
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0356TS383_5-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS383_5-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      N       7          2.472
LGA    A     315      D       8          1.081
LGA    I     316      L       9          4.802
LGA    Y     317      R      10           -
LGA    H     318      D      11           -
LGA    S     319      F      12           -
LGA    T     320      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    Y     321      L      63           #
LGA    T     322      C      64          3.248
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    G     323      I     316          5.203
LGA    R     324      -       -           -
LGA    P     325      Y     317          4.845
LGA    P     326      H     318           -
LGA    D     327      S     319           -
LGA    E     328      T     320          3.357
LGA    P     329      Y     321          2.774
LGA    A     330      T     322          2.341
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    V     331      D     327          2.859
LGA    L     332      E     328          1.887
LGA    G     333      P     329          1.079
LGA    V     334      A     330          1.243
LGA    A     335      V     331          0.944
LGA    L     336      L     332          1.142
LGA    N     337      G     333          1.344
LGA    E     338      V     334          1.205
LGA    V     339      A     335          0.978
LGA    F     340      L     336          0.564
LGA    V     341      N     337          0.972
LGA    P     342      E     338          1.192
LGA    I     343      V     339          3.848
LGA    L     344      F     340           #
LGA    Q     345      V     341           -
LGA    K     346      P     342           -
LGA    Q     347      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34  124    5.0     22    2.65     4.55     13.821     0.801

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.871196 * X  +   0.191927 * Y  +   0.451865 * Z  +  14.906806
  Y_new =  -0.196525 * X  +  -0.707112 * Y  +   0.679242 * Z  + 132.792343
  Z_new =   0.449884 * X  +  -0.680556 * Y  +  -0.578315 * Z  + 113.287804 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.275156    0.866436  [ DEG:  -130.3568     49.6432 ]
  Theta =  -0.466635   -2.674957  [ DEG:   -26.7362   -153.2638 ]
  Phi   =  -0.221867    2.919725  [ DEG:   -12.7121    167.2879 ]
 
# 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: T0356TS383_5-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_5-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  124   5.0   22   2.65    4.55  13.821
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_5-D1
PFRMAT TS
TARGET t0356
MODEL 5
PARENT 2bmoA
ATOM    745  N   ASP   314      75.309  83.582  82.071  1.00  0.00
ATOM    746  CA  ASP   314      74.880  82.336  82.691  1.00  0.00
ATOM    747  C   ASP   314      75.686  81.165  82.171  1.00  0.00
ATOM    748  O   ASP   314      76.274  81.223  81.075  1.00  0.00
ATOM    749  N   ALA   315      75.695  80.101  82.965  1.00  0.00
ATOM    750  CA  ALA   315      76.180  78.803  82.535  1.00  0.00
ATOM    751  C   ALA   315      75.041  77.851  82.225  1.00  0.00
ATOM    752  O   ALA   315      73.900  78.041  82.672  1.00  0.00
ATOM    753  N   ILE   316      75.372  76.824  81.446  1.00  0.00
ATOM    754  CA  ILE   316      74.455  75.757  81.064  1.00  0.00
ATOM    755  C   ILE   316      75.116  74.412  81.362  1.00  0.00
ATOM    756  O   ILE   316      76.165  74.096  80.791  1.00  0.00
ATOM    757  N   TYR   317      74.511  73.638  82.259  1.00  0.00
ATOM    758  CA  TYR   317      74.865  72.229  82.483  1.00  0.00
ATOM    759  C   TYR   317      73.809  71.373  81.782  1.00  0.00
ATOM    760  O   TYR   317      72.649  71.315  82.199  1.00  0.00
ATOM    761  N   HIS   318      74.211  70.717  80.695  1.00  0.00
ATOM    762  CA  HIS   318      73.262  69.984  79.859  1.00  0.00
ATOM    763  C   HIS   318      72.460  68.921  80.612  1.00  0.00
ATOM    764  O   HIS   318      73.029  68.098  81.331  1.00  0.00
ATOM    765  N   SER   319      71.142  68.938  80.431  1.00  0.00
ATOM    766  CA  SER   319      70.278  67.862  80.890  1.00  0.00
ATOM    767  C   SER   319      69.859  67.878  82.350  1.00  0.00
ATOM    768  O   SER   319      68.982  67.103  82.740  1.00  0.00
ATOM    769  N   THR   320      70.466  68.754  83.156  1.00  0.00
ATOM    770  CA  THR   320      70.341  68.677  84.626  1.00  0.00
ATOM    771  C   THR   320      69.094  69.384  85.174  1.00  0.00
ATOM    772  O   THR   320      69.173  70.265  86.028  1.00  0.00
ATOM    773  N   TYR   321      67.935  68.962  84.687  1.00  0.00
ATOM    774  CA  TYR   321      66.657  69.619  84.971  1.00  0.00
ATOM    775  C   TYR   321      66.288  69.611  86.452  1.00  0.00
ATOM    776  O   TYR   321      65.541  70.461  86.900  1.00  0.00
ATOM    777  N   THR   322      66.812  68.663  87.218  1.00  0.00
ATOM    778  CA  THR   322      66.508  68.632  88.648  1.00  0.00
ATOM    779  C   THR   322      67.495  69.454  89.486  1.00  0.00
ATOM    780  O   THR   322      67.300  69.607  90.687  1.00  0.00
ATOM    781  N   GLY   323      68.545  69.974  88.859  1.00  0.00
ATOM    782  CA  GLY   323      69.466  70.915  89.499  1.00  0.00
ATOM    783  C   GLY   323      69.936  70.492  90.878  1.00  0.00
ATOM    784  O   GLY   323      70.411  69.371  91.069  1.00  0.00
ATOM    785  N   ARG   324      69.799  71.396  91.847  1.00  0.00
ATOM    786  CA  ARG   324      70.260  71.142  93.213  1.00  0.00
ATOM    787  C   ARG   324      69.252  70.390  94.085  1.00  0.00
ATOM    788  O   ARG   324      69.430  70.309  95.306  1.00  0.00
ATOM    789  N   PRO   325      68.202  69.827  93.490  1.00  0.00
ATOM    790  CA  PRO   325      67.239  69.041  94.261  1.00  0.00
ATOM    791  C   PRO   325      67.777  67.637  94.570  1.00  0.00
ATOM    792  O   PRO   325      68.588  67.077  93.826  1.00  0.00
ATOM    793  N   PRO   326      63.021  61.707  89.801  1.00  0.00
ATOM    794  CA  PRO   326      62.203  60.982  88.816  1.00  0.00
ATOM    795  C   PRO   326      61.010  61.779  88.264  1.00  0.00
ATOM    796  O   PRO   326      60.824  61.842  87.038  1.00  0.00
ATOM    797  N   ASP   327      60.226  62.407  89.133  1.00  0.00
ATOM    798  CA  ASP   327      59.035  63.114  88.667  1.00  0.00
ATOM    799  C   ASP   327      59.378  64.367  87.867  1.00  0.00
ATOM    800  O   ASP   327      58.731  64.659  86.859  1.00  0.00
ATOM    801  N   GLU   328      60.392  65.115  88.296  1.00  0.00
ATOM    802  CA  GLU   328      60.773  66.308  87.557  1.00  0.00
ATOM    803  C   GLU   328      61.357  65.967  86.207  1.00  0.00
ATOM    804  O   GLU   328      61.002  66.584  85.204  1.00  0.00
ATOM    805  N   PRO   329      62.248  64.976  86.177  1.00  0.00
ATOM    806  CA  PRO   329      62.884  64.566  84.927  1.00  0.00
ATOM    807  C   PRO   329      61.856  64.084  83.920  1.00  0.00
ATOM    808  O   PRO   329      61.959  64.415  82.738  1.00  0.00
ATOM    809  N   ALA   330      60.860  63.327  84.379  1.00  0.00
ATOM    810  CA  ALA   330      59.785  62.857  83.496  1.00  0.00
ATOM    811  C   ALA   330      58.978  64.016  82.909  1.00  0.00
ATOM    812  O   ALA   330      58.641  64.009  81.724  1.00  0.00
ATOM    813  N   VAL   331      58.688  65.022  83.728  1.00  0.00
ATOM    814  CA  VAL   331      57.945  66.185  83.258  1.00  0.00
ATOM    815  C   VAL   331      58.735  66.960  82.200  1.00  0.00
ATOM    816  O   VAL   331      58.204  67.308  81.140  1.00  0.00
ATOM    817  N   LEU   332      60.003  67.229  82.488  1.00  0.00
ATOM    818  CA  LEU   332      60.868  67.948  81.557  1.00  0.00
ATOM    819  C   LEU   332      61.128  67.187  80.269  1.00  0.00
ATOM    820  O   LEU   332      61.134  67.777  79.190  1.00  0.00
ATOM    821  N   GLY   333      61.329  65.872  80.370  1.00  0.00
ATOM    822  CA  GLY   333      61.570  65.049  79.182  1.00  0.00
ATOM    823  C   GLY   333      60.368  65.044  78.251  1.00  0.00
ATOM    824  O   GLY   333      60.522  65.106  77.027  1.00  0.00
ATOM    825  N   VAL   334      59.172  64.988  78.824  1.00  0.00
ATOM    826  CA  VAL   334      57.953  64.979  78.031  1.00  0.00
ATOM    827  C   VAL   334      57.757  66.291  77.282  1.00  0.00
ATOM    828  O   VAL   334      57.421  66.287  76.096  1.00  0.00
ATOM    829  N   ALA   335      57.985  67.419  77.949  1.00  0.00
ATOM    830  CA  ALA   335      57.828  68.706  77.282  1.00  0.00
ATOM    831  C   ALA   335      58.937  68.972  76.267  1.00  0.00
ATOM    832  O   ALA   335      58.688  69.573  75.218  1.00  0.00
ATOM    833  N   LEU   336      60.146  68.504  76.566  1.00  0.00
ATOM    834  CA  LEU   336      61.273  68.610  75.635  1.00  0.00
ATOM    835  C   LEU   336      60.934  68.013  74.267  1.00  0.00
ATOM    836  O   LEU   336      61.246  68.604  73.226  1.00  0.00
ATOM    837  N   ASN   337      60.305  66.838  74.285  1.00  0.00
ATOM    838  CA  ASN   337      59.897  66.158  73.045  1.00  0.00
ATOM    839  C   ASN   337      58.954  67.030  72.208  1.00  0.00
ATOM    840  O   ASN   337      59.091  67.092  70.975  1.00  0.00
ATOM    841  N   GLU   338      58.003  67.686  72.869  1.00  0.00
ATOM    842  CA  GLU   338      57.078  68.598  72.196  1.00  0.00
ATOM    843  C   GLU   338      57.806  69.836  71.676  1.00  0.00
ATOM    844  O   GLU   338      57.638  70.222  70.516  1.00  0.00
ATOM    845  N   VAL   339      58.629  70.438  72.535  1.00  0.00
ATOM    846  CA  VAL   339      59.356  71.670  72.203  1.00  0.00
ATOM    847  C   VAL   339      60.339  71.551  71.048  1.00  0.00
ATOM    848  O   VAL   339      60.543  72.505  70.301  1.00  0.00
ATOM    849  N   PHE   340      60.953  70.383  70.906  1.00  0.00
ATOM    850  CA  PHE   340      61.911  70.155  69.829  1.00  0.00
ATOM    851  C   PHE   340      61.290  70.439  68.455  1.00  0.00
ATOM    852  O   PHE   340      61.961  70.952  67.563  1.00  0.00
ATOM    853  N   VAL   341      59.997  70.149  68.318  1.00  0.00
ATOM    854  CA  VAL   341      59.277  70.386  67.061  1.00  0.00
ATOM    855  C   VAL   341      59.032  71.868  66.779  1.00  0.00
ATOM    856  O   VAL   341      58.849  72.258  65.623  1.00  0.00
ATOM    857  N   PRO   342      59.025  72.680  67.835  1.00  0.00
ATOM    858  CA  PRO   342      58.716  74.106  67.741  1.00  0.00
ATOM    859  C   PRO   342      59.967  74.976  67.660  1.00  0.00
ATOM    860  O   PRO   342      60.023  75.927  66.875  1.00  0.00
ATOM    861  N   ILE   343      60.962  74.663  68.487  1.00  0.00
ATOM    862  CA  ILE   343      62.169  75.493  68.595  1.00  0.00
ATOM    863  C   ILE   343      63.481  74.772  68.272  1.00  0.00
ATOM    864  O   ILE   343      64.546  75.385  68.300  1.00  0.00
ATOM    865  N   LEU   344      63.398  73.485  67.938  1.00  0.00
ATOM    866  CA  LEU   344      64.582  72.710  67.551  1.00  0.00
ATOM    867  C   LEU   344      65.213  71.926  68.691  1.00  0.00
ATOM    868  O   LEU   344      64.939  72.189  69.862  1.00  0.00
ATOM    869  N   GLN   345      66.072  70.968  68.349  1.00  0.00
ATOM    870  CA  GLN   345      66.681  70.063  69.338  1.00  0.00
ATOM    871  C   GLN   345      67.531  70.768  70.400  1.00  0.00
ATOM    872  O   GLN   345      67.379  70.501  71.595  1.00  0.00
ATOM    873  N   LYS   346      68.436  71.639  69.970  1.00  0.00
ATOM    874  CA  LYS   346      69.348  72.303  70.905  1.00  0.00
ATOM    875  C   LYS   346      68.584  73.126  71.950  1.00  0.00
ATOM    876  O   LYS   346      68.816  73.002  73.165  1.00  0.00
ATOM    877  N   GLN   347      67.656  73.951  71.483  1.00  0.00
ATOM    878  CA  GLN   347      66.924  74.817  72.393  1.00  0.00
ATOM    879  C   GLN   347      65.953  74.036  73.281  1.00  0.00
ATOM    880  O   GLN   347      65.742  74.406  74.436  1.00  0.00
TER
END
