
#######################################################
#                                                     #
#                        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   90 (   90),  selected   90 , name T0316TS393_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS393_5-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284           -
LGA    S     285      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    T     286      L     288          4.101
LGA    S     287      E     289          2.582
LGA    L     288      A     290          3.973
LGA    E     289      S     291          5.227
LGA    A     290      -       -           -
LGA    S     291      -       -           -
LGA    Q     292      -       -           -
LGA    V     293      -       -           -
LGA    H     294      -       -           -
LGA    F     295      -       -           -
LGA    T     296      -       -           -
LGA    R     297      -       -           -
LGA    E     298      -       -           -
LGA    M     299      -       -           -
LGA    P     300      -       -           -
LGA    E     301      -       -           -
LGA    E     302      -       -           -
LGA    F     303      -       -           -
LGA    T     304      -       -           -
LGA    L     305      -       -           -
LGA    E     306      -       -           -
LGA    C     307      -       -           -
LGA    T     308      -       -           -
LGA    A     309      -       -           -
LGA    K     310      -       -           -
LGA    F     311      -       -           -
LGA    R     312      -       -           -
LGA    Y     313      Q     292           #
LGA    R     314      V     293           -
LGA    Q     315      H     294           -
LGA    P     316      F     295           -
LGA    D     317      T     296           -
LGA    S     318      -       -           -
LGA    K     319      -       -           -
LGA    V     320      -       -           -
LGA    T     321      -       -           -
LGA    V     322      -       -           -
LGA    H     323      R     297           #
LGA    V     324      E     298          4.909
LGA    K     325      M     299           #
LGA    G     326      P     300          2.363
LGA    E     327      E     301          1.136
LGA    K     328      E     302          3.810
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    T     329      K     328          3.845
LGA    E     330      T     329          2.219
LGA    V     331      E     330          1.313
LGA    I     332      V     331          1.624
LGA    F     333      I     332          1.960
LGA    A     334      F     333          2.719
LGA    E     335      A     334          2.081
LGA    P     336      E     335          2.385
LGA    Q     337      P     336          2.090
LGA    R     338      Q     337          3.109
LGA    A     339      R     338          3.767
LGA    I     340      A     339          2.785
LGA    T     341      -       -           -
LGA    P     342      -       -           -
LGA    G     343      -       -           -
LGA    Q     344      -       -           -
LGA    A     345      -       -           -
LGA    V     346      I     340          3.743
LGA    V     347      T     341          1.456
LGA    F     348      P     342          1.996
LGA    Y     349      G     343          3.311
LGA    D     350      Q     344          1.596
LGA    G     351      A     345          4.549
LGA    E     352      V     346          4.718
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    E     353      I     360          4.932
LGA    -       -      D     361           -
LGA    C     354      N     362          2.617
LGA    L     355      A     363          3.548
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    G     356      Y     372          4.585
LGA    G     357      I     373          3.841
LGA    G     358      -       -           -
LGA    L     359      -       -           -
LGA    I     360      -       -           -
LGA    D     361      -       -           -
LGA    N     362      -       -           -
LGA    A     363      -       -           -
LGA    Y     364      -       -           -
LGA    R     365      -       -           -
LGA    D     366      -       -           -
LGA    G     367      -       -           -
LGA    Q     368      -       -           -
LGA    V     369      -       -           -
LGA    C     370      -       -           -
LGA    Q     371      -       -           -
LGA    Y     372      -       -           -
LGA    I     373      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     32    3.30     3.12     20.740     0.940

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.215645 * X  +  -0.930558 * Y  +  -0.295904 * Z  +  38.249485
  Y_new =   0.976334 * X  +  -0.210563 * Y  +  -0.049343 * Z  +   8.042296
  Z_new =  -0.016390 * X  +  -0.299541 * Y  +   0.953942 * Z  +  -9.883951 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.304254    2.837338  [ DEG:   -17.4325    162.5675 ]
  Theta =   0.016391    3.125202  [ DEG:     0.9391    179.0609 ]
  Phi   =   1.788179   -1.353414  [ DEG:   102.4551    -77.5449 ]
 
# 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: T0316TS393_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS393_5-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   90   90   5.0   32   3.30    3.12  20.740
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS393_5-D3
PFRMAT TS
TARGET T0316
MODEL 5
PARENT N/A
ATOM    284  CA  MET   284      31.568  10.763   2.882  1.00 25.00           C
ATOM    285  CA  SER   285      29.797   7.424   2.265  1.00 25.00           C
ATOM    286  CA  THR   286      28.283   7.221  -1.233  1.00 25.00           C
ATOM    287  CA  SER   287      31.663   8.734  -2.199  1.00 25.00           C
ATOM    288  CA  LEU   288      34.818   6.873  -1.040  1.00 25.00           C
ATOM    289  CA  GLU   289      37.947   9.046  -1.057  1.00 25.00           C
ATOM    290  CA  ALA   290      40.842  11.101  -2.402  1.00 25.00           C
ATOM    291  CA  SER   291      42.683  13.143  -5.061  1.00 25.00           C
ATOM    292  CA  GLN   292      46.334  12.203  -4.808  1.00 25.00           C
ATOM    293  CA  VAL   293      47.330  13.908  -8.053  1.00 25.00           C
ATOM    294  CA  HIS   294      50.434  12.550  -9.794  1.00 25.00           C
ATOM    295  CA  PHE   295      52.197  11.598 -13.044  1.00 25.00           C
ATOM    296  CA  THR   296      54.211  13.802 -15.359  1.00 25.00           C
ATOM    297  CA  ARG   297      57.768  14.857 -15.957  1.00 25.00           C
ATOM    298  CA  GLU   298      61.000  16.753 -16.354  1.00 25.00           C
ATOM    299  CA  MET   299      61.383  20.123 -14.682  1.00 25.00           C
ATOM    300  CA  PRO   300      61.960  23.775 -13.887  1.00 25.00           C
ATOM    301  CA  GLU   301      62.850  23.510 -10.168  1.00 25.00           C
ATOM    302  CA  GLU   302      62.163  24.922  -6.749  1.00 25.00           C
ATOM    303  CA  PHE   303      59.225  27.175  -7.422  1.00 25.00           C
ATOM    304  CA  THR   304      55.965  25.548  -6.469  1.00 25.00           C
ATOM    305  CA  LEU   305      53.627  22.541  -6.398  1.00 25.00           C
ATOM    306  CA  GLU   306      50.457  20.779  -5.239  1.00 25.00           C
ATOM    307  CA  CYS   307      47.338  18.742  -5.813  1.00 25.00           C
ATOM    308  CA  THR   308      44.671  17.017  -3.830  1.00 25.00           C
ATOM    309  CA  ALA   309      41.046  17.991  -4.216  1.00 25.00           C
ATOM    310  CA  LYS   310      40.695  16.005  -0.972  1.00 25.00           C
ATOM    311  CA  PHE   311      37.279  16.310   0.548  1.00 25.00           C
ATOM    312  CA  ARG   312      35.341  15.116   3.606  1.00 25.00           C
ATOM    313  CA  TYR   313      35.198  18.310   5.603  1.00 25.00           C
ATOM    314  CA  ARG   314      34.710  20.330   8.736  1.00 25.00           C
ATOM    315  CA  GLN   315      36.444  21.936  11.697  1.00 25.00           C
ATOM    316  CA  PRO   316      36.447  23.804  15.031  1.00 25.00           C
ATOM    317  CA  ASP   317      32.990  23.975  16.709  1.00 25.00           C
ATOM    318  CA  SER   318      32.653  21.257  19.308  1.00 25.00           C
ATOM    319  CA  LYS   319      33.489  17.773  20.498  1.00 25.00           C
ATOM    320  CA  VAL   320      32.767  14.370  22.054  1.00 25.00           C
ATOM    321  CA  THR   321      30.492  12.154  24.121  1.00 25.00           C
ATOM    322  CA  VAL   322      27.894   9.419  23.917  1.00 25.00           C
ATOM    323  CA  HIS   323      26.426   5.982  23.064  1.00 25.00           C
ATOM    324  CA  VAL   324      27.872   3.262  20.871  1.00 25.00           C
ATOM    325  CA  LYS   325      26.976   0.248  18.757  1.00 25.00           C
ATOM    326  CA  GLY   326      26.703  -1.272  15.317  1.00 25.00           C
ATOM    327  CA  GLU   327      28.737   0.302  12.521  1.00 25.00           C
ATOM    328  CA  LYS   328      29.731   1.537   9.098  1.00 25.00           C
ATOM    329  CA  THR   329      31.203   2.256   5.705  1.00 25.00           C
ATOM    330  CA  GLU   330      28.875   2.356   2.655  1.00 25.00           C
ATOM    331  CA  VAL   331      27.365   2.289  -0.872  1.00 25.00           C
ATOM    332  CA  ILE   332      24.209   4.264  -1.517  1.00 25.00           C
ATOM    333  CA  PHE   333      22.013   6.441  -3.650  1.00 25.00           C
ATOM    334  CA  ALA   334      18.231   6.647  -3.460  1.00 25.00           C
ATOM    335  CA  GLU   335      15.864   8.502  -5.746  1.00 25.00           C
ATOM    336  CA  PRO   336      15.557  10.764  -8.778  1.00 25.00           C
ATOM    337  CA  GLN   337      18.862  11.287 -10.627  1.00 25.00           C
ATOM    338  CA  ARG   338      21.524  11.924 -13.303  1.00 25.00           C
ATOM    339  CA  ALA   339      25.058  13.209 -14.158  1.00 25.00           C
ATOM    340  CA  ILE   340      26.163  16.837 -14.481  1.00 25.00           C
ATOM    341  CA  THR   341      27.763  18.952 -11.715  1.00 25.00           C
ATOM    342  CA  PRO   342      29.424  20.781 -14.605  1.00 25.00           C
ATOM    343  CA  GLY   343      30.749  18.401 -17.250  1.00 25.00           C
ATOM    344  CA  GLN   344      30.964  14.804 -18.557  1.00 25.00           C
ATOM    345  CA  ALA   345      30.220  13.804 -15.015  1.00 25.00           C
ATOM    346  CA  VAL   346      29.770  14.454 -11.321  1.00 25.00           C
ATOM    347  CA  VAL   347      30.715  14.751  -7.622  1.00 25.00           C
ATOM    348  CA  PHE   348      32.799  15.463  -4.495  1.00 25.00           C
ATOM    349  CA  TYR   349      32.271  15.942  -0.770  1.00 25.00           C
ATOM    350  CA  ASP   350      30.167  18.957  -1.555  1.00 25.00           C
ATOM    351  CA  GLY   351      26.604  18.234  -2.797  1.00 25.00           C
ATOM    352  CA  GLU   352      27.460  14.661  -3.876  1.00 25.00           C
ATOM    353  CA  GLU   353      27.468  10.922  -4.507  1.00 25.00           C
ATOM    354  CA  CYS   354      30.643  10.366  -6.532  1.00 25.00           C
ATOM    355  CA  LEU   355      33.246   9.578  -9.202  1.00 25.00           C
ATOM    356  CA  GLY   356      35.280  12.758  -8.632  1.00 25.00           C
ATOM    357  CA  GLY   357      34.302  14.451 -11.914  1.00 25.00           C
ATOM    358  CA  GLY   358      33.246  17.930 -12.806  1.00 25.00           C
ATOM    359  CA  LEU   359      32.791  18.252  -9.016  1.00 25.00           C
ATOM    360  CA  ILE   360      29.953  20.048  -7.284  1.00 25.00           C
ATOM    361  CA  ASP   361      28.473  23.165  -8.998  1.00 25.00           C
ATOM    362  CA  ASN   362      27.313  26.544  -7.683  1.00 25.00           C
ATOM    363  CA  ALA   363      27.320  30.248  -8.428  1.00 25.00           C
ATOM    364  CA  TYR   364      25.839  33.586  -7.354  1.00 25.00           C
ATOM    365  CA  ARG   365      25.382  35.505  -4.169  1.00 25.00           C
ATOM    366  CA  ASP   366      26.752  37.761  -1.406  1.00 25.00           C
ATOM    367  CA  GLY   367      28.643  40.411  -3.304  1.00 25.00           C
ATOM    368  CA  GLN   368      31.344  39.942  -0.690  1.00 25.00           C
ATOM    369  CA  VAL   369      33.265  37.029  -2.316  1.00 25.00           C
ATOM    370  CA  CYS   370      37.015  36.762  -1.576  1.00 25.00           C
ATOM    371  CA  GLN   371      40.013  38.122   0.350  1.00 25.00           C
ATOM    372  CA  TYR   372      42.620  35.449   1.220  1.00 25.00           C
ATOM    373  CA  ILE   373      44.666  38.637   1.744  1.00 25.00           C
TER
END
