
#######################################################
#                                                     #
#                        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   36 (  177),  selected   36 , name T0320TS102_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS102_2-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    N     229      N     242           #
LGA    S     230      P     243           #
LGA    L     231      A     244           #
LGA    P     232      -       -           -
LGA    N     233      -       -           -
LGA    P     234      L     245           #
LGA    H     235      -       -           -
LGA    L     236      -       -           -
LGA    I     251      H     246          3.238
LGA    I     252      -       -           -
LGA    H     253      -       -           -
LGA    A     254      F     247          2.698
LGA    F     255      E     248          1.636
LGA    G     256      W     249          3.760
LGA    A     266      E     250          2.384
LGA    I     267      I     251          1.798
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    N     268      S     265          2.318
LGA    T     269      A     266          1.879
LGA    S     270      I     267          2.260
LGA    P     271      N     268          0.293
LGA    I     272      T     269          2.331
LGA    G     290      S     270          1.392
LGA    W     291      P     271          1.548
LGA    Y     292      I     272          1.840
LGA    L     293      S     273          1.369
LGA    V     294      V     274          2.830
LGA    D     295      V     275          2.598
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    D     296      E     278          1.354
LGA    T     297      R     279          4.454
LGA    -       -      F     280           -
LGA    L     298      S     281          4.664
LGA    E     299      K     282          3.827
LGA    R     300      Y     283           #
LGA    A     301      H     284           -
LGA    G     302      D     285           -
LGA    R     303      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    I     304      A     301           #
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   73    5.0     21    2.63     9.52     21.775     0.769

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.036618 * X  +  -0.114774 * Y  +  -0.992717 * Z  +  76.154083
  Y_new =  -0.353219 * X  +   0.930748 * Y  +  -0.094580 * Z  +  21.954540
  Z_new =   0.934824 * X  +   0.347183 * Y  +  -0.074622 * Z  +  -5.171143 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.782511   -1.359082  [ DEG:   102.1304    -77.8696 ]
  Theta =  -1.207763   -1.933830  [ DEG:   -69.1997   -110.8003 ]
  Phi   =  -1.674096    1.467497  [ DEG:   -95.9186     84.0814 ]
 
# 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: T0320TS102_2-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS102_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   73   5.0   21   2.63    9.52  21.775
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS102_2-D2
PFRMAT TS
TARGET T0320
MODEL 2
PARENT 1vdx_A
ATOM    629  N   ASN   229       7.006   5.544   4.910  1.00  1.00
ATOM    630  CA  ASN   229       7.217   4.165   4.495  1.00  1.00
ATOM    631  C   ASN   229       5.881   3.428   4.475  1.00  1.00
ATOM    632  O   ASN   229       5.687   2.518   3.680  1.00  1.00
ATOM    633  CB  ASN   229       8.219   3.486   5.427  1.00  1.00
ATOM    634  N   SER   230       4.974   3.849   5.356  1.00  1.00
ATOM    635  CA  SER   230       3.615   3.317   5.464  1.00  1.00
ATOM    636  C   SER   230       2.868   4.076   6.562  1.00  1.00
ATOM    637  O   SER   230       3.459   4.478   7.551  1.00  1.00
ATOM    638  CB  SER   230       3.613   1.791   5.732  1.00  1.00
ATOM    639  N   LEU   231       1.572   4.280   6.357  1.00  1.00
ATOM    640  CA  LEU   231       0.710   4.997   7.294  1.00  1.00
ATOM    641  C   LEU   231       0.144   4.071   8.375  1.00  1.00
ATOM    642  O   LEU   231      -0.217   2.932   8.098  1.00  1.00
ATOM    643  CB  LEU   231      -0.484   5.652   6.547  1.00  1.00
ATOM    644  N   PRO   232       0.067   4.570   9.603  1.00  1.00
ATOM    645  CA  PRO   232      -0.462   3.798  10.723  1.00  1.00
ATOM    646  C   PRO   232      -1.901   4.222  10.989  1.00  1.00
ATOM    647  O   PRO   232      -2.820   3.402  10.963  1.00  1.00
ATOM    648  CB  PRO   232       0.384   4.038  11.972  1.00  1.00
ATOM    649  N   ASN   233      -2.085   5.512  11.240  1.00  1.00
ATOM    650  CA  ASN   233      -3.401   6.082  11.497  1.00  1.00
ATOM    651  C   ASN   233      -3.614   7.258  10.546  1.00  1.00
ATOM    652  O   ASN   233      -3.125   8.366  10.790  1.00  1.00
ATOM    653  CB  ASN   233      -3.488   6.542  12.955  1.00  1.00
ATOM    654  N   PRO   234      -4.332   7.008   9.458  1.00  1.00
ATOM    655  CA  PRO   234      -4.589   8.041   8.468  1.00  1.00
ATOM    656  C   PRO   234      -5.267   9.299   9.021  1.00  1.00
ATOM    657  O   PRO   234      -4.826  10.410   8.723  1.00  1.00
ATOM    658  CB  PRO   234      -5.411   7.463   7.315  1.00  1.00
ATOM    659  N   HIS   235      -6.339   9.146   9.802  1.00  1.00
ATOM    660  CA  HIS   235      -7.016  10.319  10.363  1.00  1.00
ATOM    661  C   HIS   235      -6.003  11.167  11.133  1.00  1.00
ATOM    662  O   HIS   235      -5.987  12.397  11.023  1.00  1.00
ATOM    663  CB  HIS   235      -8.156   9.907  11.304  1.00  1.00
ATOM    664  N   LEU   236      -5.156  10.495  11.907  1.00  1.00
ATOM    665  CA  LEU   236      -4.142  11.186  12.688  1.00  1.00
ATOM    666  C   LEU   236      -3.132  11.977  11.866  1.00  1.00
ATOM    667  O   LEU   236      -2.897  13.168  12.136  1.00  1.00
ATOM    668  CB  LEU   236      -3.360  10.117  13.474  1.00  1.00
ATOM    669  N   ILE   251      -2.523  11.318  10.878  1.00  1.00
ATOM    670  CA  ILE   251      -1.528  11.965  10.022  1.00  1.00
ATOM    671  C   ILE   251      -2.121  13.190   9.349  1.00  1.00
ATOM    672  O   ILE   251      -1.620  14.302   9.487  1.00  1.00
ATOM    673  CB  ILE   251      -1.030  11.006   8.937  1.00  1.00
ATOM    674  N   ILE   252      -3.195  12.958   8.612  1.00  1.00
ATOM    675  CA  ILE   252      -3.907  14.003   7.894  1.00  1.00
ATOM    676  C   ILE   252      -4.274  15.203   8.789  1.00  1.00
ATOM    677  O   ILE   252      -4.152  16.341   8.365  1.00  1.00
ATOM    678  CB  ILE   252      -5.184  13.412   7.241  1.00  1.00
ATOM    679  N   HIS   253      -4.713  14.958  10.019  1.00  1.00
ATOM    680  CA  HIS   253      -5.062  16.052  10.926  1.00  1.00
ATOM    681  C   HIS   253      -3.788  16.701  11.449  1.00  1.00
ATOM    682  O   HIS   253      -3.716  17.914  11.628  1.00  1.00
ATOM    683  CB  HIS   253      -5.885  15.535  12.108  1.00  1.00
ATOM    684  N   ALA   254      -2.774  15.885  11.708  1.00  1.00
ATOM    685  CA  ALA   254      -1.503  16.415  12.189  1.00  1.00
ATOM    686  C   ALA   254      -0.910  17.342  11.110  1.00  1.00
ATOM    687  O   ALA   254      -0.509  18.474  11.391  1.00  1.00
ATOM    688  CB  ALA   254      -0.529  15.268  12.477  1.00  1.00
ATOM    689  N   PHE   255      -0.874  16.858   9.872  1.00  1.00
ATOM    690  CA  PHE   255      -0.319  17.632   8.774  1.00  1.00
ATOM    691  C   PHE   255      -1.140  18.864   8.439  1.00  1.00
ATOM    692  O   PHE   255      -0.586  19.899   8.077  1.00  1.00
ATOM    693  CB  PHE   255      -0.178  16.761   7.522  1.00  1.00
ATOM    694  N   GLY   256      -2.458  18.753   8.539  1.00  1.00
ATOM    695  CA  GLY   256      -3.304  19.892   8.241  1.00  1.00
ATOM    696  C   GLY   256      -3.086  21.007   9.244  1.00  1.00
ATOM    697  O   GLY   256      -3.244  22.177   8.910  1.00  1.00
ATOM    698  N   ALA   266      -2.700  20.667  10.468  1.00  1.00
ATOM    699  CA  ALA   266      -2.485  21.714  11.456  1.00  1.00
ATOM    700  C   ALA   266      -1.197  22.477  11.148  1.00  1.00
ATOM    701  O   ALA   266      -0.907  23.505  11.759  1.00  1.00
ATOM    702  CB  ALA   266      -2.443  21.129  12.870  1.00  1.00
ATOM    703  N   ILE   267      -0.443  21.979  10.174  1.00  1.00
ATOM    704  CA  ILE   267       0.808  22.614   9.765  1.00  1.00
ATOM    705  C   ILE   267       0.701  23.175   8.347  1.00  1.00
ATOM    706  O   ILE   267       1.695  23.636   7.786  1.00  1.00
ATOM    707  CB  ILE   267       1.956  21.595   9.833  1.00  1.00
ATOM    708  N   ASN   268      -0.505  23.158   7.782  1.00  1.00
ATOM    709  CA  ASN   268      -0.715  23.631   6.417  1.00  1.00
ATOM    710  C   ASN   268      -0.069  24.974   6.062  1.00  1.00
ATOM    711  O   ASN   268       0.621  25.081   5.056  1.00  1.00
ATOM    712  CB  ASN   268      -2.211  23.679   6.111  1.00  1.00
ATOM    713  N   THR   269      -0.270  25.988   6.891  1.00  1.00
ATOM    714  CA  THR   269       0.266  27.313   6.609  1.00  1.00
ATOM    715  C   THR   269       1.418  27.772   7.498  1.00  1.00
ATOM    716  O   THR   269       1.777  28.950   7.485  1.00  1.00
ATOM    717  CB  THR   269      -0.872  28.339   6.697  1.00  1.00
ATOM    718  N   SER   270       1.996  26.855   8.267  1.00  1.00
ATOM    719  CA  SER   270       3.100  27.201   9.158  1.00  1.00
ATOM    720  C   SER   270       4.193  28.024   8.502  1.00  1.00
ATOM    721  O   SER   270       4.635  27.718   7.395  1.00  1.00
ATOM    722  CB  SER   270       3.752  25.943   9.740  1.00  1.00
ATOM    723  N   PRO   271       4.625  29.070   9.198  1.00  1.00
ATOM    724  CA  PRO   271       5.715  29.926   8.737  1.00  1.00
ATOM    725  C   PRO   271       6.914  29.470   9.568  1.00  1.00
ATOM    726  O   PRO   271       6.993  29.745  10.761  1.00  1.00
ATOM    727  CB  PRO   271       5.393  31.400   9.002  1.00  1.00
ATOM    728  N   ILE   272       7.839  28.756   8.942  1.00  1.00
ATOM    729  CA  ILE   272       8.996  28.224   9.659  1.00  1.00
ATOM    730  C   ILE   272      10.180  29.171   9.730  1.00  1.00
ATOM    731  O   ILE   272      11.126  28.939  10.474  1.00  1.00
ATOM    732  CB  ILE   272       9.432  26.912   9.013  1.00  1.00
ATOM    733  N   GLY   290      10.115  30.247   8.963  1.00  1.00
ATOM    734  CA  GLY   290      11.202  31.196   8.958  1.00  1.00
ATOM    735  C   GLY   290      11.681  31.466   7.547  1.00  1.00
ATOM    736  O   GLY   290      11.086  31.039   6.557  1.00  1.00
ATOM    737  N   TRP   291      12.778  32.190   7.451  1.00  1.00
ATOM    738  CA  TRP   291      13.320  32.511   6.158  1.00  1.00
ATOM    739  C   TRP   291      14.828  32.453   6.229  1.00  1.00
ATOM    740  O   TRP   291      15.412  32.461   7.314  1.00  1.00
ATOM    741  CB  TRP   291      12.852  33.904   5.741  1.00  1.00
ATOM    742  N   TYR   292      15.446  32.356   5.060  1.00  1.00
ATOM    743  CA  TYR   292      16.898  32.324   4.935  1.00  1.00
ATOM    744  C   TYR   292      17.211  33.085   3.663  1.00  1.00
ATOM    745  O   TYR   292      16.301  33.474   2.936  1.00  1.00
ATOM    746  CB  TYR   292      17.444  30.884   4.844  1.00  1.00
ATOM    747  N   LEU   293      18.489  33.307   3.394  1.00  1.00
ATOM    748  CA  LEU   293      18.895  34.020   2.195  1.00  1.00
ATOM    749  C   LEU   293      19.454  33.080   1.120  1.00  1.00
ATOM    750  O   LEU   293      20.477  32.425   1.328  1.00  1.00
ATOM    751  CB  LEU   293      19.969  35.068   2.524  1.00  1.00
ATOM    752  N   VAL   294      18.776  33.000  -0.022  1.00  1.00
ATOM    753  CA  VAL   294      19.271  32.171  -1.115  1.00  1.00
ATOM    754  C   VAL   294      20.525  32.903  -1.578  1.00  1.00
ATOM    755  O   VAL   294      20.438  33.964  -2.198  1.00  1.00
ATOM    756  CB  VAL   294      18.260  32.109  -2.255  1.00  1.00
ATOM    757  N   ASP   295      21.696  32.358  -1.262  1.00  1.00
ATOM    758  CA  ASP   295      22.924  33.042  -1.629  1.00  1.00
ATOM    759  C   ASP   295      23.899  32.235  -2.452  1.00  1.00
ATOM    760  O   ASP   295      24.886  32.768  -2.947  1.00  1.00
ATOM    761  CB  ASP   295      23.634  33.545  -0.371  1.00  1.00
ATOM    762  N   ASP   296      23.631  30.949  -2.606  1.00  1.00
ATOM    763  CA  ASP   296      24.535  30.114  -3.375  1.00  1.00
ATOM    764  C   ASP   296      23.825  28.906  -3.977  1.00  1.00
ATOM    765  O   ASP   296      22.710  28.551  -3.581  1.00  1.00
ATOM    766  CB  ASP   296      25.712  29.650  -2.488  1.00  1.00
ATOM    767  N   THR   297      24.487  28.293  -4.943  1.00  1.00
ATOM    768  CA  THR   297      23.976  27.119  -5.605  1.00  1.00
ATOM    769  C   THR   297      25.089  26.065  -5.426  1.00  1.00
ATOM    770  O   THR   297      26.273  26.377  -5.596  1.00  1.00
ATOM    771  CB  THR   297      23.705  27.429  -7.103  1.00  1.00
ATOM    772  N   LEU   298      24.738  24.849  -5.034  1.00  1.00
ATOM    773  CA  LEU   298      25.760  23.840  -4.819  1.00  1.00
ATOM    774  C   LEU   298      25.569  22.568  -5.619  1.00  1.00
ATOM    775  O   LEU   298      24.453  22.101  -5.832  1.00  1.00
ATOM    776  CB  LEU   298      25.828  23.485  -3.330  1.00  1.00
ATOM    777  N   GLU   299      26.685  22.017  -6.070  1.00  1.00
ATOM    778  CA  GLU   299      26.678  20.753  -6.780  1.00  1.00
ATOM    779  C   GLU   299      27.081  19.773  -5.699  1.00  1.00
ATOM    780  O   GLU   299      28.116  19.950  -5.063  1.00  1.00
ATOM    781  CB  GLU   299      27.724  20.729  -7.891  1.00  1.00
ATOM    782  N   ARG   300      26.267  18.751  -5.468  1.00  1.00
ATOM    783  CA  ARG   300      26.589  17.794  -4.426  1.00  1.00
ATOM    784  C   ARG   300      26.632  16.322  -4.819  1.00  1.00
ATOM    785  O   ARG   300      25.981  15.872  -5.769  1.00  1.00
ATOM    786  CB  ARG   300      25.632  17.964  -3.247  1.00  1.00
ATOM    787  N   ALA   301      27.412  15.581  -4.046  1.00  1.00
ATOM    788  CA  ALA   301      27.595  14.152  -4.229  1.00  1.00
ATOM    789  C   ALA   301      26.944  13.459  -3.043  1.00  1.00
ATOM    790  O   ALA   301      27.178  13.847  -1.894  1.00  1.00
ATOM    791  CB  ALA   301      29.088  13.836  -4.251  1.00  1.00
ATOM    792  N   GLY   302      26.125  12.451  -3.320  1.00  1.00
ATOM    793  CA  GLY   302      25.463  11.703  -2.264  1.00  1.00
ATOM    794  C   GLY   302      26.025  10.290  -2.210  1.00  1.00
ATOM    795  O   GLY   302      26.255   9.661  -3.242  1.00  1.00
ATOM    796  N   ARG   303      26.274   9.813  -0.997  1.00  1.00
ATOM    797  CA  ARG   303      26.783   8.463  -0.782  1.00  1.00
ATOM    798  C   ARG   303      25.813   7.784   0.165  1.00  1.00
ATOM    799  O   ARG   303      25.586   8.256   1.275  1.00  1.00
ATOM    800  CB  ARG   303      28.186   8.456  -0.134  1.00  1.00
ATOM    801  N   ILE   304      25.236   6.674  -0.280  1.00  1.00
ATOM    802  CA  ILE   304      24.276   5.930   0.527  1.00  1.00
ATOM    803  C   ILE   304      24.980   4.981   1.491  1.00  1.00
ATOM    804  O   ILE   304      25.789   4.148   1.089  1.00  1.00
ATOM    805  CB  ILE   304      23.312   5.170  -0.389  1.00  1.00
TER
END
