATOM    386  O   ASP    46      13.978  34.834  11.892  1.00  0.00              
ATOM    387  CB  ASP    46      12.017  35.424  13.883  1.00  0.00              
ATOM    388  CG  ASP    46      10.652  35.778  13.326  1.00  0.00              
ATOM    389  OD1 ASP    46       9.970  34.872  12.805  1.00  0.00              
ATOM    390  OD2 ASP    46      10.265  36.962  13.412  1.00  0.00              
ATOM    391  N   GLN    47      15.462  36.057  13.059  1.00  0.00              
ATOM    392  CA  GLN    47      16.628  35.444  12.434  1.00  0.00              
ATOM    393  C   GLN    47      16.307  34.042  11.925  1.00  0.00              
ATOM    394  O   GLN    47      16.349  33.784  10.722  1.00  0.00              
ATOM    395  CB  GLN    47      17.143  36.316  11.287  1.00  0.00              
ATOM    396  CG  GLN    47      18.646  36.238  11.075  1.00  0.00              
ATOM    397  CD  GLN    47      19.051  36.579   9.653  1.00  0.00              
ATOM    398  OE1 GLN    47      20.212  36.890   9.387  1.00  0.00              
ATOM    399  NE2 GLN    47      18.093  36.521   8.736  1.00  0.00              
ATOM    400  N   GLU    48      15.987  33.142  12.848  1.00  0.00              
ATOM    401  CA  GLU    48      15.658  31.766  12.494  1.00  0.00              
ATOM    402  C   GLU    48      14.921  31.700  11.161  1.00  0.00              
ATOM    403  O   GLU    48      14.904  30.661  10.500  1.00  0.00              
ATOM    404  CB  GLU    48      16.925  30.910  12.438  1.00  0.00              
ATOM    405  CG  GLU    48      17.053  29.915  13.580  1.00  0.00              
ATOM    406  CD  GLU    48      18.191  28.934  13.373  1.00  0.00              
ATOM    407  OE1 GLU    48      19.362  29.364  13.416  1.00  0.00              
ATOM    408  OE2 GLU    48      17.910  27.734  13.168  1.00  0.00              
ATOM    409  N   ASN    49      14.313  32.815  10.771  1.00  0.00              
ATOM    410  CA  ASN    49      13.574  32.887   9.517  1.00  0.00              
ATOM    411  C   ASN    49      14.484  32.615   8.323  1.00  0.00              
ATOM    412  O   ASN    49      14.234  31.704   7.534  1.00  0.00              
ATOM    413  CB  ASN    49      12.408  31.895   9.525  1.00  0.00              
ATOM    414  CG  ASN    49      11.167  32.450   8.852  1.00  0.00              
ATOM    415  OD1 ASN    49      10.203  31.723   8.613  1.00  0.00              
ATOM    416  ND2 ASN    49      11.190  33.740   8.543  1.00  0.00              
ATOM    417  N   GLN    50      15.540  33.412   8.199  1.00  0.00              
ATOM    418  CA  GLN    50      16.490  33.259   7.102  1.00  0.00              
ATOM    419  C   GLN    50      16.526  31.820   6.601  1.00  0.00              
ATOM    420  O   GLN    50      17.234  31.502   5.644  1.00  0.00              
ATOM    421  CB  GLN    50      16.139  34.208   5.955  1.00  0.00              
ATOM    422  CG  GLN    50      17.264  35.154   5.567  1.00  0.00              
ATOM    423  CD  GLN    50      16.986  35.888   4.269  1.00  0.00              
ATOM    424  OE1 GLN    50      17.844  36.605   3.755  1.00  0.00              
ATOM    425  NE2 GLN    50      15.781  35.712   3.738  1.00  0.00              
ATOM    426  N   VAL    51      15.758  30.951   7.253  1.00  0.00              
ATOM    427  CA  VAL    51      15.700  29.513   6.865  1.00  0.00              
ATOM    428  C   VAL    51      15.815  29.343   5.354  1.00  0.00              
ATOM    429  O   VAL    51      16.276  28.311   4.869  1.00  0.00              
ATOM    430  CB  VAL    51      16.814  28.698   7.549  1.00  0.00              
ATOM    431  CG1 VAL    51      16.335  28.163   8.890  1.00  0.00              
ATOM    432  CG2 VAL    51      18.065  29.546   7.721  1.00  0.00              
ATOM    433  N   THR    52      15.392  30.364   4.615  1.00  0.00              
ATOM    434  CA  THR    52      15.447  30.330   3.125  1.00  0.00              
ATOM    435  C   THR    52      16.861  30.035   2.633  1.00  0.00              
ATOM    436  O   THR    52      17.048  29.442   1.571  1.00  0.00              
ATOM    437  CB  THR    52      14.484  29.275   2.549  1.00  0.00              
ATOM    438  OG1 THR    52      14.192  28.292   3.550  1.00  0.00              
ATOM    439  CG2 THR    52      13.188  29.930   2.095  1.00  0.00              
ATOM    440  N   SER    53      17.853  30.454   3.412  1.00  0.00              
ATOM    441  CA  SER    53      19.250  30.237   3.057  1.00  0.00              
ATOM    442  C   SER    53      19.441  28.890   2.368  1.00  0.00              
ATOM    443  O   SER    53      20.263  28.756   1.462  1.00  0.00              
ATOM    444  CB  SER    53      19.756  31.365   2.156  1.00  0.00              
ATOM    445  OG  SER    53      20.974  31.899   2.644  1.00  0.00              
ATOM    446  N   LEU    54      18.675  27.894   2.803  1.00  0.00              
ATOM    447  CA  LEU    54      18.758  26.557   2.228  1.00  0.00              
ATOM    448  C   LEU    54      18.718  26.607   0.705  1.00  0.00              
ATOM    449  O   LEU    54      18.957  25.603   0.035  1.00  0.00              
ATOM    450  CB  LEU    54      20.030  25.850   2.700  1.00  0.00              
ATOM    451  CG  LEU    54      19.876  24.389   3.126  1.00  0.00              
ATOM    452  CD1 LEU    54      21.069  23.565   2.666  1.00  0.00              
ATOM    453  CD2 LEU    54      18.578  23.807   2.590  1.00  0.00              
ATOM    454  N   ILE    55      18.416  27.783   0.164  1.00  0.00              
ATOM    455  CA  ILE    55      18.344  27.971  -1.312  1.00  0.00              
ATOM    456  C   ILE    55      18.478  26.640  -2.046  1.00  0.00              
ATOM    457  O   ILE    55      17.670  26.313  -2.914  1.00  0.00              
ATOM    458  CB  ILE    55      17.024  28.644  -1.732  1.00  0.00              
ATOM    459  CG2 ILE    55      17.119  30.153  -1.562  1.00  0.00              
ATOM    460  CG1 ILE    55      15.856  28.081  -0.921  1.00  0.00              
ATOM    461  CD1 ILE    55      14.878  29.133  -0.446  1.00  0.00              
ATOM    462  N   VAL    56      19.506  25.875  -1.688  1.00  0.00              
ATOM    463  CA  VAL    56      19.754  24.549  -2.325  1.00  0.00              
ATOM    464  C   VAL    56      18.443  23.855  -2.681  1.00  0.00              
ATOM    465  O   VAL    56      18.158  23.611  -3.853  1.00  0.00              
ATOM    466  CB  VAL    56      20.614  24.685  -3.595  1.00  0.00              
ATOM    467  CG1 VAL    56      22.048  24.262  -3.315  1.00  0.00              
ATOM    468  CG2 VAL    56      20.564  26.112  -4.121  1.00  0.00              
ATOM    469  N   ILE    57      17.651  23.539  -1.661  1.00  0.00              
ATOM    470  CA  ILE    57      16.342  22.857  -1.870  1.00  0.00              
ATOM    471  C   ILE    57      15.782  23.149  -3.258  1.00  0.00              
ATOM    472  O   ILE    57      15.076  22.325  -3.839  1.00  0.00              
ATOM    473  CB  ILE    57      16.464  21.332  -1.687  1.00  0.00              
ATOM    474  CG2 ILE    57      16.059  20.931  -0.277  1.00  0.00              
ATOM    475  CG1 ILE    57      17.890  20.872  -1.992  1.00  0.00              
ATOM    476  CD1 ILE    57      18.194  19.468  -1.515  1.00  0.00              
ATOM    477  N   LEU    58      16.100  24.328  -3.782  1.00  0.00              
ATOM    478  CA  LEU    58      15.630  24.732  -5.101  1.00  0.00              
ATOM    479  C   LEU    58      16.045  23.722  -6.167  1.00  0.00              
ATOM    480  O   LEU    58      15.904  23.976  -7.364  1.00  0.00              
ATOM    481  CB  LEU    58      14.109  24.901  -5.100  1.00  0.00              
ATOM    482  CG  LEU    58      13.565  26.150  -5.795  1.00  0.00              
ATOM    483  CD1 LEU    58      12.139  25.923  -6.271  1.00  0.00              
ATOM    484  CD2 LEU    58      14.465  26.556  -6.953  1.00  0.00              
ATOM    485  N   SER    59      16.555  22.578  -5.724  1.00  0.00              
ATOM    486  CA  SER    59      16.989  21.529  -6.639  1.00  0.00              
ATOM    487  C   SER    59      17.667  22.118  -7.871  1.00  0.00              
ATOM    488  O   SER    59      18.202  21.388  -8.706  1.00  0.00              
ATOM    489  CB  SER    59      17.938  20.560  -5.929  1.00  0.00              
ATOM    490  OG  SER    59      17.313  19.307  -5.706  1.00  0.00              
ATOM    491  N   PHE    60      17.642  23.442  -7.978  1.00  0.00              
ATOM    492  CA  PHE    60      18.253  24.132  -9.108  1.00  0.00              
ATOM    493  C   PHE    60      19.482  23.383  -9.611  1.00  0.00              
ATOM    494  O   PHE    60      20.261  23.910 -10.405  1.00  0.00              
ATOM    495  CB  PHE    60      17.241  24.303 -10.243  1.00  0.00              
ATOM    496  CG  PHE    60      16.927  25.736 -10.565  1.00  0.00              
ATOM    497  CD1 PHE    60      17.367  26.758  -9.740  1.00  0.00              
ATOM    498  CD2 PHE    60      16.193  26.063 -11.691  1.00  0.00              
ATOM    499  CE1 PHE    60      17.079  28.077 -10.035  1.00  0.00              
ATOM    500  CE2 PHE    60      15.905  27.383 -11.987  1.00  0.00              
ATOM    501  CZ  PHE    60      16.344  28.387 -11.164  1.00  0.00              
ATOM    502  N   MET    61      19.650  22.150  -9.145  1.00  0.00              
ATOM    503  CA  MET    61      20.785  21.326  -9.546  1.00  0.00              
ATOM    504  C   MET    61      21.180  21.599 -10.993  1.00  0.00              
ATOM    505  O   MET    61      22.221  22.200 -11.259  1.00  0.00              
ATOM    506  CB  MET    61      21.978  21.569  -8.619  1.00  0.00              
ATOM    507  CG  MET    61      22.637  20.298  -8.109  1.00  0.00              
ATOM    508  SD  MET    61      23.929  20.625  -6.894  1.00  0.00              
ATOM    509  CE  MET    61      23.972  19.064  -6.018  1.00  0.00              
ATOM    510  N   ILE    62      20.342  21.154 -11.925  1.00  0.00              
ATOM    511  CA  ILE    62      20.607  21.355 -13.377  1.00  0.00              
ATOM    512  C   ILE    62      20.579  22.834 -13.745  1.00  0.00              
ATOM    513  O   ILE    62      20.181  23.202 -14.850  1.00  0.00              
ATOM    514  CB  ILE    62      21.967  20.760 -13.789  1.00  0.00              
ATOM    515  CG2 ILE    62      21.844  19.262 -14.025  1.00  0.00              
ATOM    516  CG1 ILE    62      23.024  21.055 -12.723  1.00  0.00              
ATOM    517  CD1 ILE    62      24.322  20.302 -12.924  1.00  0.00              
ATOM    518  N   VAL    63      21.005  23.679 -12.811  1.00  0.00              
ATOM    519  CA  VAL    63      21.029  25.152 -13.040  1.00  0.00              
ATOM    520  C   VAL    63      20.634  25.913 -11.778  1.00  0.00              
ATOM    521  O   VAL    63      20.399  25.315 -10.729  1.00  0.00              
ATOM    522  CB  VAL    63      22.418  25.629 -13.502  1.00  0.00              
ATOM    523  CG1 VAL    63      22.556  25.486 -15.010  1.00  0.00              
ATOM    524  CG2 VAL    63      23.513  24.856 -12.783  1.00  0.00              
TER
END
