
#######################################################
#                                                     #
#                        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_1-D2
# Molecule2: number of CA atoms  144 ( 1137),  selected  144 , name T0310_D2.pdb
# PARAMETERS: T0310TS393_1-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          3.028
LGA    G     217      G     217          3.125
LGA    I     218      I     218          2.393
LGA    C     219      C     219          1.141
LGA    H     220      H     220          0.990
LGA    M     221      M     221          1.517
LGA    Y     222      Y     222          2.229
LGA    V     223      V     223          0.757
LGA    D     224      D     224          0.217
LGA    S     225      S     225          1.421
LGA    E     226      E     226          1.221
LGA    A     227      A     227          2.335
LGA    S     228      S     228          0.658
LGA    V     229      V     229          2.029
LGA    D     230      D     230          2.521
LGA    K     231      K     231          0.400
LGA    V     232      V     232          1.139
LGA    T     233      T     233          1.275
LGA    R     234      R     234          1.228
LGA    L     235      L     235          0.237
LGA    V     236      V     236          0.450
LGA    R     237      R     237          0.900
LGA    D     238      D     238          0.969
LGA    S     239      S     239          1.266
LGA    K     240      K     240          2.300
LGA    C     241      C     241          3.019
LGA    -       -      E     242           -
LGA    E     242      Y     243          2.241
LGA    Y     243      P     244          4.743
LGA    P     244      A     245          3.744
LGA    A     245      -       -           -
LGA    A     246      A     246          4.346
LGA    C     247      C     247           #
LGA    N     248      N     248          3.517
LGA    A     249      A     249          1.568
LGA    L     250      L     250          4.461
LGA    E     251      E     251          1.216
LGA    T     252      T     252          4.785
LGA    L     253      L     253          4.168
LGA    L     254      -       -           -
LGA    I     255      L     254           #
LGA    H     256      I     255          2.202
LGA    R     257      H     256          3.668
LGA    D     258      R     257           -
LGA    -       -      D     258           -
LGA    L     259      L     259          4.290
LGA    L     260      L     260          2.764
LGA    R     261      R     261          3.014
LGA    T     262      T     262          0.918
LGA    P     263      P     263          1.744
LGA    L     264      L     264           #
LGA    F     265      F     265           #
LGA    D     266      D     266          3.627
LGA    Q     267      Q     267          3.631
LGA    I     268      I     268          5.463
LGA    I     269      I     269          3.651
LGA    D     270      D     270          2.188
LGA    M     271      M     271          4.772
LGA    L     272      L     272          4.187
LGA    R     273      R     273          1.685
LGA    -       -      V     274           -
LGA    -       -      E     275           -
LGA    V     274      Q     276          3.687
LGA    E     275      V     277          1.761
LGA    Q     276      K     278           #
LGA    V     277      I     279           #
LGA    K     278      H     280           #
LGA    I     279      A     281           #
LGA    H     280      G     282          4.045
LGA    A     281      P     283           #
LGA    G     282      K     284          4.408
LGA    P     283      -       -           -
LGA    K     284      -       -           -
LGA    F     285      -       -           -
LGA    A     286      -       -           -
LGA    S     287      F     285          4.560
LGA    Y     288      A     286          2.829
LGA    L     289      S     287           #
LGA    T     290      Y     288           -
LGA    F     291      L     289           -
LGA    -       -      T     290           -
LGA    V     292      F     291           #
LGA    K     293      V     292          2.746
LGA    S     294      K     293          3.804
LGA    L     295      -       -           -
LGA    R     296      -       -           -
LGA    T     297      -       -           -
LGA    E     298      S     294           #
LGA    Y     299      L     295           -
LGA    G     300      R     296           -
LGA    D     301      T     297           #
LGA    L     302      E     298           #
LGA    E     303      Y     299          4.079
LGA    -       -      G     300           -
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    -       -      E     303           -
LGA    L     304      L     304          2.634
LGA    C     305      C     305          2.666
LGA    I     306      I     306          2.444
LGA    E     307      E     307          3.047
LGA    V     308      V     308          2.750
LGA    V     309      V     309          2.926
LGA    D     310      D     310          3.121
LGA    N     311      N     311          3.271
LGA    V     312      V     312          0.475
LGA    Q     313      Q     313          1.061
LGA    D     314      D     314          1.297
LGA    A     315      A     315          0.690
LGA    I     316      I     316          0.580
LGA    D     317      D     317          1.330
LGA    H     318      H     318          1.239
LGA    I     319      I     319          0.372
LGA    H     320      H     320          0.957
LGA    K     321      K     321          1.527
LGA    Y     322      Y     322          1.973
LGA    G     323      G     323          2.747
LGA    S     324      S     324          1.304
LGA    S     325      S     325          0.532
LGA    H     326      H     326          0.347
LGA    T     327      T     327          0.742
LGA    D     328      D     328          2.297
LGA    V     329      V     329          1.460
LGA    I     330      I     330          2.363
LGA    V     331      V     331          3.272
LGA    T     332      T     332          3.804
LGA    E     333      E     333          4.404
LGA    D     334      D     334          1.203
LGA    E     335      E     335          4.062
LGA    N     336      N     336          3.574
LGA    T     337      T     337          3.378
LGA    A     338      A     338          3.080
LGA    E     339      E     339          2.773
LGA    F     340      F     340          2.452
LGA    F     341      F     341          1.892
LGA    L     342      L     342          1.846
LGA    Q     343      Q     343          1.773
LGA    H     344      H     344          1.351
LGA    V     345      V     345          1.589
LGA    D     346      D     346          2.817
LGA    S     347      S     347          1.336
LGA    A     348      A     348          2.185
LGA    C     349      C     349          3.047
LGA    V     350      V     350          2.652
LGA    F     351      F     351          1.750
LGA    W     352      W     352          0.782
LGA    N     353      N     353          2.122
LGA    A     354      A     354          1.165
LGA    S     355      S     355          0.334
LGA    T     356      T     356          1.498
LGA    R     357      R     357          1.617
LGA    F     358      F     358          2.019
LGA    S     359      S     359          2.254

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  144  144    5.0    116    2.61    87.93     50.913     4.278

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.849955 * X  +  -0.525784 * Y  +   0.033580 * Z  + 136.380280
  Y_new =  -0.014309 * X  +   0.040675 * Y  +   0.999070 * Z  +   2.721359
  Z_new =  -0.526661 * X  +  -0.849645 * Y  +   0.027049 * Z  +  21.789488 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.538972    1.602621  [ DEG:   -88.1766     91.8234 ]
  Theta =   0.554668    2.586925  [ DEG:    31.7801    148.2199 ]
  Phi   =  -0.016834    3.124759  [ DEG:    -0.9645    179.0355 ]
 
# 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_1-D2                               
REMARK     2: T0310_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0310TS393_1-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  116   2.61   87.93  50.913
REMARK  ---------------------------------------------------------- 
MOLECULE T0310TS393_1-D2
PFRMAT TS
TARGET T0310
MODEL 1
PARENT N/A
ATOM    216  CA  GLU   216     137.495   9.015  19.068  1.00 25.00           C
ATOM    217  CA  GLY   217     138.585  11.003  22.175  1.00 25.00           C
ATOM    218  CA  ILE   218     137.083  13.996  20.464  1.00 25.00           C
ATOM    219  CA  CYS   219     138.173  16.263  23.257  1.00 25.00           C
ATOM    220  CA  HIS   220     137.023  19.931  23.322  1.00 25.00           C
ATOM    221  CA  MET   221     137.721  21.968  26.469  1.00 25.00           C
ATOM    222  CA  TYR   222     138.943  24.342  29.179  1.00 25.00           C
ATOM    223  CA  VAL   223     140.254  27.757  30.165  1.00 25.00           C
ATOM    224  CA  ASP   224     137.696  30.154  31.656  1.00 25.00           C
ATOM    225  CA  SER   225     137.655  33.244  33.800  1.00 25.00           C
ATOM    226  CA  GLU   226     139.154  32.873  37.215  1.00 25.00           C
ATOM    227  CA  ALA   227     140.954  29.539  37.449  1.00 25.00           C
ATOM    228  CA  SER   228     144.750  30.088  37.753  1.00 25.00           C
ATOM    229  CA  VAL   229     146.126  30.700  34.278  1.00 25.00           C
ATOM    230  CA  ASP   230     149.219  28.657  35.243  1.00 25.00           C
ATOM    231  CA  LYS   231     147.011  25.616  35.979  1.00 25.00           C
ATOM    232  CA  VAL   232     145.288  26.014  32.582  1.00 25.00           C
ATOM    233  CA  THR   233     148.698  26.216  30.849  1.00 25.00           C
ATOM    234  CA  ARG   234     149.838  23.047  32.671  1.00 25.00           C
ATOM    235  CA  LEU   235     146.636  21.244  31.594  1.00 25.00           C
ATOM    236  CA  VAL   236     147.209  22.339  27.969  1.00 25.00           C
ATOM    237  CA  ARG   237     150.816  21.060  28.128  1.00 25.00           C
ATOM    238  CA  ASP   238     149.592  17.709  29.521  1.00 25.00           C
ATOM    239  CA  SER   239     147.013  17.450  26.701  1.00 25.00           C
ATOM    240  CA  LYS   240     149.735  18.190  24.111  1.00 25.00           C
ATOM    241  CA  CYS   241     150.067  15.770  21.182  1.00 25.00           C
ATOM    242  CA  GLU   242     150.778  12.070  21.673  1.00 25.00           C
ATOM    243  CA  TYR   243     151.007   9.623  18.767  1.00 25.00           C
ATOM    244  CA  PRO   244     149.069   9.142  15.594  1.00 25.00           C
ATOM    245  CA  ALA   245     146.090   9.374  17.954  1.00 25.00           C
ATOM    246  CA  ALA   246     145.436   5.766  19.127  1.00 25.00           C
ATOM    247  CA  CYS   247     145.847   6.583  22.774  1.00 25.00           C
ATOM    248  CA  ASN   248     143.236   9.282  23.247  1.00 25.00           C
ATOM    249  CA  ALA   249     144.512  12.804  22.609  1.00 25.00           C
ATOM    250  CA  LEU   250     142.079  14.393  20.192  1.00 25.00           C
ATOM    251  CA  GLU   251     141.190  18.004  19.855  1.00 25.00           C
ATOM    252  CA  THR   252     142.220  19.394  23.208  1.00 25.00           C
ATOM    253  CA  LEU   253     142.595  22.203  25.747  1.00 25.00           C
ATOM    254  CA  LEU   254     142.428  26.023  25.613  1.00 25.00           C
ATOM    255  CA  ILE   255     144.226  29.231  26.740  1.00 25.00           C
ATOM    256  CA  HIS   256     141.083  31.371  26.721  1.00 25.00           C
ATOM    257  CA  ARG   257     140.333  33.790  29.561  1.00 25.00           C
ATOM    258  CA  ASP   258     142.597  35.904  31.813  1.00 25.00           C
ATOM    259  CA  LEU   259     145.699  34.439  30.111  1.00 25.00           C
ATOM    260  CA  LEU   260     144.218  35.235  26.670  1.00 25.00           C
ATOM    261  CA  ARG   261     143.491  38.826  27.787  1.00 25.00           C
ATOM    262  CA  THR   262     147.085  39.184  29.061  1.00 25.00           C
ATOM    263  CA  PRO   263     150.315  37.187  28.991  1.00 25.00           C
ATOM    264  CA  LEU   264     148.562  36.571  25.649  1.00 25.00           C
ATOM    265  CA  PHE   265     150.259  36.653  22.217  1.00 25.00           C
ATOM    266  CA  ASP   266     153.408  35.063  23.709  1.00 25.00           C
ATOM    267  CA  GLN   267     151.283  32.325  25.336  1.00 25.00           C
ATOM    268  CA  ILE   268     149.538  31.657  21.993  1.00 25.00           C
ATOM    269  CA  ILE   269     152.935  31.418  20.240  1.00 25.00           C
ATOM    270  CA  ASP   270     154.166  28.959  22.906  1.00 25.00           C
ATOM    271  CA  MET   271     151.006  26.842  22.447  1.00 25.00           C
ATOM    272  CA  LEU   272     151.539  26.827  18.655  1.00 25.00           C
ATOM    273  CA  ARG   273     155.178  25.739  19.144  1.00 25.00           C
ATOM    274  CA  VAL   274     154.048  22.923  21.481  1.00 25.00           C
ATOM    275  CA  GLU   275     151.162  21.714  19.372  1.00 25.00           C
ATOM    276  CA  GLN   276     147.492  21.959  20.303  1.00 25.00           C
ATOM    277  CA  VAL   277     143.929  23.242  20.705  1.00 25.00           C
ATOM    278  CA  LYS   278     140.586  24.891  19.779  1.00 25.00           C
ATOM    279  CA  ILE   279     139.179  27.871  17.956  1.00 25.00           C
ATOM    280  CA  HIS   280     136.585  30.643  17.822  1.00 25.00           C
ATOM    281  CA  ALA   281     136.051  34.229  19.093  1.00 25.00           C
ATOM    282  CA  GLY   282     136.716  37.973  19.052  1.00 25.00           C
ATOM    283  CA  PRO   283     139.129  40.917  18.644  1.00 25.00           C
ATOM    284  CA  LYS   284     141.790  41.356  15.924  1.00 25.00           C
ATOM    285  CA  PHE   285     143.959  38.668  17.578  1.00 25.00           C
ATOM    286  CA  ALA   286     140.956  36.296  17.720  1.00 25.00           C
ATOM    287  CA  SER   287     140.239  36.942  14.013  1.00 25.00           C
ATOM    288  CA  TYR   288     143.902  36.223  13.155  1.00 25.00           C
ATOM    289  CA  LEU   289     143.756  32.961  15.156  1.00 25.00           C
ATOM    290  CA  THR   290     140.555  31.947  13.315  1.00 25.00           C
ATOM    291  CA  PHE   291     142.222  32.695   9.950  1.00 25.00           C
ATOM    292  CA  VAL   292     145.255  30.583  10.956  1.00 25.00           C
ATOM    293  CA  LYS   293     142.944  27.702  11.968  1.00 25.00           C
ATOM    294  CA  SER   294     141.125  27.949   8.607  1.00 25.00           C
ATOM    295  CA  LEU   295     144.478  27.878   6.758  1.00 25.00           C
ATOM    296  CA  ARG   296     145.543  24.791   8.758  1.00 25.00           C
ATOM    297  CA  THR   297     142.230  23.067   7.909  1.00 25.00           C
ATOM    298  CA  GLU   298     142.726  23.888   4.200  1.00 25.00           C
ATOM    299  CA  TYR   299     146.277  22.460   4.334  1.00 25.00           C
ATOM    300  CA  GLY   300     146.078  19.854   7.099  1.00 25.00           C
ATOM    301  CA  ASP   301     144.704  17.512   9.781  1.00 25.00           C
ATOM    302  CA  LEU   302     145.768  18.664  13.201  1.00 25.00           C
ATOM    303  CA  GLU   303     142.401  19.903  14.399  1.00 25.00           C
ATOM    304  CA  LEU   304     143.990  23.152  15.667  1.00 25.00           C
ATOM    305  CA  CYS   305     144.449  26.618  16.993  1.00 25.00           C
ATOM    306  CA  ILE   306     144.356  29.150  19.821  1.00 25.00           C
ATOM    307  CA  GLU   307     141.056  29.624  21.627  1.00 25.00           C
ATOM    308  CA  VAL   308     137.598  30.217  23.125  1.00 25.00           C
ATOM    309  CA  VAL   309     135.689  32.176  25.750  1.00 25.00           C
ATOM    310  CA  ASP   310     133.499  34.546  27.755  1.00 25.00           C
ATOM    311  CA  ASN   311     132.504  32.988  31.049  1.00 25.00           C
ATOM    312  CA  VAL   312     131.057  29.819  29.588  1.00 25.00           C
ATOM    313  CA  GLN   313     128.157  30.094  27.101  1.00 25.00           C
ATOM    314  CA  ASP   314     130.642  30.412  24.203  1.00 25.00           C
ATOM    315  CA  ALA   315     132.528  27.321  25.449  1.00 25.00           C
ATOM    316  CA  ILE   316     129.238  25.370  25.666  1.00 25.00           C
ATOM    317  CA  ASP   317     128.345  26.433  22.097  1.00 25.00           C
ATOM    318  CA  HIS   318     131.795  25.308  20.871  1.00 25.00           C
ATOM    319  CA  ILE   319     131.340  21.930  22.618  1.00 25.00           C
ATOM    320  CA  HIS   320     127.899  21.523  20.989  1.00 25.00           C
ATOM    321  CA  LYS   321     129.398  22.336  17.561  1.00 25.00           C
ATOM    322  CA  TYR   322     130.615  19.084  16.085  1.00 25.00           C
ATOM    323  CA  GLY   323     130.054  16.692  19.010  1.00 25.00           C
ATOM    324  CA  SER   324     131.415  13.133  19.206  1.00 25.00           C
ATOM    325  CA  SER   325     130.515  13.438  22.905  1.00 25.00           C
ATOM    326  CA  HIS   326     133.807  12.091  24.316  1.00 25.00           C
ATOM    327  CA  THR   327     135.910  13.610  27.115  1.00 25.00           C
ATOM    328  CA  ASP   328     137.364  16.983  28.193  1.00 25.00           C
ATOM    329  CA  VAL   329     135.637  19.604  30.410  1.00 25.00           C
ATOM    330  CA  ILE   330     134.354  23.035  31.454  1.00 25.00           C
ATOM    331  CA  VAL   331     136.448  24.789  34.092  1.00 25.00           C
ATOM    332  CA  THR   332     135.521  25.627  37.707  1.00 25.00           C
ATOM    333  CA  GLU   333     135.277  29.354  37.133  1.00 25.00           C
ATOM    334  CA  ASP   334     134.257  29.528  40.789  1.00 25.00           C
ATOM    335  CA  GLU   335     130.503  29.459  40.150  1.00 25.00           C
ATOM    336  CA  ASN   336     126.972  29.661  38.681  1.00 25.00           C
ATOM    337  CA  THR   337     128.429  29.912  35.149  1.00 25.00           C
ATOM    338  CA  ALA   338     130.642  26.859  35.818  1.00 25.00           C
ATOM    339  CA  GLU   339     127.604  24.906  37.092  1.00 25.00           C
ATOM    340  CA  PHE   340     125.635  25.875  33.954  1.00 25.00           C
ATOM    341  CA  PHE   341     128.545  24.729  31.744  1.00 25.00           C
ATOM    342  CA  LEU   342     128.692  21.395  33.624  1.00 25.00           C
ATOM    343  CA  GLN   343     124.919  20.936  33.155  1.00 25.00           C
ATOM    344  CA  HIS   344     125.270  21.666  29.412  1.00 25.00           C
ATOM    345  CA  VAL   345     127.656  19.852  27.048  1.00 25.00           C
ATOM    346  CA  ASP   346     128.021  16.950  29.440  1.00 25.00           C
ATOM    347  CA  SER   347     130.271  14.447  27.770  1.00 25.00           C
ATOM    348  CA  ALA   348     130.427  11.454  30.055  1.00 25.00           C
ATOM    349  CA  CYS   349     133.244  10.503  32.391  1.00 25.00           C
ATOM    350  CA  VAL   350     132.841  14.144  33.335  1.00 25.00           C
ATOM    351  CA  PHE   351     135.180  16.672  35.015  1.00 25.00           C
ATOM    352  CA  TRP   352     136.711  19.794  36.456  1.00 25.00           C
ATOM    353  CA  ASN   353     139.685  20.702  34.337  1.00 25.00           C
ATOM    354  CA  ALA   354     142.682  18.455  34.722  1.00 25.00           C
ATOM    355  CA  SER   355     143.258  16.383  31.578  1.00 25.00           C
ATOM    356  CA  THR   356     142.521  14.308  28.472  1.00 25.00           C
ATOM    357  CA  ARG   357     145.085  11.469  28.637  1.00 25.00           C
ATOM    358  CA  PHE   358     142.644   9.349  30.690  1.00 25.00           C
ATOM    359  CA  SER   359     140.003   7.791  28.499  1.00 25.00           C
TER
END
