
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms  144 ( 1137),  selected  144 , name T0310_D2.pdb
# PARAMETERS: T0310TS393_2-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          2.716
LGA    G     217      G     217          2.509
LGA    I     218      I     218          1.392
LGA    C     219      C     219          0.937
LGA    H     220      H     220          2.158
LGA    M     221      M     221          3.133
LGA    Y     222      Y     222          3.350
LGA    V     223      V     223          0.823
LGA    D     224      D     224          0.557
LGA    S     225      S     225          1.594
LGA    E     226      E     226          1.282
LGA    A     227      A     227          1.811
LGA    S     228      S     228          1.176
LGA    V     229      V     229          2.559
LGA    D     230      D     230          3.488
LGA    K     231      K     231          0.844
LGA    V     232      V     232          1.381
LGA    T     233      T     233          2.215
LGA    R     234      R     234          1.897
LGA    L     235      L     235          0.449
LGA    V     236      V     236          0.520
LGA    R     237      R     237          1.239
LGA    D     238      D     238          1.348
LGA    S     239      S     239          1.062
LGA    K     240      K     240          1.342
LGA    C     241      C     241          2.005
LGA    E     242      E     242          1.275
LGA    Y     243      Y     243          1.056
LGA    P     244      P     244          3.618
LGA    A     245      A     245          0.630
LGA    A     246      A     246          3.276
LGA    C     247      C     247          4.227
LGA    N     248      N     248          2.840
LGA    A     249      A     249          2.923
LGA    L     250      L     250          2.619
LGA    E     251      E     251          2.421
LGA    T     252      T     252          3.725
LGA    L     253      L     253          1.548
LGA    L     254      L     254          1.942
LGA    I     255      I     255          2.699
LGA    H     256      H     256          1.841
LGA    R     257      R     257          1.902
LGA    D     258      D     258          2.500
LGA    L     259      L     259          2.444
LGA    L     260      L     260          2.196
LGA    R     261      R     261          3.508
LGA    T     262      T     262          2.583
LGA    P     263      P     263          2.330
LGA    -       -      L     264           -
LGA    L     264      F     265          0.611
LGA    F     265      D     266          0.940
LGA    D     266      Q     267          1.259
LGA    Q     267      I     268          1.187
LGA    I     268      I     269          1.657
LGA    I     269      D     270          1.914
LGA    D     270      M     271          2.279
LGA    M     271      L     272          2.683
LGA    L     272      R     273          2.931
LGA    R     273      V     274          3.349
LGA    -       -      E     275           -
LGA    V     274      Q     276          2.436
LGA    E     275      V     277          3.897
LGA    Q     276      K     278          2.667
LGA    V     277      I     279          2.425
LGA    K     278      H     280          4.639
LGA    I     279      A     281          4.343
LGA    H     280      G     282           -
LGA    -       -      P     283           -
LGA    -       -      K     284           -
LGA    A     281      F     285           #
LGA    G     282      A     286           -
LGA    P     283      S     287           -
LGA    K     284      -       -           -
LGA    F     285      -       -           -
LGA    A     286      Y     288          1.290
LGA    S     287      -       -           -
LGA    Y     288      -       -           -
LGA    L     289      -       -           -
LGA    T     290      L     289          4.146
LGA    F     291      T     290           -
LGA    V     292      -       -           -
LGA    K     293      -       -           -
LGA    S     294      F     291           #
LGA    L     295      V     292          2.522
LGA    R     296      -       -           -
LGA    T     297      -       -           -
LGA    E     298      -       -           -
LGA    Y     299      -       -           -
LGA    G     300      K     293          3.128
LGA    D     301      S     294          6.038
LGA    -       -      L     295           -
LGA    -       -      R     296           -
LGA    -       -      T     297           -
LGA    L     302      E     298           #
LGA    -       -      Y     299           -
LGA    -       -      G     300           -
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    E     303      E     303          3.464
LGA    L     304      L     304          3.744
LGA    C     305      C     305          3.906
LGA    I     306      I     306          2.048
LGA    E     307      E     307          1.846
LGA    V     308      V     308          2.497
LGA    V     309      V     309          2.632
LGA    D     310      D     310          2.843
LGA    N     311      N     311          2.923
LGA    V     312      V     312          0.627
LGA    Q     313      Q     313          1.321
LGA    D     314      D     314          1.285
LGA    A     315      A     315          0.825
LGA    I     316      I     316          1.356
LGA    D     317      D     317          2.134
LGA    H     318      H     318          1.906
LGA    I     319      I     319          1.216
LGA    H     320      H     320          2.185
LGA    K     321      K     321          2.974
LGA    Y     322      Y     322          1.765
LGA    G     323      G     323          4.323
LGA    S     324      S     324          2.109
LGA    S     325      S     325          1.920
LGA    H     326      H     326          1.993
LGA    T     327      T     327          1.138
LGA    D     328      D     328          0.830
LGA    V     329      V     329          0.751
LGA    I     330      I     330          1.281
LGA    V     331      V     331          1.828
LGA    T     332      T     332          1.808
LGA    E     333      E     333          2.021
LGA    D     334      D     334          2.317
LGA    E     335      E     335          3.181
LGA    N     336      N     336          2.171
LGA    T     337      T     337          2.304
LGA    A     338      A     338          2.391
LGA    E     339      E     339          2.013
LGA    F     340      F     340          1.271
LGA    F     341      F     341          1.492
LGA    L     342      L     342          1.838
LGA    Q     343      Q     343          1.451
LGA    H     344      H     344          1.258
LGA    V     345      V     345          1.323
LGA    D     346      D     346          1.525
LGA    S     347      S     347          1.685
LGA    A     348      A     348          0.927
LGA    C     349      C     349          1.810
LGA    V     350      V     350          1.262
LGA    F     351      F     351          0.718
LGA    W     352      W     352          1.184
LGA    N     353      N     353          1.029
LGA    A     354      A     354          0.916
LGA    S     355      S     355          1.959
LGA    T     356      T     356          2.057
LGA    R     357      R     357          0.725
LGA    F     358      F     358          1.931
LGA    S     359      S     359          2.590

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  144  144    5.0    126    2.31    84.13     60.327     5.236

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.063528 * X  +   0.993777 * Y  +   0.091500 * Z  + 134.471146
  Y_new =   0.061554 * X  +  -0.095413 * Y  +   0.993533 * Z  +   6.513911
  Z_new =   0.996080 * X  +  -0.057485 * Y  +  -0.067233 * Z  +  19.919121 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.434190    0.707403  [ DEG:  -139.4688     40.5312 ]
  Theta =  -1.482223   -1.659370  [ DEG:   -84.9251    -95.0749 ]
  Phi   =   0.769616   -2.371977  [ DEG:    44.0957   -135.9043 ]
 
# 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_2-D2                               
REMARK     2: T0310_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0310TS393_2-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  126   2.31   84.13  60.327
REMARK  ---------------------------------------------------------- 
MOLECULE T0310TS393_2-D2
PFRMAT TS
TARGET T0310
MODEL 2
PARENT N/A
ATOM    216  CA  GLU   216     137.602  11.175  18.426  1.00 25.00           C
ATOM    217  CA  GLY   217     136.908  12.894  21.748  1.00 25.00           C
ATOM    218  CA  ILE   218     135.893  15.867  19.603  1.00 25.00           C
ATOM    219  CA  CYS   219     137.616  17.835  22.323  1.00 25.00           C
ATOM    220  CA  HIS   220     139.339  19.718  25.084  1.00 25.00           C
ATOM    221  CA  MET   221     141.481  20.576  28.169  1.00 25.00           C
ATOM    222  CA  TYR   222     140.271  23.993  29.175  1.00 25.00           C
ATOM    223  CA  VAL   223     140.551  27.708  29.920  1.00 25.00           C
ATOM    224  CA  ASP   224     137.567  29.577  31.398  1.00 25.00           C
ATOM    225  CA  SER   225     138.219  32.536  33.583  1.00 25.00           C
ATOM    226  CA  GLU   226     139.174  33.060  37.201  1.00 25.00           C
ATOM    227  CA  ALA   227     141.406  30.017  36.981  1.00 25.00           C
ATOM    228  CA  SER   228     145.094  30.431  37.944  1.00 25.00           C
ATOM    229  CA  VAL   229     145.495  30.764  34.188  1.00 25.00           C
ATOM    230  CA  ASP   230     149.018  29.282  34.414  1.00 25.00           C
ATOM    231  CA  LYS   231     147.569  25.966  35.667  1.00 25.00           C
ATOM    232  CA  VAL   232     145.069  25.934  32.767  1.00 25.00           C
ATOM    233  CA  THR   233     147.907  26.594  30.281  1.00 25.00           C
ATOM    234  CA  ARG   234     149.941  23.730  31.806  1.00 25.00           C
ATOM    235  CA  LEU   235     146.917  21.398  31.523  1.00 25.00           C
ATOM    236  CA  VAL   236     146.453  22.405  27.857  1.00 25.00           C
ATOM    237  CA  ARG   237     150.159  21.721  27.174  1.00 25.00           C
ATOM    238  CA  ASP   238     149.857  18.284  28.838  1.00 25.00           C
ATOM    239  CA  SER   239     146.775  17.495  26.703  1.00 25.00           C
ATOM    240  CA  LYS   240     148.669  18.539  23.542  1.00 25.00           C
ATOM    241  CA  CYS   241     150.350  15.255  22.617  1.00 25.00           C
ATOM    242  CA  GLU   242     151.725  13.072  25.338  1.00 25.00           C
ATOM    243  CA  TYR   243     149.743  10.351  23.669  1.00 25.00           C
ATOM    244  CA  PRO   244     150.581  10.366  19.962  1.00 25.00           C
ATOM    245  CA  ALA   245     147.209   9.696  18.341  1.00 25.00           C
ATOM    246  CA  ALA   246     144.668   7.004  19.262  1.00 25.00           C
ATOM    247  CA  CYS   247     144.654   8.127  22.836  1.00 25.00           C
ATOM    248  CA  ASN   248     141.500  10.030  21.926  1.00 25.00           C
ATOM    249  CA  ALA   249     143.595  12.854  20.382  1.00 25.00           C
ATOM    250  CA  LEU   250     142.509  15.220  23.214  1.00 25.00           C
ATOM    251  CA  GLU   251     143.528  17.870  20.686  1.00 25.00           C
ATOM    252  CA  THR   252     143.098  21.349  22.155  1.00 25.00           C
ATOM    253  CA  LEU   253     142.402  24.642  23.863  1.00 25.00           C
ATOM    254  CA  LEU   254     140.030  27.435  24.850  1.00 25.00           C
ATOM    255  CA  ILE   255     142.198  30.355  25.957  1.00 25.00           C
ATOM    256  CA  HIS   256     139.222  32.409  27.094  1.00 25.00           C
ATOM    257  CA  ARG   257     138.069  36.021  27.229  1.00 25.00           C
ATOM    258  CA  ASP   258     139.312  37.021  30.711  1.00 25.00           C
ATOM    259  CA  LEU   259     142.293  34.642  30.357  1.00 25.00           C
ATOM    260  CA  LEU   260     143.113  36.140  26.929  1.00 25.00           C
ATOM    261  CA  ARG   261     142.945  39.670  28.404  1.00 25.00           C
ATOM    262  CA  THR   262     145.281  38.618  31.251  1.00 25.00           C
ATOM    263  CA  PRO   263     148.088  36.409  29.821  1.00 25.00           C
ATOM    264  CA  LEU   264     147.350  33.890  27.069  1.00 25.00           C
ATOM    265  CA  PHE   265     150.845  34.767  25.771  1.00 25.00           C
ATOM    266  CA  ASP   266     152.275  31.622  27.425  1.00 25.00           C
ATOM    267  CA  GLN   267     149.518  29.498  25.827  1.00 25.00           C
ATOM    268  CA  ILE   268     150.281  31.039  22.405  1.00 25.00           C
ATOM    269  CA  ILE   269     154.008  30.287  22.869  1.00 25.00           C
ATOM    270  CA  ASP   270     153.186  26.667  23.807  1.00 25.00           C
ATOM    271  CA  MET   271     150.980  26.336  20.694  1.00 25.00           C
ATOM    272  CA  LEU   272     153.803  27.731  18.515  1.00 25.00           C
ATOM    273  CA  ARG   273     156.264  25.238  20.063  1.00 25.00           C
ATOM    274  CA  VAL   274     153.821  22.367  19.382  1.00 25.00           C
ATOM    275  CA  GLU   275     155.339  20.922  16.195  1.00 25.00           C
ATOM    276  CA  GLN   276     153.554  23.792  14.490  1.00 25.00           C
ATOM    277  CA  VAL   277     150.415  25.813  15.346  1.00 25.00           C
ATOM    278  CA  LYS   278     148.311  28.889  16.110  1.00 25.00           C
ATOM    279  CA  ILE   279     145.325  29.734  18.292  1.00 25.00           C
ATOM    280  CA  HIS   280     145.549  33.145  19.810  1.00 25.00           C
ATOM    281  CA  ALA   281     145.340  36.358  21.809  1.00 25.00           C
ATOM    282  CA  GLY   282     143.938  39.851  21.954  1.00 25.00           C
ATOM    283  CA  PRO   283     140.785  42.078  22.173  1.00 25.00           C
ATOM    284  CA  LYS   284     138.014  39.636  21.163  1.00 25.00           C
ATOM    285  CA  PHE   285     137.907  41.169  17.655  1.00 25.00           C
ATOM    286  CA  ALA   286     141.711  40.831  17.364  1.00 25.00           C
ATOM    287  CA  SER   287     141.492  37.165  18.453  1.00 25.00           C
ATOM    288  CA  TYR   288     138.759  36.528  15.846  1.00 25.00           C
ATOM    289  CA  LEU   289     140.922  38.166  13.142  1.00 25.00           C
ATOM    290  CA  THR   290     143.898  35.985  14.169  1.00 25.00           C
ATOM    291  CA  PHE   291     141.697  32.856  13.995  1.00 25.00           C
ATOM    292  CA  VAL   292     140.480  33.874  10.510  1.00 25.00           C
ATOM    293  CA  LYS   293     144.100  34.401   9.374  1.00 25.00           C
ATOM    294  CA  SER   294     145.055  30.951  10.735  1.00 25.00           C
ATOM    295  CA  LEU   295     142.099  29.373   8.878  1.00 25.00           C
ATOM    296  CA  ARG   296     143.166  31.123   5.643  1.00 25.00           C
ATOM    297  CA  THR   297     146.745  29.844   6.102  1.00 25.00           C
ATOM    298  CA  GLU   298     145.431  26.289   6.659  1.00 25.00           C
ATOM    299  CA  TYR   299     143.303  26.555   3.486  1.00 25.00           C
ATOM    300  CA  GLY   300     141.579  23.864   5.492  1.00 25.00           C
ATOM    301  CA  ASP   301     142.832  22.171   8.593  1.00 25.00           C
ATOM    302  CA  LEU   302     143.117  21.234  12.315  1.00 25.00           C
ATOM    303  CA  GLU   303     144.790  20.428  15.651  1.00 25.00           C
ATOM    304  CA  LEU   304     141.869  22.316  17.293  1.00 25.00           C
ATOM    305  CA  CYS   305     138.789  24.454  17.578  1.00 25.00           C
ATOM    306  CA  ILE   306     140.649  26.949  19.684  1.00 25.00           C
ATOM    307  CA  GLU   307     137.428  29.047  19.697  1.00 25.00           C
ATOM    308  CA  VAL   308     136.058  31.189  22.538  1.00 25.00           C
ATOM    309  CA  VAL   309     134.380  32.651  25.624  1.00 25.00           C
ATOM    310  CA  ASP   310     131.752  34.611  27.523  1.00 25.00           C
ATOM    311  CA  ASN   311     131.451  32.816  30.870  1.00 25.00           C
ATOM    312  CA  VAL   312     130.559  29.783  28.832  1.00 25.00           C
ATOM    313  CA  GLN   313     127.782  29.822  26.195  1.00 25.00           C
ATOM    314  CA  ASP   314     130.357  30.570  23.461  1.00 25.00           C
ATOM    315  CA  ALA   315     132.541  27.674  24.690  1.00 25.00           C
ATOM    316  CA  ILE   316     129.510  25.334  24.639  1.00 25.00           C
ATOM    317  CA  ASP   317     128.681  26.445  21.070  1.00 25.00           C
ATOM    318  CA  HIS   318     132.302  25.802  20.002  1.00 25.00           C
ATOM    319  CA  ILE   319     132.175  22.316  21.585  1.00 25.00           C
ATOM    320  CA  HIS   320     128.900  21.572  19.745  1.00 25.00           C
ATOM    321  CA  LYS   321     130.466  22.719  16.444  1.00 25.00           C
ATOM    322  CA  TYR   322     132.637  19.676  16.173  1.00 25.00           C
ATOM    323  CA  GLY   323     129.588  17.414  16.215  1.00 25.00           C
ATOM    324  CA  SER   324     130.523  15.612  19.483  1.00 25.00           C
ATOM    325  CA  SER   325     128.720  14.055  22.427  1.00 25.00           C
ATOM    326  CA  HIS   326     132.278  13.476  23.670  1.00 25.00           C
ATOM    327  CA  THR   327     134.997  14.730  26.012  1.00 25.00           C
ATOM    328  CA  ASP   328     134.779  18.322  27.246  1.00 25.00           C
ATOM    329  CA  VAL   329     136.513  20.419  29.826  1.00 25.00           C
ATOM    330  CA  ILE   330     135.631  23.788  31.369  1.00 25.00           C
ATOM    331  CA  VAL   331     137.951  25.221  34.085  1.00 25.00           C
ATOM    332  CA  THR   332     136.701  27.797  36.523  1.00 25.00           C
ATOM    333  CA  GLU   333     136.787  28.956  40.126  1.00 25.00           C
ATOM    334  CA  ASP   334     134.098  31.439  39.105  1.00 25.00           C
ATOM    335  CA  GLU   335     131.975  29.502  41.561  1.00 25.00           C
ATOM    336  CA  ASN   336     128.286  29.455  40.532  1.00 25.00           C
ATOM    337  CA  THR   337     129.287  29.687  36.842  1.00 25.00           C
ATOM    338  CA  ALA   338     131.748  26.790  37.302  1.00 25.00           C
ATOM    339  CA  GLU   339     129.013  24.701  38.982  1.00 25.00           C
ATOM    340  CA  PHE   340     126.622  25.460  36.089  1.00 25.00           C
ATOM    341  CA  PHE   341     129.308  24.422  33.564  1.00 25.00           C
ATOM    342  CA  LEU   342     129.887  21.159  35.484  1.00 25.00           C
ATOM    343  CA  GLN   343     126.120  20.466  35.492  1.00 25.00           C
ATOM    344  CA  HIS   344     125.969  21.106  31.719  1.00 25.00           C
ATOM    345  CA  VAL   345     128.108  20.926  28.663  1.00 25.00           C
ATOM    346  CA  ASP   346     127.520  17.436  27.357  1.00 25.00           C
ATOM    347  CA  SER   347     129.889  14.597  28.252  1.00 25.00           C
ATOM    348  CA  ALA   348     130.834  10.909  28.632  1.00 25.00           C
ATOM    349  CA  CYS   349     133.596  11.238  31.287  1.00 25.00           C
ATOM    350  CA  VAL   350     133.687  14.978  31.967  1.00 25.00           C
ATOM    351  CA  PHE   351     135.986  16.928  34.291  1.00 25.00           C
ATOM    352  CA  TRP   352     137.756  20.232  34.906  1.00 25.00           C
ATOM    353  CA  ASN   353     141.491  20.602  35.643  1.00 25.00           C
ATOM    354  CA  ALA   354     142.180  17.204  34.154  1.00 25.00           C
ATOM    355  CA  SER   355     141.970  15.877  30.606  1.00 25.00           C
ATOM    356  CA  THR   356     140.546  13.453  28.037  1.00 25.00           C
ATOM    357  CA  ARG   357     143.783  11.516  28.698  1.00 25.00           C
ATOM    358  CA  PHE   358     141.898   9.104  30.999  1.00 25.00           C
ATOM    359  CA  SER   359     139.866   7.698  28.060  1.00 25.00           C
TER
END
