
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms  144 ( 1137),  selected  144 , name T0310_D2.pdb
# PARAMETERS: T0310TS393_4-D2.T0310_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      E     216           -
LGA    -       -      G     217           -
LGA    E     216      I     218           #
LGA    G     217      C     219           -
LGA    I     218      -       -           -
LGA    C     219      H     220           #
LGA    H     220      M     221           -
LGA    M     221      Y     222           #
LGA    Y     222      V     223           #
LGA    V     223      D     224          1.413
LGA    D     224      S     225          3.162
LGA    S     225      E     226           #
LGA    -       -      A     227           -
LGA    -       -      S     228           -
LGA    E     226      V     229          3.301
LGA    A     227      D     230           #
LGA    -       -      K     231           -
LGA    S     228      V     232          4.288
LGA    V     229      T     233           -
LGA    D     230      R     234           -
LGA    K     231      L     235           -
LGA    -       -      V     236           -
LGA    -       -      R     237           -
LGA    -       -      D     238           -
LGA    -       -      S     239           -
LGA    -       -      K     240           -
LGA    -       -      C     241           -
LGA    -       -      E     242           -
LGA    -       -      Y     243           -
LGA    -       -      P     244           -
LGA    -       -      A     245           -
LGA    -       -      A     246           -
LGA    -       -      C     247           -
LGA    -       -      N     248           -
LGA    -       -      A     249           -
LGA    -       -      L     250           -
LGA    -       -      E     251           -
LGA    V     232      T     252           #
LGA    T     233      L     253           #
LGA    R     234      -       -           -
LGA    L     235      -       -           -
LGA    V     236      L     254          4.412
LGA    R     237      -       -           -
LGA    D     238      -       -           -
LGA    S     239      -       -           -
LGA    K     240      -       -           -
LGA    C     241      -       -           -
LGA    E     242      -       -           -
LGA    Y     243      -       -           -
LGA    P     244      -       -           -
LGA    A     245      -       -           -
LGA    A     246      -       -           -
LGA    C     247      -       -           -
LGA    N     248      -       -           -
LGA    A     249      -       -           -
LGA    L     250      -       -           -
LGA    E     251      -       -           -
LGA    T     252      I     255          4.901
LGA    L     253      H     256          3.485
LGA    L     254      R     257          5.092
LGA    -       -      D     258           -
LGA    -       -      L     259           -
LGA    -       -      L     260           -
LGA    -       -      R     261           -
LGA    -       -      T     262           -
LGA    -       -      P     263           -
LGA    I     255      L     264           #
LGA    H     256      F     265          2.343
LGA    R     257      D     266          3.085
LGA    D     258      Q     267          2.206
LGA    L     259      I     268          2.203
LGA    L     260      I     269          2.197
LGA    R     261      D     270          1.784
LGA    T     262      M     271          1.335
LGA    P     263      L     272          0.569
LGA    -       -      R     273           -
LGA    -       -      V     274           -
LGA    -       -      E     275           -
LGA    L     264      Q     276           #
LGA    F     265      V     277           #
LGA    D     266      K     278          3.692
LGA    Q     267      I     279          1.185
LGA    I     268      H     280          3.479
LGA    I     269      -       -           -
LGA    D     270      -       -           -
LGA    M     271      A     281          3.014
LGA    L     272      G     282          3.995
LGA    R     273      P     283           -
LGA    -       -      K     284           -
LGA    -       -      F     285           -
LGA    -       -      A     286           -
LGA    -       -      S     287           -
LGA    -       -      Y     288           -
LGA    -       -      L     289           -
LGA    -       -      T     290           -
LGA    -       -      F     291           -
LGA    V     274      V     292          2.141
LGA    E     275      K     293          0.736
LGA    Q     276      S     294          3.069
LGA    -       -      L     295           -
LGA    V     277      R     296           #
LGA    K     278      T     297          3.134
LGA    I     279      E     298          4.295
LGA    H     280      Y     299           #
LGA    A     281      -       -           -
LGA    G     282      -       -           -
LGA    P     283      -       -           -
LGA    K     284      -       -           -
LGA    F     285      -       -           -
LGA    A     286      -       -           -
LGA    S     287      -       -           -
LGA    Y     288      -       -           -
LGA    L     289      -       -           -
LGA    T     290      G     300          4.482
LGA    F     291      D     301          2.454
LGA    V     292      L     302          0.675
LGA    K     293      -       -           -
LGA    S     294      -       -           -
LGA    L     295      E     303          4.009
LGA    R     296      -       -           -
LGA    T     297      -       -           -
LGA    E     298      -       -           -
LGA    Y     299      -       -           -
LGA    G     300      -       -           -
LGA    D     301      L     304           #
LGA    L     302      C     305          4.557
LGA    E     303      I     306           #
LGA    L     304      E     307           #
LGA    -       -      V     308           -
LGA    -       -      V     309           -
LGA    -       -      D     310           -
LGA    -       -      N     311           -
LGA    -       -      V     312           -
LGA    -       -      Q     313           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      D     317           -
LGA    -       -      H     318           -
LGA    -       -      I     319           -
LGA    -       -      H     320           -
LGA    -       -      K     321           -
LGA    -       -      Y     322           -
LGA    C     305      G     323           #
LGA    I     306      S     324           -
LGA    E     307      -       -           -
LGA    V     308      -       -           -
LGA    V     309      -       -           -
LGA    D     310      -       -           -
LGA    N     311      -       -           -
LGA    V     312      -       -           -
LGA    Q     313      -       -           -
LGA    D     314      -       -           -
LGA    A     315      -       -           -
LGA    I     316      -       -           -
LGA    D     317      -       -           -
LGA    H     318      -       -           -
LGA    I     319      -       -           -
LGA    H     320      -       -           -
LGA    K     321      -       -           -
LGA    Y     322      -       -           -
LGA    G     323      -       -           -
LGA    S     324      -       -           -
LGA    S     325      S     325          5.416
LGA    H     326      H     326          5.205
LGA    T     327      T     327           #
LGA    D     328      D     328          4.256
LGA    V     329      V     329          2.805
LGA    I     330      I     330          1.366
LGA    V     331      V     331          1.558
LGA    T     332      T     332          3.528
LGA    E     333      -       -           -
LGA    D     334      -       -           -
LGA    E     335      -       -           -
LGA    N     336      -       -           -
LGA    T     337      -       -           -
LGA    A     338      E     333          0.750
LGA    E     339      -       -           -
LGA    F     340      D     334          2.306
LGA    -       -      E     335           -
LGA    -       -      N     336           -
LGA    F     341      T     337          4.636
LGA    L     342      A     338          4.734
LGA    Q     343      -       -           -
LGA    H     344      -       -           -
LGA    V     345      E     339          4.096
LGA    D     346      F     340           -
LGA    S     347      -       -           -
LGA    A     348      -       -           -
LGA    C     349      -       -           -
LGA    V     350      F     341          1.144
LGA    F     351      L     342           #
LGA    -       -      Q     343           -
LGA    -       -      H     344           -
LGA    -       -      V     345           -
LGA    -       -      D     346           -
LGA    -       -      S     347           -
LGA    -       -      A     348           -
LGA    -       -      C     349           -
LGA    -       -      V     350           -
LGA    -       -      F     351           -
LGA    -       -      W     352           -
LGA    W     352      N     353           #
LGA    N     353      A     354           -
LGA    A     354      S     355           -
LGA    S     355      T     356           -
LGA    T     356      R     357           -
LGA    R     357      F     358           -
LGA    F     358      S     359           -
LGA    S     359      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  144  144    5.0     44    3.31    18.18     17.549     1.289

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.154618 * X  +   0.010171 * Y  +   0.987922 * Z  + 124.818573
  Y_new =   0.734849 * X  +   0.667190 * Y  +  -0.121879 * Z  +  16.045467
  Z_new =  -0.660371 * X  +   0.744818 * Y  +   0.095686 * Z  +  17.767782 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.443028   -1.698565  [ DEG:    82.6794    -97.3206 ]
  Theta =   0.721313    2.420280  [ DEG:    41.3282    138.6718 ]
  Phi   =   1.363413   -1.778179  [ DEG:    78.1178   -101.8822 ]
 
# 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_4-D2                               
REMARK     2: T0310_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0310TS393_4-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   44   3.31   18.18  17.549
REMARK  ---------------------------------------------------------- 
MOLECULE T0310TS393_4-D2
PFRMAT TS
TARGET T0310
MODEL 4
PARENT N/A
ATOM    216  CA  GLU   216     127.250  17.443  20.713  1.00 25.00           C
ATOM    217  CA  GLY   217     126.977  20.833  22.514  1.00 25.00           C
ATOM    218  CA  ILE   218     125.767  22.938  25.440  1.00 25.00           C
ATOM    219  CA  CYS   219     129.345  24.239  25.683  1.00 25.00           C
ATOM    220  CA  HIS   220     131.044  27.565  26.289  1.00 25.00           C
ATOM    221  CA  MET   221     132.945  30.545  27.768  1.00 25.00           C
ATOM    222  CA  TYR   222     135.874  32.346  29.395  1.00 25.00           C
ATOM    223  CA  VAL   223     138.268  31.166  32.092  1.00 25.00           C
ATOM    224  CA  ASP   224     141.050  33.168  33.591  1.00 25.00           C
ATOM    225  CA  SER   225     143.107  36.153  34.696  1.00 25.00           C
ATOM    226  CA  GLU   226     146.011  33.768  34.956  1.00 25.00           C
ATOM    227  CA  ALA   227     146.310  30.651  32.689  1.00 25.00           C
ATOM    228  CA  SER   228     144.182  28.884  30.124  1.00 25.00           C
ATOM    229  CA  VAL   229     144.915  30.703  26.930  1.00 25.00           C
ATOM    230  CA  ASP   230     145.194  33.214  24.051  1.00 25.00           C
ATOM    231  CA  LYS   231     145.671  30.345  21.561  1.00 25.00           C
ATOM    232  CA  VAL   232     142.592  28.566  22.984  1.00 25.00           C
ATOM    233  CA  THR   233     140.549  31.789  22.659  1.00 25.00           C
ATOM    234  CA  ARG   234     141.703  32.184  19.029  1.00 25.00           C
ATOM    235  CA  LEU   235     140.710  28.559  18.293  1.00 25.00           C
ATOM    236  CA  VAL   236     137.267  29.158  19.858  1.00 25.00           C
ATOM    237  CA  ARG   237     136.821  32.311  17.729  1.00 25.00           C
ATOM    238  CA  ASP   238     137.785  30.352  14.583  1.00 25.00           C
ATOM    239  CA  SER   239     135.261  27.615  15.484  1.00 25.00           C
ATOM    240  CA  LYS   240     132.539  30.260  15.996  1.00 25.00           C
ATOM    241  CA  CYS   241     133.208  31.328  12.360  1.00 25.00           C
ATOM    242  CA  GLU   242     131.934  28.313  10.394  1.00 25.00           C
ATOM    243  CA  TYR   243     128.255  27.724  11.345  1.00 25.00           C
ATOM    244  CA  PRO   244     127.255  31.189  12.413  1.00 25.00           C
ATOM    245  CA  ALA   245     125.474  29.233  15.081  1.00 25.00           C
ATOM    246  CA  ALA   246     123.104  26.207  15.152  1.00 25.00           C
ATOM    247  CA  CYS   247     125.823  23.631  14.442  1.00 25.00           C
ATOM    248  CA  ASN   248     128.307  22.557  17.115  1.00 25.00           C
ATOM    249  CA  ALA   249     127.410  25.150  19.728  1.00 25.00           C
ATOM    250  CA  LEU   250     129.790  27.406  21.668  1.00 25.00           C
ATOM    251  CA  GLU   251     132.422  30.083  21.892  1.00 25.00           C
ATOM    252  CA  THR   252     135.226  31.953  23.531  1.00 25.00           C
ATOM    253  CA  LEU   253     137.884  30.225  25.619  1.00 25.00           C
ATOM    254  CA  LEU   254     140.020  32.810  27.506  1.00 25.00           C
ATOM    255  CA  ILE   255     142.573  35.435  28.472  1.00 25.00           C
ATOM    256  CA  HIS   256     146.195  34.379  29.025  1.00 25.00           C
ATOM    257  CA  ARG   257     149.532  32.633  28.504  1.00 25.00           C
ATOM    258  CA  ASP   258     151.599  29.714  29.872  1.00 25.00           C
ATOM    259  CA  LEU   259     149.445  27.234  27.900  1.00 25.00           C
ATOM    260  CA  LEU   260     149.926  29.309  24.717  1.00 25.00           C
ATOM    261  CA  ARG   261     153.712  29.362  25.295  1.00 25.00           C
ATOM    262  CA  THR   262     153.716  25.563  25.777  1.00 25.00           C
ATOM    263  CA  PRO   263     152.529  25.084  22.194  1.00 25.00           C
ATOM    264  CA  LEU   264     149.698  26.177  19.993  1.00 25.00           C
ATOM    265  CA  PHE   265     150.128  29.530  18.193  1.00 25.00           C
ATOM    266  CA  ASP   266     150.489  27.711  14.842  1.00 25.00           C
ATOM    267  CA  GLN   267     147.314  25.697  15.563  1.00 25.00           C
ATOM    268  CA  ILE   268     145.434  28.922  16.421  1.00 25.00           C
ATOM    269  CA  ILE   269     146.643  30.524  13.159  1.00 25.00           C
ATOM    270  CA  ASP   270     145.482  27.450  11.192  1.00 25.00           C
ATOM    271  CA  MET   271     142.056  27.624  12.894  1.00 25.00           C
ATOM    272  CA  LEU   272     141.786  31.344  12.028  1.00 25.00           C
ATOM    273  CA  ARG   273     142.686  30.585   8.382  1.00 25.00           C
ATOM    274  CA  VAL   274     140.023  27.835   8.272  1.00 25.00           C
ATOM    275  CA  GLU   275     138.783  24.391   7.219  1.00 25.00           C
ATOM    276  CA  GLN   276     138.746  20.811   8.634  1.00 25.00           C
ATOM    277  CA  VAL   277     140.829  18.585  10.836  1.00 25.00           C
ATOM    278  CA  LYS   278     141.447  17.343  14.357  1.00 25.00           C
ATOM    279  CA  ILE   279     142.943  17.698  17.832  1.00 25.00           C
ATOM    280  CA  HIS   280     142.707  14.952  20.420  1.00 25.00           C
ATOM    281  CA  ALA   281     143.062  12.602  23.300  1.00 25.00           C
ATOM    282  CA  GLY   282     144.476  10.803  26.300  1.00 25.00           C
ATOM    283  CA  PRO   283     147.597  10.508  28.455  1.00 25.00           C
ATOM    284  CA  LYS   284     147.143  14.264  27.861  1.00 25.00           C
ATOM    285  CA  PHE   285     150.801  14.557  26.765  1.00 25.00           C
ATOM    286  CA  ALA   286     150.342  11.614  24.359  1.00 25.00           C
ATOM    287  CA  SER   287     147.201  13.256  22.909  1.00 25.00           C
ATOM    288  CA  TYR   288     149.109  16.544  22.438  1.00 25.00           C
ATOM    289  CA  LEU   289     151.944  14.673  20.670  1.00 25.00           C
ATOM    290  CA  THR   290     149.409  12.950  18.374  1.00 25.00           C
ATOM    291  CA  PHE   291     147.811  16.333  17.558  1.00 25.00           C
ATOM    292  CA  VAL   292     151.259  17.796  16.756  1.00 25.00           C
ATOM    293  CA  LYS   293     152.017  14.818  14.469  1.00 25.00           C
ATOM    294  CA  SER   294     148.664  15.304  12.684  1.00 25.00           C
ATOM    295  CA  LEU   295     149.427  19.027  12.209  1.00 25.00           C
ATOM    296  CA  ARG   296     152.873  18.162  10.778  1.00 25.00           C
ATOM    297  CA  THR   297     151.270  15.654   8.369  1.00 25.00           C
ATOM    298  CA  GLU   298     148.739  18.304   7.255  1.00 25.00           C
ATOM    299  CA  TYR   299     151.578  20.806   6.669  1.00 25.00           C
ATOM    300  CA  GLY   300     148.882  22.818   8.492  1.00 25.00           C
ATOM    301  CA  ASP   301     145.620  22.043  10.374  1.00 25.00           C
ATOM    302  CA  LEU   302     142.792  22.800  12.801  1.00 25.00           C
ATOM    303  CA  GLU   303     140.159  22.184  15.479  1.00 25.00           C
ATOM    304  CA  LEU   304     138.269  22.625  18.744  1.00 25.00           C
ATOM    305  CA  CYS   305     139.253  19.777  21.099  1.00 25.00           C
ATOM    306  CA  ILE   306     140.786  21.530  24.069  1.00 25.00           C
ATOM    307  CA  GLU   307     142.761  22.057  27.264  1.00 25.00           C
ATOM    308  CA  VAL   308     145.744  23.542  29.110  1.00 25.00           C
ATOM    309  CA  VAL   309     148.450  22.802  31.732  1.00 25.00           C
ATOM    310  CA  ASP   310     148.666  22.634  35.489  1.00 25.00           C
ATOM    311  CA  ASN   311     145.800  24.187  37.439  1.00 25.00           C
ATOM    312  CA  VAL   312     142.375  22.505  37.869  1.00 25.00           C
ATOM    313  CA  GLN   313     143.609  18.883  37.730  1.00 25.00           C
ATOM    314  CA  ASP   314     140.252  17.659  39.108  1.00 25.00           C
ATOM    315  CA  ALA   315     138.390  19.726  36.475  1.00 25.00           C
ATOM    316  CA  ILE   316     140.601  18.250  33.719  1.00 25.00           C
ATOM    317  CA  ASP   317     139.901  14.715  35.015  1.00 25.00           C
ATOM    318  CA  HIS   318     136.141  15.438  35.028  1.00 25.00           C
ATOM    319  CA  ILE   319     136.353  16.741  31.434  1.00 25.00           C
ATOM    320  CA  HIS   320     138.247  13.586  30.375  1.00 25.00           C
ATOM    321  CA  LYS   321     135.584  11.397  32.045  1.00 25.00           C
ATOM    322  CA  TYR   322     133.547  11.689  28.845  1.00 25.00           C
ATOM    323  CA  GLY   323     131.112  14.278  30.268  1.00 25.00           C
ATOM    324  CA  SER   324     127.517  13.784  29.127  1.00 25.00           C
ATOM    325  CA  SER   325     126.730  15.944  26.081  1.00 25.00           C
ATOM    326  CA  HIS   326     130.198  15.915  24.626  1.00 25.00           C
ATOM    327  CA  THR   327     130.478  19.337  26.214  1.00 25.00           C
ATOM    328  CA  ASP   328     133.531  21.579  26.800  1.00 25.00           C
ATOM    329  CA  VAL   329     135.685  22.344  29.760  1.00 25.00           C
ATOM    330  CA  ILE   330     137.186  23.964  32.848  1.00 25.00           C
ATOM    331  CA  VAL   331     140.632  25.466  32.351  1.00 25.00           C
ATOM    332  CA  THR   332     141.556  28.328  34.700  1.00 25.00           C
ATOM    333  CA  GLU   333     143.597  29.149  37.787  1.00 25.00           C
ATOM    334  CA  ASP   334     142.243  32.582  38.688  1.00 25.00           C
ATOM    335  CA  GLU   335     141.207  31.309  42.090  1.00 25.00           C
ATOM    336  CA  ASN   336     137.468  32.052  42.473  1.00 25.00           C
ATOM    337  CA  THR   337     136.898  31.208  38.780  1.00 25.00           C
ATOM    338  CA  ALA   338     138.808  27.917  39.213  1.00 25.00           C
ATOM    339  CA  GLU   339     136.690  27.062  42.286  1.00 25.00           C
ATOM    340  CA  PHE   340     133.490  27.809  40.319  1.00 25.00           C
ATOM    341  CA  PHE   341     134.694  25.562  37.460  1.00 25.00           C
ATOM    342  CA  LEU   342     135.450  22.755  39.952  1.00 25.00           C
ATOM    343  CA  GLN   343     131.957  23.135  41.478  1.00 25.00           C
ATOM    344  CA  HIS   344     130.389  22.969  37.987  1.00 25.00           C
ATOM    345  CA  VAL   345     131.093  19.542  36.564  1.00 25.00           C
ATOM    346  CA  ASP   346     131.026  15.939  35.445  1.00 25.00           C
ATOM    347  CA  SER   347     127.891  16.823  33.448  1.00 25.00           C
ATOM    348  CA  ALA   348     125.819  18.609  30.788  1.00 25.00           C
ATOM    349  CA  CYS   349     126.964  22.234  31.144  1.00 25.00           C
ATOM    350  CA  VAL   350     130.486  23.583  31.791  1.00 25.00           C
ATOM    351  CA  PHE   351     132.913  26.523  31.634  1.00 25.00           C
ATOM    352  CA  TRP   352     136.241  27.127  29.841  1.00 25.00           C
ATOM    353  CA  ASN   353     138.086  25.941  26.687  1.00 25.00           C
ATOM    354  CA  ALA   354     135.371  26.163  24.024  1.00 25.00           C
ATOM    355  CA  SER   355     133.461  24.242  21.364  1.00 25.00           C
ATOM    356  CA  THR   356     132.349  20.759  20.242  1.00 25.00           C
ATOM    357  CA  ARG   357     133.595  22.002  16.840  1.00 25.00           C
ATOM    358  CA  PHE   358     131.400  19.415  15.063  1.00 25.00           C
ATOM    359  CA  SER   359     129.406  16.209  14.917  1.00 25.00           C
TER
END
