
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  136 ( 1077),  selected  136 , name T0339_D1.pdb
# PARAMETERS: T0339TS393_3-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      K       3           -
LGA    -       -      V       4           -
LGA    V       4      Y       5          5.331
LGA    -       -      M       6           -
LGA    Y       5      D       7           #
LGA    M       6      Y       8          2.117
LGA    D       7      E     289           -
LGA    Y       8      A     290           -
LGA    -       -      Y     291           -
LGA    -       -      E     292           -
LGA    E     289      A     293          4.604
LGA    A     290      H     294          4.474
LGA    Y     291      M     295          3.567
LGA    E     292      R     296          2.451
LGA    A     293      D     297          2.738
LGA    H     294      V     298          2.776
LGA    M     295      R     299          1.516
LGA    R     296      D     300          0.580
LGA    D     297      Y     301          1.143
LGA    V     298      L     302          2.173
LGA    R     299      E     303          2.103
LGA    D     300      E     304          1.343
LGA    Y     301      R     305          2.183
LGA    L     302      L     306           #
LGA    E     303      E     307           #
LGA    E     304      A     308          3.061
LGA    -       -      E     309           -
LGA    R     305      F     310           #
LGA    L     306      G     311           #
LGA    E     307      Q     312           #
LGA    A     308      -       -           -
LGA    E     309      -       -           -
LGA    F     310      -       -           -
LGA    G     311      K     313          6.019
LGA    Q     312      R     314          1.199
LGA    K     313      -       -           -
LGA    R     314      I     315          2.644
LGA    I     315      H     316          2.421
LGA    H     316      L     317          3.573
LGA    L     317      N     318          1.869
LGA    N     318      S     319          2.115
LGA    S     319      Q     320          3.481
LGA    Q     320      F     321          2.575
LGA    F     321      P     322          5.151
LGA    P     322      G     323          5.250
LGA    G     323      T     324           -
LGA    T     324      -       -           -
LGA    Q     325      Q     325          4.948
LGA    R     326      R     326          3.020
LGA    L     327      L     327          1.249
LGA    P     328      P     328          2.567
LGA    N     329      N     329          4.169
LGA    T     330      T     330          2.994
LGA    C     331      C     331           #
LGA    N     332      N     332           #
LGA    F     333      F     333           -
LGA    S     334      -       -           -
LGA    I     335      -       -           -
LGA    R     336      -       -           -
LGA    G     337      S     334           #
LGA    P     338      I     335          5.565
LGA    -       -      R     336           -
LGA    -       -      G     337           -
LGA    -       -      P     338           -
LGA    -       -      R     339           -
LGA    -       -      L     340           -
LGA    R     339      Q     341          2.217
LGA    L     340      G     342          2.505
LGA    Q     341      H     343          3.229
LGA    G     342      V     344          2.623
LGA    H     343      V     345          1.864
LGA    V     344      L     346          1.698
LGA    V     345      A     347          1.597
LGA    L     346      Q     348          3.650
LGA    A     347      C     349          4.027
LGA    Q     348      -       -           -
LGA    C     349      R     350          0.715
LGA    R     350      V     351          1.128
LGA    V     351      L     352          5.415
LGA    L     352      M     353          2.150
LGA    M     353      A     354          2.475
LGA    A     354      S     355          2.216
LGA    S     355      V     356           #
LGA    V     356      G     357          4.111
LGA    G     357      A     358          3.123
LGA    A     358      A     359          5.631
LGA    A     359      -       -           -
LGA    C     360      -       -           -
LGA    H     361      -       -           -
LGA    S     362      -       -           -
LGA    D     363      C     360          5.168
LGA    H     364      H     361          4.438
LGA    G     365      S     362           #
LGA    -       -      D     363           -
LGA    -       -      H     364           -
LGA    -       -      G     365           -
LGA    -       -      D     366           -
LGA    -       -      Q     367           -
LGA    -       -      P     368           -
LGA    D     366      S     369           #
LGA    Q     367      P     370           -
LGA    P     368      -       -           -
LGA    S     369      V     371           #
LGA    P     370      L     372          1.704
LGA    V     371      -       -           -
LGA    L     372      L     373          4.871
LGA    L     373      S     374          3.901
LGA    S     374      Y     375          0.748
LGA    Y     375      G     376          3.517
LGA    G     376      -       -           -
LGA    V     377      V     377          3.692
LGA    P     378      P     378          2.913
LGA    F     379      F     379          2.939
LGA    D     380      -       -           -
LGA    V     381      D     380          1.974
LGA    A     382      V     381          3.513
LGA    R     383      A     382          4.690
LGA    N     384      R     383          3.677
LGA    A     385      N     384          2.080
LGA    L     386      A     385          3.374
LGA    R     387      L     386          3.166
LGA    -       -      R     387           -
LGA    L     388      L     388          1.178
LGA    S     389      S     389          1.197
LGA    V     390      V     390          2.570
LGA    G     391      G     391          3.013
LGA    R     392      R     392           #
LGA    S     393      S     393          2.418
LGA    T     394      T     394          1.762
LGA    T     395      T     395          0.976
LGA    R     396      R     396          1.227
LGA    A     397      A     397          2.263
LGA    E     398      E     398          2.171
LGA    V     399      V     399          0.840
LGA    D     400      D     400          1.851
LGA    L     401      L     401          2.317
LGA    V     402      V     402          1.114
LGA    V     403      V     403          1.207
LGA    Q     404      Q     404          2.149
LGA    D     405      D     405          1.679
LGA    L     406      L     406          0.878
LGA    K     407      K     407          2.221
LGA    Q     408      Q     408          2.374
LGA    A     409      A     409          1.139
LGA    V     410      V     410          1.573
LGA    A     411      A     411          2.500
LGA    Q     412      Q     412          2.138
LGA    L     413      L     413          1.356
LGA    E     414      E     414          2.247
LGA    D     415      D     415          2.546
LGA    Q     416      Q     416          2.494

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  136  136    5.0     97    2.99    41.24     43.388     3.140

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.227527 * X  +  -0.704707 * Y  +   0.672026 * Z  +  -9.245765
  Y_new =  -0.905915 * X  +  -0.099926 * Y  +  -0.411500 * Z  + -14.192835
  Z_new =   0.357140 * X  +  -0.702426 * Y  +  -0.615669 * Z  +  14.714401 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.290469    0.851124  [ DEG:  -131.2342     48.7658 ]
  Theta =  -0.365204   -2.776388  [ DEG:   -20.9247   -159.0753 ]
  Phi   =  -1.816864    1.324729  [ DEG:  -104.0986     75.9014 ]
 
# 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_3-D1                               
REMARK     2: T0339_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0339TS393_3-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   97   2.99   41.24  43.388
REMARK  ---------------------------------------------------------- 
MOLECULE T0339TS393_3-D1
PFRMAT TS
TARGET T0339
MODEL 3
PARENT N/A
ATOM      1  CA  GLU     1       0.182 -35.801  22.498  1.00 25.00           C
ATOM      2  CA  ARG     2      -3.025 -34.316  23.992  1.00 25.00           C
ATOM      3  CA  LYS     3      -6.072 -32.793  22.365  1.00 25.00           C
ATOM      4  CA  VAL     4      -7.340 -33.247  18.770  1.00 25.00           C
ATOM      5  CA  TYR     5     -10.512 -31.083  19.158  1.00 25.00           C
ATOM      6  CA  MET     6     -10.297 -28.279  16.538  1.00 25.00           C
ATOM      7  CA  ASP     7     -12.651 -25.322  17.181  1.00 25.00           C
ATOM      8  CA  TYR     8     -14.665 -22.891  19.263  1.00 25.00           C
ATOM    289  CA  GLU   289       1.059 -27.056   9.674  1.00 25.00           C
ATOM    290  CA  ALA   290      -0.519 -30.527  10.037  1.00 25.00           C
ATOM    291  CA  TYR   291      -3.891 -29.144   8.863  1.00 25.00           C
ATOM    292  CA  GLU   292      -2.199 -27.515   5.839  1.00 25.00           C
ATOM    293  CA  ALA   293      -0.470 -30.826   4.992  1.00 25.00           C
ATOM    294  CA  HIS   294      -3.819 -32.667   5.241  1.00 25.00           C
ATOM    295  CA  MET   295      -5.441 -30.079   2.930  1.00 25.00           C
ATOM    296  CA  ARG   296      -2.584 -30.499   0.414  1.00 25.00           C
ATOM    297  CA  ASP   297      -3.011 -34.303   0.528  1.00 25.00           C
ATOM    298  CA  VAL   298      -6.776 -33.924  -0.066  1.00 25.00           C
ATOM    299  CA  ARG   299      -6.098 -31.613  -3.044  1.00 25.00           C
ATOM    300  CA  ASP   300      -3.625 -34.157  -4.486  1.00 25.00           C
ATOM    301  CA  TYR   301      -6.218 -36.946  -4.077  1.00 25.00           C
ATOM    302  CA  LEU   302      -8.847 -34.795  -5.847  1.00 25.00           C
ATOM    303  CA  GLU   303      -6.397 -34.116  -8.711  1.00 25.00           C
ATOM    304  CA  GLU   304      -5.675 -37.864  -9.017  1.00 25.00           C
ATOM    305  CA  ARG   305      -9.431 -38.605  -9.117  1.00 25.00           C
ATOM    306  CA  LEU   306      -9.905 -35.961 -11.846  1.00 25.00           C
ATOM    307  CA  GLU   307      -7.041 -37.501 -13.869  1.00 25.00           C
ATOM    308  CA  ALA   308      -8.618 -40.971 -13.507  1.00 25.00           C
ATOM    309  CA  GLU   309     -11.991 -39.588 -14.681  1.00 25.00           C
ATOM    310  CA  PHE   310     -14.122 -38.662 -11.649  1.00 25.00           C
ATOM    311  CA  GLY   311     -15.656 -40.213  -8.518  1.00 25.00           C
ATOM    312  CA  GLN   312     -17.479 -37.001  -7.544  1.00 25.00           C
ATOM    313  CA  LYS   313     -19.560 -35.086  -4.968  1.00 25.00           C
ATOM    314  CA  ARG   314     -17.321 -32.081  -5.691  1.00 25.00           C
ATOM    315  CA  ILE   315     -15.266 -30.259  -3.025  1.00 25.00           C
ATOM    316  CA  HIS   316     -16.833 -26.757  -2.824  1.00 25.00           C
ATOM    317  CA  LEU   317     -15.212 -25.086   0.191  1.00 25.00           C
ATOM    318  CA  ASN   318     -13.407 -22.085  -1.278  1.00 25.00           C
ATOM    319  CA  SER   319     -13.793 -22.063  -5.083  1.00 25.00           C
ATOM    320  CA  GLN   320     -10.684 -21.247  -7.072  1.00 25.00           C
ATOM    321  CA  PHE   321      -8.866 -21.921  -3.803  1.00 25.00           C
ATOM    322  CA  PRO   322      -5.714 -21.697  -5.931  1.00 25.00           C
ATOM    323  CA  GLY   323      -3.127 -24.340  -4.981  1.00 25.00           C
ATOM    324  CA  THR   324      -0.507 -21.679  -4.416  1.00 25.00           C
ATOM    325  CA  GLN   325      -2.731 -20.422  -1.660  1.00 25.00           C
ATOM    326  CA  ARG   326      -4.805 -20.882   1.453  1.00 25.00           C
ATOM    327  CA  LEU   327      -6.239 -20.195   4.884  1.00 25.00           C
ATOM    328  CA  PRO   328      -5.825 -23.775   6.029  1.00 25.00           C
ATOM    329  CA  ASN   329      -7.803 -23.533   9.304  1.00 25.00           C
ATOM    330  CA  THR   330     -10.880 -24.235   7.252  1.00 25.00           C
ATOM    331  CA  CYS   331     -14.099 -24.857   5.405  1.00 25.00           C
ATOM    332  CA  ASN   332     -17.622 -25.157   6.702  1.00 25.00           C
ATOM    333  CA  PHE   333     -21.416 -25.174   7.046  1.00 25.00           C
ATOM    334  CA  SER   334     -24.186 -27.424   5.721  1.00 25.00           C
ATOM    335  CA  ILE   335     -25.508 -30.222   3.569  1.00 25.00           C
ATOM    336  CA  ARG   336     -26.869 -32.652   1.066  1.00 25.00           C
ATOM    337  CA  GLY   337     -25.499 -35.114  -1.445  1.00 25.00           C
ATOM    338  CA  PRO   338     -22.849 -37.259   0.275  1.00 25.00           C
ATOM    339  CA  ARG   339     -25.483 -37.564   2.928  1.00 25.00           C
ATOM    340  CA  LEU   340     -24.424 -35.261   5.773  1.00 25.00           C
ATOM    341  CA  GLN   341     -25.408 -38.182   8.046  1.00 25.00           C
ATOM    342  CA  GLY   342     -23.225 -40.556   5.981  1.00 25.00           C
ATOM    343  CA  HIS   343     -20.282 -38.118   6.243  1.00 25.00           C
ATOM    344  CA  VAL   344     -20.770 -37.899  10.035  1.00 25.00           C
ATOM    345  CA  VAL   345     -20.827 -41.721  10.274  1.00 25.00           C
ATOM    346  CA  LEU   346     -17.602 -41.921   8.216  1.00 25.00           C
ATOM    347  CA  ALA   347     -15.949 -39.338  10.511  1.00 25.00           C
ATOM    348  CA  GLN   348     -17.031 -41.343  13.589  1.00 25.00           C
ATOM    349  CA  CYS   349     -15.592 -44.538  12.044  1.00 25.00           C
ATOM    350  CA  ARG   350     -12.186 -43.146  12.867  1.00 25.00           C
ATOM    351  CA  VAL   351     -11.287 -40.895  15.740  1.00 25.00           C
ATOM    352  CA  LEU   352     -12.117 -37.828  13.676  1.00 25.00           C
ATOM    353  CA  MET   353     -14.337 -34.719  13.584  1.00 25.00           C
ATOM    354  CA  ALA   354     -15.933 -31.658  11.883  1.00 25.00           C
ATOM    355  CA  SER   355     -14.980 -28.081  12.628  1.00 25.00           C
ATOM    356  CA  VAL   356     -18.625 -27.560  13.458  1.00 25.00           C
ATOM    357  CA  GLY   357     -18.773 -24.727  16.005  1.00 25.00           C
ATOM    358  CA  ALA   358     -16.919 -23.428  19.043  1.00 25.00           C
ATOM    359  CA  ALA   359     -14.333 -22.230  16.561  1.00 25.00           C
ATOM    360  CA  CYS   360     -17.207 -19.999  15.350  1.00 25.00           C
ATOM    361  CA  HIS   361     -18.116 -19.264  11.754  1.00 25.00           C
ATOM    362  CA  SER   362     -19.089 -22.900  11.324  1.00 25.00           C
ATOM    363  CA  ASP   363     -22.709 -22.026  10.739  1.00 25.00           C
ATOM    364  CA  HIS   364     -23.356 -24.445  13.597  1.00 25.00           C
ATOM    365  CA  GLY   365     -23.827 -27.196  11.058  1.00 25.00           C
ATOM    366  CA  ASP   366     -21.972 -29.756   9.008  1.00 25.00           C
ATOM    367  CA  GLN   367     -20.199 -29.422   5.620  1.00 25.00           C
ATOM    368  CA  PRO   368     -20.624 -26.908   2.753  1.00 25.00           C
ATOM    369  CA  SER   369     -23.997 -25.465   1.652  1.00 25.00           C
ATOM    370  CA  PRO   370     -23.170 -22.149   3.378  1.00 25.00           C
ATOM    371  CA  VAL   371     -19.766 -22.057   1.627  1.00 25.00           C
ATOM    372  CA  LEU   372     -21.455 -22.720  -1.746  1.00 25.00           C
ATOM    373  CA  LEU   373     -23.953 -19.894  -1.076  1.00 25.00           C
ATOM    374  CA  SER   374     -21.076 -17.527  -0.190  1.00 25.00           C
ATOM    375  CA  TYR   375     -19.258 -18.488  -3.420  1.00 25.00           C
ATOM    376  CA  GLY   376     -21.797 -18.914  -6.187  1.00 25.00           C
ATOM    377  CA  VAL   377     -23.383 -22.296  -6.573  1.00 25.00           C
ATOM    378  CA  PRO   378     -26.928 -22.638  -5.270  1.00 25.00           C
ATOM    379  CA  PHE   379     -29.834 -24.283  -3.503  1.00 25.00           C
ATOM    380  CA  ASP   380     -30.703 -26.882  -0.828  1.00 25.00           C
ATOM    381  CA  VAL   381     -28.379 -29.422  -2.506  1.00 25.00           C
ATOM    382  CA  ALA   382     -25.564 -26.828  -2.592  1.00 25.00           C
ATOM    383  CA  ARG   383     -23.353 -29.447  -4.222  1.00 25.00           C
ATOM    384  CA  ASN   384     -22.710 -30.418  -0.582  1.00 25.00           C
ATOM    385  CA  ALA   385     -21.319 -32.828   2.047  1.00 25.00           C
ATOM    386  CA  LEU   386     -17.531 -32.174   2.351  1.00 25.00           C
ATOM    387  CA  ARG   387     -15.334 -29.650   4.167  1.00 25.00           C
ATOM    388  CA  LEU   388     -12.300 -30.479   6.356  1.00 25.00           C
ATOM    389  CA  SER   389     -10.673 -28.860   9.388  1.00 25.00           C
ATOM    390  CA  VAL   390      -8.249 -31.279  11.029  1.00 25.00           C
ATOM    391  CA  GLY   391      -6.619 -28.972  13.619  1.00 25.00           C
ATOM    392  CA  ARG   392      -5.052 -31.495  15.915  1.00 25.00           C
ATOM    393  CA  SER   393      -2.341 -33.313  14.014  1.00 25.00           C
ATOM    394  CA  THR   394      -2.987 -35.644  11.046  1.00 25.00           C
ATOM    395  CA  THR   395      -0.161 -36.524   8.623  1.00 25.00           C
ATOM    396  CA  ARG   396       0.971 -37.909   5.279  1.00 25.00           C
ATOM    397  CA  ALA   397       0.336 -41.683   5.136  1.00 25.00           C
ATOM    398  CA  GLU   398      -2.273 -41.375   7.922  1.00 25.00           C
ATOM    399  CA  VAL   399      -3.989 -38.520   6.032  1.00 25.00           C
ATOM    400  CA  ASP   400      -4.040 -40.631   2.838  1.00 25.00           C
ATOM    401  CA  LEU   401      -5.563 -43.565   4.772  1.00 25.00           C
ATOM    402  CA  VAL   402      -8.240 -41.246   6.229  1.00 25.00           C
ATOM    403  CA  VAL   403      -9.044 -39.930   2.724  1.00 25.00           C
ATOM    404  CA  GLN   404      -9.344 -43.518   1.419  1.00 25.00           C
ATOM    405  CA  ASP   405     -11.692 -44.400   4.313  1.00 25.00           C
ATOM    406  CA  LEU   406     -13.833 -41.317   3.548  1.00 25.00           C
ATOM    407  CA  LYS   407     -13.997 -42.318  -0.146  1.00 25.00           C
ATOM    408  CA  GLN   408     -15.056 -45.865   0.837  1.00 25.00           C
ATOM    409  CA  ALA   409     -17.780 -44.444   3.123  1.00 25.00           C
ATOM    410  CA  VAL   410     -19.032 -42.202   0.282  1.00 25.00           C
ATOM    411  CA  ALA   411     -19.130 -45.213  -2.083  1.00 25.00           C
ATOM    412  CA  GLN   412     -21.101 -47.221   0.516  1.00 25.00           C
ATOM    413  CA  LEU   413     -23.575 -44.325   0.913  1.00 25.00           C
ATOM    414  CA  GLU   414     -24.000 -44.134  -2.888  1.00 25.00           C
ATOM    415  CA  ASP   415     -24.635 -47.908  -3.031  1.00 25.00           C
ATOM    416  CA  GLN   416     -25.344 -50.038   0.026  1.00 25.00           C
TER
END
