
#######################################################
#                                                     #
#                        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  144 (  144),  selected  144 , name T0310TS393_3-D2
# Molecule2: number of CA atoms  144 ( 1137),  selected  144 , name T0310_D2.pdb
# PARAMETERS: T0310TS393_3-D2.T0310_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E     216      E     216          5.690
LGA    G     217      G     217          1.476
LGA    I     218      I     218          2.756
LGA    C     219      C     219          2.950
LGA    H     220      H     220          0.940
LGA    M     221      M     221          1.392
LGA    Y     222      Y     222          2.427
LGA    V     223      V     223          1.020
LGA    D     224      D     224          1.080
LGA    S     225      S     225          3.925
LGA    E     226      E     226          0.742
LGA    A     227      A     227          0.474
LGA    S     228      S     228          0.574
LGA    V     229      V     229          1.413
LGA    D     230      D     230          2.193
LGA    K     231      K     231          0.686
LGA    V     232      V     232          1.268
LGA    T     233      T     233          1.348
LGA    R     234      R     234          1.245
LGA    L     235      L     235          1.154
LGA    V     236      V     236          1.039
LGA    R     237      R     237          0.727
LGA    D     238      D     238          1.158
LGA    S     239      S     239          1.962
LGA    K     240      K     240          1.876
LGA    C     241      C     241          1.535
LGA    E     242      E     242          2.840
LGA    Y     243      Y     243          1.326
LGA    P     244      P     244           #
LGA    A     245      A     245          1.147
LGA    A     246      A     246          1.938
LGA    C     247      C     247          4.909
LGA    N     248      N     248          1.149
LGA    A     249      A     249          1.594
LGA    L     250      L     250          3.984
LGA    E     251      E     251          2.093
LGA    T     252      T     252          2.040
LGA    L     253      L     253          3.396
LGA    L     254      L     254          2.341
LGA    I     255      I     255           #
LGA    H     256      -       -           -
LGA    R     257      H     256           #
LGA    D     258      R     257          0.660
LGA    L     259      D     258          3.853
LGA    L     260      L     259          3.549
LGA    R     261      L     260          1.356
LGA    T     262      R     261          4.449
LGA    P     263      T     262          2.261
LGA    -       -      P     263           -
LGA    L     264      L     264          3.306
LGA    F     265      F     265          3.319
LGA    D     266      D     266          2.156
LGA    Q     267      Q     267          2.045
LGA    I     268      I     268          2.448
LGA    I     269      I     269          1.987
LGA    D     270      D     270          1.884
LGA    M     271      M     271          2.235
LGA    L     272      L     272          1.915
LGA    R     273      R     273          1.484
LGA    V     274      V     274          2.248
LGA    E     275      E     275          2.732
LGA    Q     276      Q     276          2.246
LGA    -       -      V     277           -
LGA    V     277      K     278          2.891
LGA    K     278      I     279          2.319
LGA    I     279      H     280          5.113
LGA    H     280      A     281          5.877
LGA    A     281      G     282           -
LGA    G     282      P     283           -
LGA    P     283      -       -           -
LGA    K     284      K     284          4.756
LGA    F     285      F     285           #
LGA    A     286      A     286          3.540
LGA    -       -      S     287           -
LGA    -       -      Y     288           -
LGA    S     287      L     289          4.429
LGA    Y     288      T     290           -
LGA    L     289      F     291           #
LGA    T     290      -       -           -
LGA    F     291      -       -           -
LGA    V     292      V     292          3.030
LGA    K     293      -       -           -
LGA    S     294      -       -           -
LGA    L     295      K     293          6.359
LGA    R     296      -       -           -
LGA    T     297      -       -           -
LGA    E     298      -       -           -
LGA    Y     299      -       -           -
LGA    G     300      -       -           -
LGA    D     301      S     294           #
LGA    -       -      L     295           -
LGA    -       -      R     296           -
LGA    -       -      T     297           -
LGA    -       -      E     298           -
LGA    -       -      Y     299           -
LGA    -       -      G     300           -
LGA    L     302      D     301          3.771
LGA    -       -      L     302           -
LGA    E     303      E     303          2.848
LGA    L     304      L     304          1.557
LGA    C     305      C     305          1.927
LGA    I     306      I     306          1.775
LGA    E     307      E     307          2.422
LGA    V     308      V     308          3.440
LGA    V     309      V     309          2.622
LGA    D     310      D     310          2.829
LGA    N     311      N     311          2.589
LGA    V     312      V     312          1.332
LGA    Q     313      Q     313          1.290
LGA    D     314      D     314          1.315
LGA    A     315      A     315          1.288
LGA    I     316      I     316          1.244
LGA    D     317      D     317          1.248
LGA    H     318      H     318          1.391
LGA    I     319      I     319          1.350
LGA    H     320      H     320          1.273
LGA    K     321      K     321          1.487
LGA    Y     322      Y     322          2.810
LGA    G     323      G     323          4.073
LGA    S     324      S     324          3.111
LGA    S     325      S     325          1.096
LGA    H     326      H     326          0.940
LGA    T     327      T     327          0.512
LGA    D     328      D     328          3.408
LGA    V     329      V     329          0.393
LGA    I     330      I     330          1.407
LGA    V     331      V     331          2.016
LGA    T     332      T     332          2.704
LGA    E     333      E     333          0.895
LGA    D     334      D     334          2.776
LGA    E     335      E     335          1.944
LGA    N     336      N     336          2.109
LGA    T     337      T     337          1.830
LGA    A     338      A     338          1.747
LGA    E     339      E     339          2.167
LGA    F     340      F     340          2.037
LGA    F     341      F     341          1.455
LGA    L     342      L     342          2.142
LGA    Q     343      Q     343          2.497
LGA    H     344      H     344          1.630
LGA    V     345      V     345          1.235
LGA    D     346      D     346          1.081
LGA    S     347      S     347          1.756
LGA    A     348      A     348          1.720
LGA    C     349      C     349          1.903
LGA    V     350      V     350          2.079
LGA    F     351      F     351          1.591
LGA    W     352      W     352          2.204
LGA    N     353      N     353          0.811
LGA    A     354      A     354          0.944
LGA    S     355      S     355          1.189
LGA    T     356      T     356          1.689
LGA    R     357      R     357          0.671
LGA    F     358      F     358          0.795
LGA    S     359      S     359          0.743

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  144  144    5.0    124    2.42    90.32     57.968     4.928

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.515104 * X  +   0.856630 * Y  +  -0.029199 * Z  + 136.462006
  Y_new =  -0.508575 * X  +   0.332880 * Y  +   0.794067 * Z  +   5.504237
  Z_new =   0.689941 * X  +  -0.394177 * Y  +   0.607129 * Z  +  22.309130 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.575846    2.565746  [ DEG:   -32.9936    147.0064 ]
  Theta =  -0.761408   -2.380185  [ DEG:   -43.6255   -136.3745 ]
  Phi   =  -0.779021    2.362572  [ DEG:   -44.6346    135.3654 ]
 
# 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: T0310TS393_3-D2                               
REMARK     2: T0310_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0310TS393_3-D2.T0310_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  144  144   5.0  124   2.42   90.32  57.968
REMARK  ---------------------------------------------------------- 
MOLECULE T0310TS393_3-D2
PFRMAT TS
TARGET T0310
MODEL 3
PARENT N/A
ATOM    216  CA  GLU   216     140.983   9.495  19.125  1.00 25.00           C
ATOM    217  CA  GLY   217     138.517  12.032  20.525  1.00 25.00           C
ATOM    218  CA  ILE   218     136.683  15.173  21.530  1.00 25.00           C
ATOM    219  CA  CYS   219     135.267  18.530  22.455  1.00 25.00           C
ATOM    220  CA  HIS   220     137.401  20.881  24.636  1.00 25.00           C
ATOM    221  CA  MET   221     140.503  22.101  26.381  1.00 25.00           C
ATOM    222  CA  TYR   222     139.858  25.795  26.991  1.00 25.00           C
ATOM    223  CA  VAL   223     139.986  28.912  29.193  1.00 25.00           C
ATOM    224  CA  ASP   224     137.542  31.004  31.094  1.00 25.00           C
ATOM    225  CA  SER   225     136.504  30.908  34.726  1.00 25.00           C
ATOM    226  CA  GLU   226     139.100  32.965  36.553  1.00 25.00           C
ATOM    227  CA  ALA   227     141.471  30.366  35.025  1.00 25.00           C
ATOM    228  CA  SER   228     144.077  30.066  37.764  1.00 25.00           C
ATOM    229  CA  VAL   229     146.521  30.440  34.874  1.00 25.00           C
ATOM    230  CA  ASP   230     149.318  27.913  35.552  1.00 25.00           C
ATOM    231  CA  LYS   231     146.737  25.099  35.842  1.00 25.00           C
ATOM    232  CA  VAL   232     145.149  26.180  32.529  1.00 25.00           C
ATOM    233  CA  THR   233     148.593  26.195  30.855  1.00 25.00           C
ATOM    234  CA  ARG   234     149.297  22.685  32.215  1.00 25.00           C
ATOM    235  CA  LEU   235     145.921  21.464  30.882  1.00 25.00           C
ATOM    236  CA  VAL   236     146.702  22.975  27.450  1.00 25.00           C
ATOM    237  CA  ARG   237     150.119  21.247  27.440  1.00 25.00           C
ATOM    238  CA  ASP   238     148.463  17.913  28.341  1.00 25.00           C
ATOM    239  CA  SER   239     145.933  18.375  25.504  1.00 25.00           C
ATOM    240  CA  LYS   240     148.780  19.124  23.054  1.00 25.00           C
ATOM    241  CA  CYS   241     152.144  17.476  23.200  1.00 25.00           C
ATOM    242  CA  GLU   242     150.775  13.992  23.521  1.00 25.00           C
ATOM    243  CA  TYR   243     150.296  10.229  23.759  1.00 25.00           C
ATOM    244  CA  PRO   244     151.279   8.918  20.329  1.00 25.00           C
ATOM    245  CA  ALA   245     148.219  10.689  18.898  1.00 25.00           C
ATOM    246  CA  ALA   246     146.234   8.150  20.810  1.00 25.00           C
ATOM    247  CA  CYS   247     145.071  10.105  23.847  1.00 25.00           C
ATOM    248  CA  ASN   248     141.351  10.834  24.469  1.00 25.00           C
ATOM    249  CA  ALA   249     142.202  14.282  22.988  1.00 25.00           C
ATOM    250  CA  LEU   250     141.532  15.991  19.658  1.00 25.00           C
ATOM    251  CA  GLU   251     142.028  19.222  21.595  1.00 25.00           C
ATOM    252  CA  THR   252     139.022  20.758  19.908  1.00 25.00           C
ATOM    253  CA  LEU   253     138.440  24.336  21.031  1.00 25.00           C
ATOM    254  CA  LEU   254     136.313  26.846  22.938  1.00 25.00           C
ATOM    255  CA  ILE   255     134.995  29.450  20.519  1.00 25.00           C
ATOM    256  CA  HIS   256     136.549  32.910  20.402  1.00 25.00           C
ATOM    257  CA  ARG   257     138.652  35.350  22.506  1.00 25.00           C
ATOM    258  CA  ASP   258     138.031  37.560  25.570  1.00 25.00           C
ATOM    259  CA  LEU   259     139.720  34.960  27.819  1.00 25.00           C
ATOM    260  CA  LEU   260     142.726  34.829  25.450  1.00 25.00           C
ATOM    261  CA  ARG   261     142.965  38.651  25.502  1.00 25.00           C
ATOM    262  CA  THR   262     142.847  38.631  29.331  1.00 25.00           C
ATOM    263  CA  PRO   263     145.888  36.349  29.441  1.00 25.00           C
ATOM    264  CA  LEU   264     147.593  33.302  27.906  1.00 25.00           C
ATOM    265  CA  PHE   265     147.971  33.439  24.097  1.00 25.00           C
ATOM    266  CA  ASP   266     151.775  33.698  24.460  1.00 25.00           C
ATOM    267  CA  GLN   267     151.780  30.686  26.825  1.00 25.00           C
ATOM    268  CA  ILE   268     149.678  28.687  24.324  1.00 25.00           C
ATOM    269  CA  ILE   269     152.106  29.608  21.510  1.00 25.00           C
ATOM    270  CA  ASP   270     155.068  28.501  23.670  1.00 25.00           C
ATOM    271  CA  MET   271     153.314  25.179  24.416  1.00 25.00           C
ATOM    272  CA  LEU   272     152.664  24.654  20.678  1.00 25.00           C
ATOM    273  CA  ARG   273     156.348  25.373  19.912  1.00 25.00           C
ATOM    274  CA  VAL   274     157.421  22.862  22.599  1.00 25.00           C
ATOM    275  CA  GLU   275     156.119  20.408  20.029  1.00 25.00           C
ATOM    276  CA  GLN   276     154.947  21.725  16.628  1.00 25.00           C
ATOM    277  CA  VAL   277     153.496  25.142  15.798  1.00 25.00           C
ATOM    278  CA  LYS   278     150.279  26.995  16.579  1.00 25.00           C
ATOM    279  CA  ILE   279     147.252  28.829  17.790  1.00 25.00           C
ATOM    280  CA  HIS   280     146.188  32.276  18.951  1.00 25.00           C
ATOM    281  CA  ALA   281     146.408  36.021  19.302  1.00 25.00           C
ATOM    282  CA  GLY   282     144.786  39.367  18.251  1.00 25.00           C
ATOM    283  CA  PRO   283     141.541  41.182  17.612  1.00 25.00           C
ATOM    284  CA  LYS   284     139.362  38.034  17.673  1.00 25.00           C
ATOM    285  CA  PHE   285     138.891  38.256  13.879  1.00 25.00           C
ATOM    286  CA  ALA   286     142.674  38.620  13.407  1.00 25.00           C
ATOM    287  CA  SER   287     143.271  35.563  15.636  1.00 25.00           C
ATOM    288  CA  TYR   288     140.721  33.553  13.605  1.00 25.00           C
ATOM    289  CA  LEU   289     142.451  34.601  10.352  1.00 25.00           C
ATOM    290  CA  THR   290     145.840  33.539  11.783  1.00 25.00           C
ATOM    291  CA  PHE   291     144.374  30.152  12.810  1.00 25.00           C
ATOM    292  CA  VAL   292     142.933  29.682   9.292  1.00 25.00           C
ATOM    293  CA  LYS   293     146.340  30.524   7.759  1.00 25.00           C
ATOM    294  CA  SER   294     148.037  27.994  10.079  1.00 25.00           C
ATOM    295  CA  LEU   295     145.481  25.324   9.079  1.00 25.00           C
ATOM    296  CA  ARG   296     146.113  26.073   5.375  1.00 25.00           C
ATOM    297  CA  THR   297     149.889  25.776   5.934  1.00 25.00           C
ATOM    298  CA  GLU   298     149.387  22.421   7.713  1.00 25.00           C
ATOM    299  CA  TYR   299     147.225  21.176   4.808  1.00 25.00           C
ATOM    300  CA  GLY   300     144.889  19.775   7.383  1.00 25.00           C
ATOM    301  CA  ASP   301     144.817  17.713  10.632  1.00 25.00           C
ATOM    302  CA  LEU   302     146.770  16.973  13.828  1.00 25.00           C
ATOM    303  CA  GLU   303     145.499  19.813  16.087  1.00 25.00           C
ATOM    304  CA  LEU   304     144.137  22.969  17.614  1.00 25.00           C
ATOM    305  CA  CYS   305     141.077  24.306  15.889  1.00 25.00           C
ATOM    306  CA  ILE   306     141.188  27.489  18.043  1.00 25.00           C
ATOM    307  CA  GLU   307     140.652  29.637  21.147  1.00 25.00           C
ATOM    308  CA  VAL   308     139.198  31.110  24.339  1.00 25.00           C
ATOM    309  CA  VAL   309     135.696  32.081  25.411  1.00 25.00           C
ATOM    310  CA  ASP   310     133.440  34.384  27.440  1.00 25.00           C
ATOM    311  CA  ASN   311     131.025  34.031  30.302  1.00 25.00           C
ATOM    312  CA  VAL   312     131.121  30.286  30.415  1.00 25.00           C
ATOM    313  CA  GLN   313     127.877  29.997  28.402  1.00 25.00           C
ATOM    314  CA  ASP   314     129.786  30.748  25.169  1.00 25.00           C
ATOM    315  CA  ALA   315     132.380  28.071  26.051  1.00 25.00           C
ATOM    316  CA  ILE   316     129.580  25.546  26.723  1.00 25.00           C
ATOM    317  CA  ASP   317     127.971  26.395  23.353  1.00 25.00           C
ATOM    318  CA  HIS   318     131.341  25.921  21.597  1.00 25.00           C
ATOM    319  CA  ILE   319     131.792  22.532  23.323  1.00 25.00           C
ATOM    320  CA  HIS   320     128.276  21.478  22.226  1.00 25.00           C
ATOM    321  CA  LYS   321     129.058  22.529  18.627  1.00 25.00           C
ATOM    322  CA  TYR   322     130.327  18.955  18.817  1.00 25.00           C
ATOM    323  CA  GLY   323     130.252  15.565  17.000  1.00 25.00           C
ATOM    324  CA  SER   324     129.175  13.371  19.893  1.00 25.00           C
ATOM    325  CA  SER   325     131.054  13.032  23.195  1.00 25.00           C
ATOM    326  CA  HIS   326     134.398  11.787  24.507  1.00 25.00           C
ATOM    327  CA  THR   327     136.127  14.309  26.771  1.00 25.00           C
ATOM    328  CA  ASP   328     138.147  16.606  28.940  1.00 25.00           C
ATOM    329  CA  VAL   329     136.820  20.089  29.724  1.00 25.00           C
ATOM    330  CA  ILE   330     136.192  23.777  30.632  1.00 25.00           C
ATOM    331  CA  VAL   331     137.772  25.705  33.448  1.00 25.00           C
ATOM    332  CA  THR   332     135.906  26.639  36.605  1.00 25.00           C
ATOM    333  CA  GLU   333     138.297  27.743  39.346  1.00 25.00           C
ATOM    334  CA  ASP   334     135.278  27.285  41.574  1.00 25.00           C
ATOM    335  CA  GLU   335     131.930  27.292  39.921  1.00 25.00           C
ATOM    336  CA  ASN   336     128.635  28.580  38.455  1.00 25.00           C
ATOM    337  CA  THR   337     130.078  28.320  34.917  1.00 25.00           C
ATOM    338  CA  ALA   338     131.221  24.733  35.621  1.00 25.00           C
ATOM    339  CA  GLU   339     127.730  23.849  36.923  1.00 25.00           C
ATOM    340  CA  PHE   340     126.149  25.354  33.776  1.00 25.00           C
ATOM    341  CA  PHE   341     128.539  23.325  31.576  1.00 25.00           C
ATOM    342  CA  LEU   342     127.639  20.136  33.497  1.00 25.00           C
ATOM    343  CA  GLN   343     123.911  20.883  33.040  1.00 25.00           C
ATOM    344  CA  HIS   344     124.454  21.423  29.287  1.00 25.00           C
ATOM    345  CA  VAL   345     127.063  19.055  27.933  1.00 25.00           C
ATOM    346  CA  ASP   346     126.707  15.363  27.086  1.00 25.00           C
ATOM    347  CA  SER   347     130.363  14.934  28.130  1.00 25.00           C
ATOM    348  CA  ALA   348     131.301  11.365  29.216  1.00 25.00           C
ATOM    349  CA  CYS   349     134.663  11.903  30.908  1.00 25.00           C
ATOM    350  CA  VAL   350     134.246  15.081  32.961  1.00 25.00           C
ATOM    351  CA  PHE   351     135.572  18.293  34.495  1.00 25.00           C
ATOM    352  CA  TRP   352     137.047  19.361  37.858  1.00 25.00           C
ATOM    353  CA  ASN   353     140.066  21.250  36.609  1.00 25.00           C
ATOM    354  CA  ALA   354     141.583  18.382  34.644  1.00 25.00           C
ATOM    355  CA  SER   355     144.258  16.731  32.493  1.00 25.00           C
ATOM    356  CA  THR   356     142.751  16.121  29.013  1.00 25.00           C
ATOM    357  CA  ARG   357     144.073  12.562  28.512  1.00 25.00           C
ATOM    358  CA  PHE   358     142.312  11.431  31.720  1.00 25.00           C
ATOM    359  CA  SER   359     139.222   9.544  30.685  1.00 25.00           C
TER
END
