
#######################################################
#                                                     #
#                        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  136 (  136),  selected  136 , name T0339TS393_1-D1
# Molecule2: number of CA atoms  136 ( 1077),  selected  136 , name T0339_D1.pdb
# PARAMETERS: T0339TS393_1-D1.T0339_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E       1      E       1           -
LGA    R       2      R       2           -
LGA    -       -      K       3           -
LGA    -       -      V       4           -
LGA    K       3      Y       5           #
LGA    V       4      M       6           -
LGA    -       -      D       7           -
LGA    Y       5      Y       8          4.125
LGA    M       6      E     289           -
LGA    D       7      A     290           -
LGA    Y       8      Y     291           -
LGA    E     289      E     292          1.589
LGA    -       -      A     293           -
LGA    A     290      H     294          3.544
LGA    Y     291      M     295          2.926
LGA    E     292      R     296          2.450
LGA    A     293      D     297          2.518
LGA    H     294      V     298          1.866
LGA    M     295      R     299          0.686
LGA    R     296      D     300          1.113
LGA    D     297      Y     301          1.310
LGA    V     298      L     302          0.699
LGA    R     299      E     303          2.046
LGA    D     300      E     304          2.620
LGA    Y     301      R     305          1.864
LGA    L     302      L     306          3.216
LGA    E     303      E     307          4.563
LGA    E     304      A     308          3.863
LGA    R     305      E     309          3.671
LGA    L     306      -       -           -
LGA    E     307      -       -           -
LGA    A     308      -       -           -
LGA    E     309      -       -           -
LGA    F     310      F     310          4.405
LGA    G     311      G     311          3.729
LGA    -       -      Q     312           -
LGA    Q     312      K     313          4.153
LGA    K     313      R     314          3.045
LGA    R     314      I     315          2.077
LGA    I     315      H     316          2.377
LGA    H     316      L     317          3.410
LGA    L     317      N     318          2.277
LGA    N     318      S     319          3.364
LGA    S     319      Q     320          4.956
LGA    Q     320      -       -           -
LGA    F     321      F     321          4.731
LGA    P     322      -       -           -
LGA    G     323      P     322           #
LGA    T     324      G     323          4.720
LGA    Q     325      T     324          4.811
LGA    R     326      Q     325          4.872
LGA    L     327      R     326          0.917
LGA    P     328      L     327          1.457
LGA    -       -      P     328           -
LGA    N     329      N     329          3.828
LGA    T     330      T     330          1.907
LGA    C     331      C     331          2.224
LGA    N     332      N     332          2.407
LGA    F     333      F     333          5.158
LGA    S     334      S     334           #
LGA    I     335      -       -           -
LGA    R     336      I     335           #
LGA    G     337      R     336          3.034
LGA    P     338      G     337          4.159
LGA    -       -      P     338           -
LGA    -       -      R     339           -
LGA    R     339      L     340          1.249
LGA    L     340      Q     341          2.605
LGA    -       -      G     342           -
LGA    Q     341      H     343          2.320
LGA    G     342      V     344          2.610
LGA    H     343      V     345          1.522
LGA    V     344      L     346          0.725
LGA    V     345      A     347          1.420
LGA    L     346      Q     348          2.375
LGA    A     347      C     349          2.505
LGA    Q     348      -       -           -
LGA    C     349      -       -           -
LGA    R     350      R     350          1.854
LGA    V     351      V     351          1.986
LGA    L     352      L     352          2.322
LGA    M     353      M     353          2.497
LGA    A     354      A     354          1.496
LGA    S     355      S     355          2.354
LGA    V     356      V     356           #
LGA    G     357      -       -           -
LGA    A     358      -       -           -
LGA    A     359      -       -           -
LGA    C     360      -       -           -
LGA    H     361      -       -           -
LGA    S     362      -       -           -
LGA    D     363      G     357          1.100
LGA    H     364      -       -           -
LGA    G     365      A     358          3.502
LGA    -       -      A     359           -
LGA    D     366      C     360          3.051
LGA    -       -      H     361           -
LGA    -       -      S     362           -
LGA    Q     367      D     363          4.744
LGA    -       -      H     364           -
LGA    -       -      G     365           -
LGA    -       -      D     366           -
LGA    -       -      Q     367           -
LGA    P     368      P     368          5.310
LGA    S     369      S     369          2.950
LGA    P     370      P     370          1.798
LGA    V     371      V     371          0.841
LGA    L     372      L     372          2.027
LGA    L     373      L     373          2.140
LGA    S     374      S     374          1.054
LGA    Y     375      Y     375          0.547
LGA    G     376      G     376          1.043
LGA    V     377      V     377          2.060
LGA    P     378      P     378          4.138
LGA    F     379      F     379          3.571
LGA    D     380      D     380          3.685
LGA    V     381      V     381          3.259
LGA    A     382      A     382          1.527
LGA    R     383      R     383           #
LGA    N     384      N     384          3.285
LGA    A     385      A     385          3.281
LGA    L     386      L     386          1.140
LGA    R     387      R     387          2.812
LGA    L     388      L     388          1.849
LGA    S     389      S     389          1.863
LGA    V     390      V     390          1.787
LGA    G     391      G     391          2.393
LGA    R     392      R     392          2.894
LGA    S     393      S     393          1.540
LGA    T     394      T     394          1.631
LGA    T     395      T     395          2.451
LGA    R     396      R     396          2.075
LGA    A     397      A     397          2.312
LGA    E     398      E     398          2.222
LGA    V     399      V     399          1.193
LGA    D     400      D     400          1.074
LGA    L     401      L     401          1.718
LGA    V     402      V     402          1.105
LGA    V     403      V     403          0.364
LGA    Q     404      Q     404          1.113
LGA    D     405      D     405          1.094
LGA    L     406      L     406          0.304
LGA    K     407      K     407          1.195
LGA    Q     408      Q     408          1.313
LGA    A     409      A     409          0.676
LGA    V     410      V     410          1.027
LGA    A     411      A     411          1.460
LGA    Q     412      Q     412          1.328
LGA    L     413      L     413          1.197
LGA    E     414      E     414          1.596
LGA    D     415      D     415          1.878
LGA    Q     416      Q     416           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  136  136    5.0    107    2.67    60.75     47.867     3.865

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.747142 * X  +  -0.427371 * Y  +   0.509051 * Z  +  -8.737823
  Y_new =  -0.539954 * X  +  -0.056349 * Y  +  -0.839806 * Z  + -11.544186
  Z_new =   0.387593 * X  +  -0.902319 * Y  +  -0.188660 * Z  +  10.528456 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.776911    1.364682  [ DEG:  -101.8095     78.1905 ]
  Theta =  -0.398019   -2.743574  [ DEG:   -22.8048   -157.1952 ]
  Phi   =  -2.515798    0.625794  [ DEG:  -144.1446     35.8554 ]
 
# 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: T0339TS393_1-D1                               
REMARK     2: T0339_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0339TS393_1-D1.T0339_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  136  136   5.0  107   2.67   60.75  47.867
REMARK  ---------------------------------------------------------- 
MOLECULE T0339TS393_1-D1
PFRMAT TS
TARGET T0339
MODEL 1
PARENT N/A
ATOM      1  CA  GLU     1      -7.920 -33.302  29.226  1.00 25.00           C
ATOM      2  CA  ARG     2      -6.427 -34.781  26.055  1.00 25.00           C
ATOM      3  CA  LYS     3      -8.437 -32.996  23.286  1.00 25.00           C
ATOM      4  CA  VAL     4      -8.214 -29.308  22.230  1.00 25.00           C
ATOM      5  CA  TYR     5      -9.349 -28.066  18.785  1.00 25.00           C
ATOM      6  CA  MET     6     -11.886 -25.833  17.083  1.00 25.00           C
ATOM      7  CA  ASP     7      -9.622 -23.411  15.206  1.00 25.00           C
ATOM      8  CA  TYR     8      -9.592 -21.187  18.322  1.00 25.00           C
ATOM    289  CA  GLU   289       0.837 -24.321   9.496  1.00 25.00           C
ATOM    290  CA  ALA   290       0.218 -27.990  10.407  1.00 25.00           C
ATOM    291  CA  TYR   291      -3.414 -27.694   9.232  1.00 25.00           C
ATOM    292  CA  GLU   292      -2.246 -26.142   5.931  1.00 25.00           C
ATOM    293  CA  ALA   293       0.269 -28.991   5.453  1.00 25.00           C
ATOM    294  CA  HIS   294      -2.485 -31.566   6.121  1.00 25.00           C
ATOM    295  CA  MET   295      -4.756 -29.837   3.567  1.00 25.00           C
ATOM    296  CA  ARG   296      -1.926 -29.875   0.987  1.00 25.00           C
ATOM    297  CA  ASP   297      -1.351 -33.606   1.638  1.00 25.00           C
ATOM    298  CA  VAL   298      -5.093 -34.285   1.192  1.00 25.00           C
ATOM    299  CA  ARG   299      -5.081 -32.333  -2.102  1.00 25.00           C
ATOM    300  CA  ASP   300      -2.055 -34.345  -3.312  1.00 25.00           C
ATOM    301  CA  TYR   301      -3.829 -37.612  -2.396  1.00 25.00           C
ATOM    302  CA  LEU   302      -6.952 -36.479  -4.303  1.00 25.00           C
ATOM    303  CA  GLU   303      -4.805 -35.619  -7.356  1.00 25.00           C
ATOM    304  CA  GLU   304      -3.141 -39.065  -7.187  1.00 25.00           C
ATOM    305  CA  ARG   305      -6.579 -40.742  -6.993  1.00 25.00           C
ATOM    306  CA  LEU   306      -7.760 -38.727 -10.027  1.00 25.00           C
ATOM    307  CA  GLU   307      -4.625 -39.763 -11.967  1.00 25.00           C
ATOM    308  CA  ALA   308      -5.244 -43.432 -11.057  1.00 25.00           C
ATOM    309  CA  GLU   309      -8.877 -43.136 -12.232  1.00 25.00           C
ATOM    310  CA  PHE   310     -11.159 -42.403  -9.260  1.00 25.00           C
ATOM    311  CA  GLY   311     -14.424 -40.898  -7.947  1.00 25.00           C
ATOM    312  CA  GLN   312     -16.560 -37.809  -8.623  1.00 25.00           C
ATOM    313  CA  LYS   313     -15.626 -36.447  -5.170  1.00 25.00           C
ATOM    314  CA  ARG   314     -17.105 -32.958  -5.801  1.00 25.00           C
ATOM    315  CA  ILE   315     -15.117 -30.848  -3.329  1.00 25.00           C
ATOM    316  CA  HIS   316     -16.380 -27.774  -1.492  1.00 25.00           C
ATOM    317  CA  LEU   317     -13.417 -25.381  -1.148  1.00 25.00           C
ATOM    318  CA  ASN   318     -13.654 -21.987  -2.792  1.00 25.00           C
ATOM    319  CA  SER   319     -15.187 -24.173  -5.496  1.00 25.00           C
ATOM    320  CA  GLN   320     -12.647 -24.164  -8.333  1.00 25.00           C
ATOM    321  CA  PHE   321     -10.183 -24.192  -5.418  1.00 25.00           C
ATOM    322  CA  PRO   322      -7.321 -24.573  -7.856  1.00 25.00           C
ATOM    323  CA  GLY   323      -3.974 -24.445  -6.155  1.00 25.00           C
ATOM    324  CA  THR   324      -3.980 -20.705  -6.618  1.00 25.00           C
ATOM    325  CA  GLN   325      -5.329 -20.296  -3.108  1.00 25.00           C
ATOM    326  CA  ARG   326      -7.247 -21.447  -0.059  1.00 25.00           C
ATOM    327  CA  LEU   327      -6.294 -19.364   3.014  1.00 25.00           C
ATOM    328  CA  PRO   328      -5.249 -22.017   5.472  1.00 25.00           C
ATOM    329  CA  ASN   329      -8.181 -23.750   7.073  1.00 25.00           C
ATOM    330  CA  THR   330     -10.187 -25.863   4.687  1.00 25.00           C
ATOM    331  CA  CYS   331     -12.709 -28.073   2.881  1.00 25.00           C
ATOM    332  CA  ASN   332     -16.172 -27.154   4.169  1.00 25.00           C
ATOM    333  CA  PHE   333     -19.455 -28.462   2.859  1.00 25.00           C
ATOM    334  CA  SER   334     -22.796 -30.104   2.457  1.00 25.00           C
ATOM    335  CA  ILE   335     -25.133 -32.886   1.432  1.00 25.00           C
ATOM    336  CA  ARG   336     -25.445 -33.792  -2.264  1.00 25.00           C
ATOM    337  CA  GLY   337     -23.959 -36.427  -4.480  1.00 25.00           C
ATOM    338  CA  PRO   338     -21.829 -37.620  -1.554  1.00 25.00           C
ATOM    339  CA  ARG   339     -25.131 -38.233   0.159  1.00 25.00           C
ATOM    340  CA  LEU   340     -23.419 -37.187   3.338  1.00 25.00           C
ATOM    341  CA  GLN   341     -24.466 -37.283   7.021  1.00 25.00           C
ATOM    342  CA  GLY   342     -23.975 -41.081   7.087  1.00 25.00           C
ATOM    343  CA  HIS   343     -20.499 -40.684   5.527  1.00 25.00           C
ATOM    344  CA  VAL   344     -19.598 -38.041   8.149  1.00 25.00           C
ATOM    345  CA  VAL   345     -20.786 -40.374  10.944  1.00 25.00           C
ATOM    346  CA  LEU   346     -18.676 -43.224   9.497  1.00 25.00           C
ATOM    347  CA  ALA   347     -15.621 -40.919   9.350  1.00 25.00           C
ATOM    348  CA  GLN   348     -16.193 -39.888  12.994  1.00 25.00           C
ATOM    349  CA  CYS   349     -16.451 -43.568  14.021  1.00 25.00           C
ATOM    350  CA  ARG   350     -13.497 -45.075  12.187  1.00 25.00           C
ATOM    351  CA  VAL   351     -11.526 -42.051  13.442  1.00 25.00           C
ATOM    352  CA  LEU   352     -11.159 -38.430  12.195  1.00 25.00           C
ATOM    353  CA  MET   353     -12.222 -35.177  13.790  1.00 25.00           C
ATOM    354  CA  ALA   354     -13.678 -33.377  10.808  1.00 25.00           C
ATOM    355  CA  SER   355     -15.877 -30.363  11.586  1.00 25.00           C
ATOM    356  CA  VAL   356     -17.524 -27.765  13.797  1.00 25.00           C
ATOM    357  CA  GLY   357     -17.265 -24.414  15.524  1.00 25.00           C
ATOM    358  CA  ALA   358     -13.901 -22.986  16.681  1.00 25.00           C
ATOM    359  CA  ALA   359     -15.640 -19.640  16.961  1.00 25.00           C
ATOM    360  CA  CYS   360     -17.036 -17.515  14.151  1.00 25.00           C
ATOM    361  CA  HIS   361     -16.408 -20.547  11.998  1.00 25.00           C
ATOM    362  CA  SER   362     -15.998 -24.086  10.680  1.00 25.00           C
ATOM    363  CA  ASP   363     -19.166 -25.675   9.387  1.00 25.00           C
ATOM    364  CA  HIS   364     -21.025 -22.774  10.911  1.00 25.00           C
ATOM    365  CA  GLY   365     -22.804 -23.483  14.238  1.00 25.00           C
ATOM    366  CA  ASP   366     -23.962 -26.637  12.384  1.00 25.00           C
ATOM    367  CA  GLN   367     -26.291 -24.429  10.388  1.00 25.00           C
ATOM    368  CA  PRO   368     -24.175 -23.380   7.467  1.00 25.00           C
ATOM    369  CA  SER   369     -27.034 -22.719   5.005  1.00 25.00           C
ATOM    370  CA  PRO   370     -26.515 -18.943   5.378  1.00 25.00           C
ATOM    371  CA  VAL   371     -22.765 -19.370   4.734  1.00 25.00           C
ATOM    372  CA  LEU   372     -23.513 -21.453   1.608  1.00 25.00           C
ATOM    373  CA  LEU   373     -25.932 -18.757   0.362  1.00 25.00           C
ATOM    374  CA  SER   374     -23.270 -16.066   0.944  1.00 25.00           C
ATOM    375  CA  TYR   375     -20.704 -18.151  -0.988  1.00 25.00           C
ATOM    376  CA  GLY   376     -22.187 -18.944  -4.385  1.00 25.00           C
ATOM    377  CA  VAL   377     -23.759 -22.380  -4.306  1.00 25.00           C
ATOM    378  CA  PRO   378     -27.357 -22.110  -3.125  1.00 25.00           C
ATOM    379  CA  PHE   379     -28.217 -24.079   0.036  1.00 25.00           C
ATOM    380  CA  ASP   380     -28.760 -27.625  -1.307  1.00 25.00           C
ATOM    381  CA  VAL   381     -25.705 -27.256  -3.587  1.00 25.00           C
ATOM    382  CA  ALA   382     -23.607 -26.044  -0.621  1.00 25.00           C
ATOM    383  CA  ARG   383     -21.351 -28.920  -1.762  1.00 25.00           C
ATOM    384  CA  ASN   384     -20.281 -32.568  -1.118  1.00 25.00           C
ATOM    385  CA  ALA   385     -20.081 -33.600   2.540  1.00 25.00           C
ATOM    386  CA  LEU   386     -17.956 -32.435   5.509  1.00 25.00           C
ATOM    387  CA  ARG   387     -14.226 -31.793   5.872  1.00 25.00           C
ATOM    388  CA  LEU   388     -12.348 -29.284   8.016  1.00 25.00           C
ATOM    389  CA  SER   389     -10.118 -27.915  10.816  1.00 25.00           C
ATOM    390  CA  VAL   390      -7.618 -30.293   9.338  1.00 25.00           C
ATOM    391  CA  GLY   391      -5.870 -30.432  12.684  1.00 25.00           C
ATOM    392  CA  ARG   392      -2.967 -29.917  15.125  1.00 25.00           C
ATOM    393  CA  SER   393      -0.970 -32.886  13.772  1.00 25.00           C
ATOM    394  CA  THR   394      -1.113 -34.837  10.523  1.00 25.00           C
ATOM    395  CA  THR   395      -0.368 -36.349   7.163  1.00 25.00           C
ATOM    396  CA  ARG   396       0.794 -39.493   5.285  1.00 25.00           C
ATOM    397  CA  ALA   397      -0.209 -43.151   5.804  1.00 25.00           C
ATOM    398  CA  GLU   398      -2.878 -42.086   8.335  1.00 25.00           C
ATOM    399  CA  VAL   399      -4.227 -39.495   5.860  1.00 25.00           C
ATOM    400  CA  ASP   400      -4.368 -42.157   3.110  1.00 25.00           C
ATOM    401  CA  LEU   401      -6.249 -44.522   5.464  1.00 25.00           C
ATOM    402  CA  VAL   402      -8.733 -41.735   6.318  1.00 25.00           C
ATOM    403  CA  VAL   403      -9.268 -41.036   2.591  1.00 25.00           C
ATOM    404  CA  GLN   404      -9.877 -44.763   1.953  1.00 25.00           C
ATOM    405  CA  ASP   405     -12.409 -44.865   4.825  1.00 25.00           C
ATOM    406  CA  LEU   406     -14.200 -41.800   3.387  1.00 25.00           C
ATOM    407  CA  LYS   407     -14.324 -43.460  -0.062  1.00 25.00           C
ATOM    408  CA  GLN   408     -15.769 -46.646   1.496  1.00 25.00           C
ATOM    409  CA  ALA   409     -18.422 -44.577   3.327  1.00 25.00           C
ATOM    410  CA  VAL   410     -19.334 -42.806   0.056  1.00 25.00           C
ATOM    411  CA  ALA   411     -19.644 -46.187  -1.717  1.00 25.00           C
ATOM    412  CA  GLN   412     -21.902 -47.481   1.093  1.00 25.00           C
ATOM    413  CA  LEU   413     -24.088 -44.348   0.812  1.00 25.00           C
ATOM    414  CA  GLU   414     -24.348 -44.841  -2.977  1.00 25.00           C
ATOM    415  CA  ASP   415     -25.352 -48.500  -2.457  1.00 25.00           C
ATOM    416  CA  GLN   416     -23.734 -49.016  -5.850  1.00 25.00           C
TER
END
