
#######################################################
#                                                     #
#                        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 T0310TS168_5-D2
# Molecule2: number of CA atoms  144 ( 1137),  selected  144 , name T0310_D2.pdb
# PARAMETERS: T0310TS168_5-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          3.157
LGA    G     217      G     217          0.983
LGA    I     218      I     218          0.658
LGA    C     219      C     219          1.081
LGA    H     220      H     220          1.224
LGA    M     221      M     221          2.159
LGA    Y     222      Y     222          2.050
LGA    V     223      V     223          1.184
LGA    D     224      D     224          1.658
LGA    S     225      S     225          1.195
LGA    E     226      E     226          1.293
LGA    A     227      A     227          1.914
LGA    S     228      S     228          2.567
LGA    V     229      V     229          2.236
LGA    D     230      D     230          2.557
LGA    K     231      K     231          1.859
LGA    V     232      V     232          1.579
LGA    T     233      T     233          1.526
LGA    R     234      R     234          2.183
LGA    L     235      L     235          1.591
LGA    V     236      V     236          1.603
LGA    R     237      R     237          1.932
LGA    D     238      D     238          1.945
LGA    S     239      S     239          1.716
LGA    K     240      K     240          3.219
LGA    C     241      C     241          3.719
LGA    E     242      -       -           -
LGA    Y     243      E     242          4.447
LGA    P     244      Y     243          3.895
LGA    A     245      P     244          4.296
LGA    A     246      A     245           #
LGA    C     247      A     246          4.524
LGA    -       -      C     247           -
LGA    N     248      N     248          1.002
LGA    A     249      A     249          1.449
LGA    L     250      L     250          2.570
LGA    E     251      E     251          2.705
LGA    T     252      T     252          3.712
LGA    L     253      L     253          3.371
LGA    L     254      L     254          2.247
LGA    I     255      I     255          2.081
LGA    H     256      H     256          0.892
LGA    R     257      R     257          1.547
LGA    D     258      D     258          2.530
LGA    L     259      L     259          2.074
LGA    L     260      L     260          1.134
LGA    R     261      R     261          1.790
LGA    T     262      T     262          0.472
LGA    P     263      P     263          4.011
LGA    -       -      L     264           -
LGA    L     264      F     265          2.580
LGA    F     265      D     266          3.151
LGA    D     266      Q     267          3.269
LGA    Q     267      I     268          2.603
LGA    I     268      I     269          2.960
LGA    I     269      D     270          3.775
LGA    D     270      M     271          3.472
LGA    M     271      L     272          3.300
LGA    L     272      R     273          3.880
LGA    R     273      V     274          4.405
LGA    -       -      E     275           -
LGA    V     274      Q     276          1.160
LGA    E     275      V     277          2.971
LGA    Q     276      K     278          1.377
LGA    V     277      I     279          1.653
LGA    K     278      H     280          5.612
LGA    -       -      A     281           -
LGA    -       -      G     282           -
LGA    -       -      P     283           -
LGA    -       -      K     284           -
LGA    I     279      F     285           #
LGA    H     280      A     286          3.815
LGA    A     281      S     287          4.802
LGA    G     282      Y     288          2.496
LGA    P     283      -       -           -
LGA    K     284      -       -           -
LGA    F     285      -       -           -
LGA    A     286      -       -           -
LGA    S     287      L     289           #
LGA    Y     288      T     290           -
LGA    L     289      -       -           -
LGA    T     290      -       -           -
LGA    F     291      F     291           #
LGA    V     292      -       -           -
LGA    K     293      -       -           -
LGA    S     294      -       -           -
LGA    L     295      V     292          1.569
LGA    R     296      K     293          3.929
LGA    T     297      S     294           -
LGA    E     298      L     295           -
LGA    Y     299      R     296           -
LGA    G     300      T     297           -
LGA    -       -      E     298           -
LGA    D     301      Y     299          4.958
LGA    L     302      G     300           #
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    E     303      E     303          3.572
LGA    L     304      L     304          1.940
LGA    C     305      C     305          2.067
LGA    I     306      I     306          2.685
LGA    E     307      E     307          2.499
LGA    V     308      V     308          2.871
LGA    V     309      V     309          3.035
LGA    D     310      D     310          3.797
LGA    N     311      N     311          3.091
LGA    V     312      V     312          1.118
LGA    Q     313      Q     313          1.987
LGA    D     314      D     314          1.866
LGA    A     315      A     315          0.933
LGA    I     316      I     316          1.255
LGA    D     317      D     317          2.346
LGA    H     318      H     318          2.215
LGA    I     319      I     319          1.079
LGA    H     320      H     320          1.633
LGA    -       -      K     321           -
LGA    K     321      Y     322          0.685
LGA    Y     322      G     323          3.274
LGA    G     323      -       -           -
LGA    S     324      S     324          3.394
LGA    S     325      S     325          2.367
LGA    H     326      H     326          2.067
LGA    T     327      T     327          0.500
LGA    D     328      D     328          0.915
LGA    V     329      V     329          0.295
LGA    I     330      I     330          0.648
LGA    V     331      V     331          0.701
LGA    T     332      T     332          1.795
LGA    E     333      E     333          0.417
LGA    D     334      D     334          0.749
LGA    E     335      E     335          0.945
LGA    N     336      N     336          1.145
LGA    T     337      T     337          0.605
LGA    A     338      A     338          0.389
LGA    E     339      E     339          0.546
LGA    F     340      F     340          0.209
LGA    F     341      F     341          0.453
LGA    L     342      L     342          0.977
LGA    Q     343      Q     343          1.169
LGA    H     344      H     344          1.263
LGA    V     345      V     345          1.191
LGA    D     346      D     346          0.525
LGA    S     347      S     347          1.846
LGA    A     348      A     348          1.559
LGA    C     349      C     349          0.766
LGA    V     350      V     350          1.093
LGA    F     351      F     351          1.174
LGA    W     352      W     352          0.934
LGA    N     353      N     353          1.366
LGA    A     354      A     354          1.227
LGA    S     355      S     355          1.079
LGA    T     356      T     356          1.688
LGA    R     357      R     357          1.776
LGA    F     358      F     358          1.368
LGA    S     359      S     359          1.109

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  144  144    5.0    123    2.36    78.86     58.112     5.004

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.817605 * X  +  -0.336953 * Y  +  -0.466888 * Z  + 134.942932
  Y_new =  -0.511018 * X  +   0.051034 * Y  +   0.858054 * Z  +   6.659634
  Z_new =  -0.265297 * X  +   0.940137 * Y  +  -0.213915 * Z  +  22.282921 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.794523   -1.347070  [ DEG:   102.8186    -77.1814 ]
  Theta =   0.268512    2.873081  [ DEG:    15.3846    164.6154 ]
  Phi   =  -2.582980    0.558612  [ DEG:  -147.9939     32.0061 ]
 
# 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: T0310TS168_5-D2                               
REMARK     2: T0310_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0310TS168_5-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  123   2.36   78.86  58.112
REMARK  ---------------------------------------------------------- 
MOLECULE T0310TS168_5-D2
PFRMAT TS
TARGET T0310
MODEL 5
PARENT N/A
ATOM    216  CA  GLU   216     134.988  10.716  19.672  1.00 25.00           C
ATOM    217  CA  GLY   217     138.433  12.309  19.696  1.00 25.00           C
ATOM    218  CA  ILE   218     136.736  15.701  19.429  1.00 25.00           C
ATOM    219  CA  CYS   219     137.049  17.726  22.618  1.00 25.00           C
ATOM    220  CA  HIS   220     136.807  21.247  24.011  1.00 25.00           C
ATOM    221  CA  MET   221     137.800  23.861  26.653  1.00 25.00           C
ATOM    222  CA  TYR   222     136.199  26.937  28.216  1.00 25.00           C
ATOM    223  CA  VAL   223     139.066  28.735  29.975  1.00 25.00           C
ATOM    224  CA  ASP   224     136.496  29.280  32.700  1.00 25.00           C
ATOM    225  CA  SER   225     137.373  32.988  33.092  1.00 25.00           C
ATOM    226  CA  GLU   226     139.735  31.915  35.876  1.00 25.00           C
ATOM    227  CA  ALA   227     142.432  29.341  36.578  1.00 25.00           C
ATOM    228  CA  SER   228     144.940  32.111  36.734  1.00 25.00           C
ATOM    229  CA  VAL   229     147.339  32.096  33.800  1.00 25.00           C
ATOM    230  CA  ASP   230     149.585  29.530  35.543  1.00 25.00           C
ATOM    231  CA  LYS   231     146.643  27.092  35.801  1.00 25.00           C
ATOM    232  CA  VAL   232     145.887  27.572  32.077  1.00 25.00           C
ATOM    233  CA  THR   233     149.561  26.910  31.221  1.00 25.00           C
ATOM    234  CA  ARG   234     149.509  23.728  33.352  1.00 25.00           C
ATOM    235  CA  LEU   235     146.322  22.562  31.577  1.00 25.00           C
ATOM    236  CA  VAL   236     147.950  23.217  28.172  1.00 25.00           C
ATOM    237  CA  ARG   237     151.040  21.221  29.239  1.00 25.00           C
ATOM    238  CA  ASP   238     148.809  18.327  30.382  1.00 25.00           C
ATOM    239  CA  SER   239     146.962  18.394  27.027  1.00 25.00           C
ATOM    240  CA  LYS   240     150.304  18.332  25.158  1.00 25.00           C
ATOM    241  CA  CYS   241     151.982  15.831  27.421  1.00 25.00           C
ATOM    242  CA  GLU   242     151.019  13.720  30.512  1.00 25.00           C
ATOM    243  CA  TYR   243     150.089  10.340  29.117  1.00 25.00           C
ATOM    244  CA  PRO   244     152.440  10.700  26.220  1.00 25.00           C
ATOM    245  CA  ALA   245     149.220  11.624  24.325  1.00 25.00           C
ATOM    246  CA  ALA   246     147.925   8.078  24.890  1.00 25.00           C
ATOM    247  CA  CYS   247     144.704   9.820  26.064  1.00 25.00           C
ATOM    248  CA  ASN   248     141.812  11.343  24.204  1.00 25.00           C
ATOM    249  CA  ALA   249     144.302  13.164  22.060  1.00 25.00           C
ATOM    250  CA  LEU   250     141.655  15.922  21.651  1.00 25.00           C
ATOM    251  CA  GLU   251     141.834  19.698  22.152  1.00 25.00           C
ATOM    252  CA  THR   252     141.683  23.279  23.423  1.00 25.00           C
ATOM    253  CA  LEU   253     143.069  26.232  25.351  1.00 25.00           C
ATOM    254  CA  LEU   254     140.087  28.517  24.721  1.00 25.00           C
ATOM    255  CA  ILE   255     140.465  32.243  24.369  1.00 25.00           C
ATOM    256  CA  HIS   256     138.460  33.150  27.401  1.00 25.00           C
ATOM    257  CA  ARG   257     138.650  36.903  26.868  1.00 25.00           C
ATOM    258  CA  ASP   258     140.819  37.279  30.001  1.00 25.00           C
ATOM    259  CA  LEU   259     143.173  34.539  28.729  1.00 25.00           C
ATOM    260  CA  LEU   260     143.428  36.297  25.337  1.00 25.00           C
ATOM    261  CA  ARG   261     144.227  39.609  27.086  1.00 25.00           C
ATOM    262  CA  THR   262     146.937  37.883  29.170  1.00 25.00           C
ATOM    263  CA  PRO   263     148.215  34.438  28.029  1.00 25.00           C
ATOM    264  CA  LEU   264     147.057  32.274  25.144  1.00 25.00           C
ATOM    265  CA  PHE   265     150.259  33.610  23.524  1.00 25.00           C
ATOM    266  CA  ASP   266     152.330  30.990  25.400  1.00 25.00           C
ATOM    267  CA  GLN   267     149.946  28.231  24.228  1.00 25.00           C
ATOM    268  CA  ILE   268     150.243  29.474  20.618  1.00 25.00           C
ATOM    269  CA  ILE   269     154.062  29.467  20.904  1.00 25.00           C
ATOM    270  CA  ASP   270     153.978  25.893  22.274  1.00 25.00           C
ATOM    271  CA  MET   271     151.727  24.807  19.372  1.00 25.00           C
ATOM    272  CA  LEU   272     154.131  26.425  16.869  1.00 25.00           C
ATOM    273  CA  ARG   273     157.086  24.614  18.499  1.00 25.00           C
ATOM    274  CA  VAL   274     155.193  21.291  18.296  1.00 25.00           C
ATOM    275  CA  GLU   275     152.849  21.691  15.315  1.00 25.00           C
ATOM    276  CA  GLN   276     150.367  24.096  13.734  1.00 25.00           C
ATOM    277  CA  VAL   277     149.304  27.464  15.151  1.00 25.00           C
ATOM    278  CA  LYS   278     148.153  31.008  15.564  1.00 25.00           C
ATOM    279  CA  ILE   279     145.036  31.791  17.610  1.00 25.00           C
ATOM    280  CA  HIS   280     143.649  35.362  17.242  1.00 25.00           C
ATOM    281  CA  ALA   281     142.243  38.641  18.432  1.00 25.00           C
ATOM    282  CA  GLY   282     139.444  41.187  18.419  1.00 25.00           C
ATOM    283  CA  PRO   283     135.689  41.780  18.405  1.00 25.00           C
ATOM    284  CA  LYS   284     135.164  38.126  19.424  1.00 25.00           C
ATOM    285  CA  PHE   285     133.462  37.409  16.070  1.00 25.00           C
ATOM    286  CA  ALA   286     136.381  39.048  14.210  1.00 25.00           C
ATOM    287  CA  SER   287     138.872  36.931  16.205  1.00 25.00           C
ATOM    288  CA  TYR   288     136.889  33.763  15.367  1.00 25.00           C
ATOM    289  CA  LEU   289     136.890  34.716  11.657  1.00 25.00           C
ATOM    290  CA  THR   290     140.674  35.288  11.779  1.00 25.00           C
ATOM    291  CA  PHE   291     141.163  31.873  13.441  1.00 25.00           C
ATOM    292  CA  VAL   292     139.011  30.223  10.737  1.00 25.00           C
ATOM    293  CA  LYS   293     141.072  31.947   8.008  1.00 25.00           C
ATOM    294  CA  SER   294     144.311  30.735   9.655  1.00 25.00           C
ATOM    295  CA  LEU   295     142.927  27.167   9.806  1.00 25.00           C
ATOM    296  CA  ARG   296     141.971  27.354   6.101  1.00 25.00           C
ATOM    297  CA  THR   297     145.490  28.593   5.232  1.00 25.00           C
ATOM    298  CA  GLU   298     147.026  25.711   7.232  1.00 25.00           C
ATOM    299  CA  TYR   299     144.777  23.209   5.402  1.00 25.00           C
ATOM    300  CA  GLY   300     144.018  22.070   8.926  1.00 25.00           C
ATOM    301  CA  ASP   301     144.894  20.910  12.365  1.00 25.00           C
ATOM    302  CA  LEU   302     147.696  19.493  14.459  1.00 25.00           C
ATOM    303  CA  GLU   303     145.176  19.512  17.307  1.00 25.00           C
ATOM    304  CA  LEU   304     144.613  22.751  19.265  1.00 25.00           C
ATOM    305  CA  CYS   305     141.211  23.291  17.556  1.00 25.00           C
ATOM    306  CA  ILE   306     140.144  26.416  19.443  1.00 25.00           C
ATOM    307  CA  GLU   307     137.076  28.519  20.247  1.00 25.00           C
ATOM    308  CA  VAL   308     135.710  31.099  22.678  1.00 25.00           C
ATOM    309  CA  VAL   309     133.962  31.952  25.970  1.00 25.00           C
ATOM    310  CA  ASP   310     133.161  34.598  28.539  1.00 25.00           C
ATOM    311  CA  ASN   311     131.557  32.100  30.902  1.00 25.00           C
ATOM    312  CA  VAL   312     130.411  29.552  28.313  1.00 25.00           C
ATOM    313  CA  GLN   313     127.885  29.461  25.435  1.00 25.00           C
ATOM    314  CA  ASP   314     130.742  29.656  22.890  1.00 25.00           C
ATOM    315  CA  ALA   315     132.552  26.786  24.666  1.00 25.00           C
ATOM    316  CA  ILE   316     129.345  24.694  24.606  1.00 25.00           C
ATOM    317  CA  ASP   317     128.926  25.397  20.865  1.00 25.00           C
ATOM    318  CA  HIS   318     132.555  24.352  20.237  1.00 25.00           C
ATOM    319  CA  ILE   319     131.992  21.117  22.210  1.00 25.00           C
ATOM    320  CA  HIS   320     128.835  20.392  20.166  1.00 25.00           C
ATOM    321  CA  LYS   321     130.773  20.984  16.917  1.00 25.00           C
ATOM    322  CA  TYR   322     133.881  18.754  16.582  1.00 25.00           C
ATOM    323  CA  GLY   323     133.036  15.290  15.370  1.00 25.00           C
ATOM    324  CA  SER   324     129.728  14.206  16.892  1.00 25.00           C
ATOM    325  CA  SER   325     130.993  13.963  20.510  1.00 25.00           C
ATOM    326  CA  HIS   326     133.637  13.999  23.245  1.00 25.00           C
ATOM    327  CA  THR   327     136.037  14.283  26.214  1.00 25.00           C
ATOM    328  CA  ASP   328     135.110  17.469  28.076  1.00 25.00           C
ATOM    329  CA  VAL   329     137.193  20.093  29.903  1.00 25.00           C
ATOM    330  CA  ILE   330     136.038  23.131  31.797  1.00 25.00           C
ATOM    331  CA  VAL   331     139.270  24.418  33.282  1.00 25.00           C
ATOM    332  CA  THR   332     138.147  25.801  36.677  1.00 25.00           C
ATOM    333  CA  GLU   333     138.487  28.343  39.398  1.00 25.00           C
ATOM    334  CA  ASP   334     134.755  28.771  39.941  1.00 25.00           C
ATOM    335  CA  GLU   335     133.229  25.596  41.344  1.00 25.00           C
ATOM    336  CA  ASN   336     129.681  26.770  40.507  1.00 25.00           C
ATOM    337  CA  THR   337     130.816  27.774  36.990  1.00 25.00           C
ATOM    338  CA  ALA   338     132.447  24.342  36.510  1.00 25.00           C
ATOM    339  CA  GLU   339     129.223  22.622  37.656  1.00 25.00           C
ATOM    340  CA  PHE   340     127.189  24.742  35.201  1.00 25.00           C
ATOM    341  CA  PHE   341     129.598  23.817  32.370  1.00 25.00           C
ATOM    342  CA  LEU   342     129.273  20.109  33.272  1.00 25.00           C
ATOM    343  CA  GLN   343     125.456  20.413  33.252  1.00 25.00           C
ATOM    344  CA  HIS   344     125.585  22.107  29.819  1.00 25.00           C
ATOM    345  CA  VAL   345     127.810  20.057  27.496  1.00 25.00           C
ATOM    346  CA  ASP   346     126.889  16.380  27.416  1.00 25.00           C
ATOM    347  CA  SER   347     128.781  14.144  24.997  1.00 25.00           C
ATOM    348  CA  ALA   348     130.809  11.356  26.543  1.00 25.00           C
ATOM    349  CA  CYS   349     132.420  12.035  29.892  1.00 25.00           C
ATOM    350  CA  VAL   350     132.644  15.170  31.980  1.00 25.00           C
ATOM    351  CA  PHE   351     135.575  16.238  34.187  1.00 25.00           C
ATOM    352  CA  TRP   352     136.127  19.684  35.729  1.00 25.00           C
ATOM    353  CA  ASN   353     139.823  20.015  36.631  1.00 25.00           C
ATOM    354  CA  ALA   354     142.924  18.294  35.194  1.00 25.00           C
ATOM    355  CA  SER   355     142.831  17.479  31.467  1.00 25.00           C
ATOM    356  CA  THR   356     140.939  14.423  30.150  1.00 25.00           C
ATOM    357  CA  ARG   357     143.921  12.074  30.661  1.00 25.00           C
ATOM    358  CA  PHE   358     141.622   9.467  32.270  1.00 25.00           C
ATOM    359  CA  SER   359     139.051   8.022  29.807  1.00 25.00           C
TER
END
