
#######################################################
#                                                     #
#                        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  120 (  120),  selected  120 , name T0356TS393_3-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS393_3-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      F     348           -
LGA    P     349      P     349           -
LGA    E     350      E     350           -
LGA    I     351      I     351           -
LGA    V     352      V     352           -
LGA    D     353      D     353           -
LGA    -       -      F     354           -
LGA    -       -      Y     355           -
LGA    F     354      L     356           #
LGA    Y     355      -       -           -
LGA    L     356      -       -           -
LGA    P     357      -       -           -
LGA    P     358      -       -           -
LGA    E     359      -       -           -
LGA    G     360      P     357           #
LGA    C     361      P     358          2.931
LGA    S     362      E     359          4.979
LGA    -       -      G     360           -
LGA    -       -      C     361           -
LGA    Y     363      S     362          2.104
LGA    R     364      Y     363          3.633
LGA    L     365      R     364           #
LGA    A     366      L     365           #
LGA    V     367      A     366          4.361
LGA    V     368      V     367          2.238
LGA    T     369      V     368          3.888
LGA    I     370      T     369          4.678
LGA    -       -      I     370           -
LGA    -       -      K     371           -
LGA    K     371      K     372          4.844
LGA    K     372      Q     373           -
LGA    Q     373      Y     374           -
LGA    Y     374      -       -           -
LGA    A     375      A     375          4.892
LGA    G     376      G     376          1.836
LGA    H     377      H     377          1.467
LGA    A     378      A     378          0.901
LGA    K     379      K     379          1.013
LGA    R     380      R     380          1.245
LGA    V     381      V     381          1.188
LGA    M     382      M     382          1.463
LGA    M     383      M     383          1.351
LGA    G     384      G     384          1.619
LGA    V     385      V     385          1.679
LGA    W     386      W     386          1.896
LGA    S     387      S     387          2.167
LGA    -       -      F     388           -
LGA    F     388      L     389          3.744
LGA    L     389      R     390          3.543
LGA    R     390      Q     391           -
LGA    Q     391      F     392           -
LGA    F     392      -       -           -
LGA    M     393      -       -           -
LGA    Y     394      -       -           -
LGA    T     395      -       -           -
LGA    K     396      M     393          4.443
LGA    F     397      Y     394          2.702
LGA    V     398      T     395          2.458
LGA    I     399      K     396          4.691
LGA    -       -      F     397           -
LGA    V     400      V     398           #
LGA    C     401      I     399           -
LGA    D     402      V     400           -
LGA    -       -      C     401           -
LGA    -       -      D     402           -
LGA    -       -      D     403           -
LGA    -       -      D     404           -
LGA    -       -      V     405           -
LGA    -       -      N     406           -
LGA    -       -      A     407           -
LGA    D     403      R     408          4.236
LGA    D     404      D     409          2.799
LGA    V     405      W     410          3.255
LGA    N     406      -       -           -
LGA    A     407      -       -           -
LGA    R     408      -       -           -
LGA    D     409      -       -           -
LGA    W     410      -       -           -
LGA    N     411      -       -           -
LGA    D     412      -       -           -
LGA    V     413      -       -           -
LGA    I     414      N     411          2.811
LGA    W     415      D     412          3.121
LGA    A     416      -       -           -
LGA    I     417      V     413          4.420
LGA    T     418      I     414           #
LGA    -       -      W     415           -
LGA    T     419      A     416           #
LGA    R     420      I     417           -
LGA    M     421      T     418           #
LGA    D     422      T     419           #
LGA    P     423      -       -           -
LGA    A     424      -       -           -
LGA    R     425      -       -           -
LGA    D     426      -       -           -
LGA    T     427      R     420          2.922
LGA    V     428      M     421          2.227
LGA    L     429      D     422          4.808
LGA    V     430      P     423          2.981
LGA    E     431      A     424          2.737
LGA    N     432      -       -           -
LGA    T     433      -       -           -
LGA    P     434      -       -           -
LGA    I     435      R     425          3.474
LGA    D     436      D     426           #
LGA    Y     437      -       -           -
LGA    L     438      T     427           #
LGA    D     439      V     428          4.821
LGA    F     440      -       -           -
LGA    A     441      -       -           -
LGA    S     442      -       -           -
LGA    P     443      -       -           -
LGA    V     444      -       -           -
LGA    S     445      -       -           -
LGA    G     446      -       -           -
LGA    L     447      -       -           -
LGA    G     448      L     429          4.716
LGA    S     449      V     430          3.378
LGA    K     450      E     431           -
LGA    -       -      N     432           -
LGA    -       -      T     433           -
LGA    -       -      P     434           -
LGA    -       -      I     435           -
LGA    -       -      D     436           -
LGA    -       -      Y     437           -
LGA    -       -      L     438           -
LGA    -       -      D     439           -
LGA    -       -      F     440           -
LGA    -       -      A     441           -
LGA    -       -      S     442           -
LGA    -       -      P     443           -
LGA    -       -      V     444           -
LGA    -       -      S     445           -
LGA    -       -      G     446           -
LGA    -       -      L     447           -
LGA    -       -      G     448           -
LGA    -       -      S     449           -
LGA    M     451      K     450          3.942
LGA    G     452      M     451          4.074
LGA    L     453      G     452           #
LGA    D     454      L     453           #
LGA    A     455      D     454           -
LGA    T     456      A     455           -
LGA    N     457      T     456           -
LGA    K     458      N     457           -
LGA    W     459      K     458           -
LGA    P     460      W     459           -
LGA    G     461      P     460           -
LGA    E     462      G     461           -
LGA    T     463      E     462           -
LGA    Q     464      T     463           -
LGA    R     465      Q     464           -
LGA    E     466      R     465           -
LGA    W     467      E     466           -
LGA    -       -      W     467           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  120  120    5.0     45    3.32    35.56     22.176     1.315

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.184023 * X  +   0.686098 * Y  +   0.703851 * Z  +  47.419079
  Y_new =  -0.807867 * X  +   0.302324 * Y  +  -0.505916 * Z  +  74.895050
  Z_new =  -0.559899 * X  +  -0.661718 * Y  +   0.498641 * Z  +  59.979290 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.925024    2.216569  [ DEG:   -52.9999    127.0001 ]
  Theta =   0.594263    2.547329  [ DEG:    34.0488    145.9512 ]
  Phi   =  -1.794763    1.346829  [ DEG:  -102.8324     77.1676 ]
 
# 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: T0356TS393_3-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS393_3-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  120  120   5.0   45   3.32   35.56  22.176
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS393_3-D3
PFRMAT TS
TARGET T0356
MODEL 3
PARENT N/A
ATOM    348  CA  PHE   348      66.475  59.423  64.143  1.00 25.00           C
ATOM    349  CA  PRO   349      67.383  62.904  65.330  1.00 25.00           C
ATOM    350  CA  GLU   350      64.719  64.432  63.128  1.00 25.00           C
ATOM    351  CA  ILE   351      63.268  63.836  66.625  1.00 25.00           C
ATOM    352  CA  VAL   352      60.617  61.238  65.900  1.00 25.00           C
ATOM    353  CA  ASP   353      59.308  59.073  68.719  1.00 25.00           C
ATOM    354  CA  PHE   354      55.591  59.594  69.082  1.00 25.00           C
ATOM    355  CA  TYR   355      52.664  58.911  71.404  1.00 25.00           C
ATOM    356  CA  LEU   356      49.796  57.771  69.235  1.00 25.00           C
ATOM    357  CA  PRO   357      47.251  58.468  71.925  1.00 25.00           C
ATOM    358  CA  PRO   358      43.565  59.442  72.365  1.00 25.00           C
ATOM    359  CA  GLU   359      44.776  61.457  75.397  1.00 25.00           C
ATOM    360  CA  GLY   360      46.513  64.809  75.562  1.00 25.00           C
ATOM    361  CA  CYS   361      49.830  66.216  74.501  1.00 25.00           C
ATOM    362  CA  SER   362      53.483  65.200  74.577  1.00 25.00           C
ATOM    363  CA  TYR   363      54.196  63.693  71.187  1.00 25.00           C
ATOM    364  CA  ARG   364      57.756  64.037  69.913  1.00 25.00           C
ATOM    365  CA  LEU   365      56.260  63.768  66.406  1.00 25.00           C
ATOM    366  CA  ALA   366      54.343  63.474  63.105  1.00 25.00           C
ATOM    367  CA  VAL   367      51.975  62.025  60.429  1.00 25.00           C
ATOM    368  CA  VAL   368      48.935  63.444  62.227  1.00 25.00           C
ATOM    369  CA  THR   369      47.819  64.260  58.652  1.00 25.00           C
ATOM    370  CA  ILE   370      46.768  66.242  55.582  1.00 25.00           C
ATOM    371  CA  LYS   371      44.466  67.007  52.662  1.00 25.00           C
ATOM    372  CA  LYS   372      40.704  66.515  52.113  1.00 25.00           C
ATOM    373  CA  GLN   373      39.587  62.932  52.034  1.00 25.00           C
ATOM    374  CA  TYR   374      43.183  62.024  52.752  1.00 25.00           C
ATOM    375  CA  ALA   375      44.662  62.041  49.220  1.00 25.00           C
ATOM    376  CA  GLY   376      48.028  61.187  47.608  1.00 25.00           C
ATOM    377  CA  HIS   377      49.641  64.212  49.316  1.00 25.00           C
ATOM    378  CA  ALA   378      48.180  63.122  52.683  1.00 25.00           C
ATOM    379  CA  LYS   379      49.541  59.581  52.154  1.00 25.00           C
ATOM    380  CA  ARG   380      52.995  61.009  51.319  1.00 25.00           C
ATOM    381  CA  VAL   381      52.900  63.159  54.486  1.00 25.00           C
ATOM    382  CA  MET   382      51.945  60.091  56.571  1.00 25.00           C
ATOM    383  CA  MET   383      54.838  58.112  55.029  1.00 25.00           C
ATOM    384  CA  GLY   384      57.255  60.973  55.828  1.00 25.00           C
ATOM    385  CA  VAL   385      55.988  61.066  59.442  1.00 25.00           C
ATOM    386  CA  TRP   386      56.478  57.279  59.736  1.00 25.00           C
ATOM    387  CA  SER   387      60.040  57.608  58.369  1.00 25.00           C
ATOM    388  CA  PHE   388      60.779  60.387  60.899  1.00 25.00           C
ATOM    389  CA  LEU   389      62.404  57.204  62.263  1.00 25.00           C
ATOM    390  CA  ARG   390      63.491  54.662  59.666  1.00 25.00           C
ATOM    391  CA  GLN   391      63.432  54.385  55.918  1.00 25.00           C
ATOM    392  CA  PHE   392      62.820  56.747  52.951  1.00 25.00           C
ATOM    393  CA  MET   393      60.400  59.174  51.242  1.00 25.00           C
ATOM    394  CA  TYR   394      57.752  56.625  52.172  1.00 25.00           C
ATOM    395  CA  THR   395      58.102  54.811  55.501  1.00 25.00           C
ATOM    396  CA  LYS   396      58.344  54.128  59.243  1.00 25.00           C
ATOM    397  CA  PHE   397      58.198  55.610  62.758  1.00 25.00           C
ATOM    398  CA  VAL   398      56.729  58.855  64.143  1.00 25.00           C
ATOM    399  CA  ILE   399      53.063  59.385  64.676  1.00 25.00           C
ATOM    400  CA  VAL   400      51.573  61.938  67.113  1.00 25.00           C
ATOM    401  CA  CYS   401      48.527  62.699  69.214  1.00 25.00           C
ATOM    402  CA  ASP   402      47.142  65.958  70.735  1.00 25.00           C
ATOM    403  CA  ASP   403      46.137  69.514  71.649  1.00 25.00           C
ATOM    404  CA  ASP   404      42.999  68.867  69.648  1.00 25.00           C
ATOM    405  CA  VAL   405      42.064  65.469  71.089  1.00 25.00           C
ATOM    406  CA  ASN   406      39.363  64.535  73.510  1.00 25.00           C
ATOM    407  CA  ALA   407      40.535  67.394  75.758  1.00 25.00           C
ATOM    408  CA  ARG   408      39.453  70.472  77.644  1.00 25.00           C
ATOM    409  CA  ASP   409      36.541  70.963  75.271  1.00 25.00           C
ATOM    410  CA  TRP   410      38.319  69.991  71.998  1.00 25.00           C
ATOM    411  CA  ASN   411      35.668  69.082  69.389  1.00 25.00           C
ATOM    412  CA  ASP   412      35.801  72.640  67.978  1.00 25.00           C
ATOM    413  CA  VAL   413      39.621  72.444  67.776  1.00 25.00           C
ATOM    414  CA  ILE   414      39.375  69.085  65.954  1.00 25.00           C
ATOM    415  CA  TRP   415      36.855  70.578  63.487  1.00 25.00           C
ATOM    416  CA  ALA   416      39.190  73.549  62.863  1.00 25.00           C
ATOM    417  CA  ILE   417      42.114  71.154  62.245  1.00 25.00           C
ATOM    418  CA  THR   418      39.978  69.145  59.781  1.00 25.00           C
ATOM    419  CA  THR   419      39.010  72.369  57.953  1.00 25.00           C
ATOM    420  CA  ARG   420      35.321  72.285  58.982  1.00 25.00           C
ATOM    421  CA  MET   421      33.483  68.963  58.621  1.00 25.00           C
ATOM    422  CA  ASP   422      30.963  71.170  56.754  1.00 25.00           C
ATOM    423  CA  PRO   423      32.655  73.896  54.715  1.00 25.00           C
ATOM    424  CA  ALA   424      32.524  72.866  51.004  1.00 25.00           C
ATOM    425  CA  ARG   425      32.980  69.382  52.524  1.00 25.00           C
ATOM    426  CA  ASP   426      35.899  67.926  54.357  1.00 25.00           C
ATOM    427  CA  THR   427      38.154  66.060  56.824  1.00 25.00           C
ATOM    428  CA  VAL   428      37.979  62.324  57.279  1.00 25.00           C
ATOM    429  CA  LEU   429      40.037  59.472  55.822  1.00 25.00           C
ATOM    430  CA  VAL   430      40.234  56.052  57.391  1.00 25.00           C
ATOM    431  CA  GLU   431      37.265  53.739  56.926  1.00 25.00           C
ATOM    432  CA  ASN   432      34.577  51.441  55.646  1.00 25.00           C
ATOM    433  CA  THR   433      33.708  53.970  52.981  1.00 25.00           C
ATOM    434  CA  PRO   434      33.781  53.217  49.257  1.00 25.00           C
ATOM    435  CA  ILE   435      36.929  55.340  49.351  1.00 25.00           C
ATOM    436  CA  ASP   436      39.567  57.460  47.527  1.00 25.00           C
ATOM    437  CA  TYR   437      42.689  55.753  48.839  1.00 25.00           C
ATOM    438  CA  LEU   438      46.208  55.205  50.145  1.00 25.00           C
ATOM    439  CA  ASP   439      45.676  51.492  50.830  1.00 25.00           C
ATOM    440  CA  PHE   440      45.312  51.157  47.033  1.00 25.00           C
ATOM    441  CA  ALA   441      47.793  48.420  45.993  1.00 25.00           C
ATOM    442  CA  SER   442      48.339  47.017  42.552  1.00 25.00           C
ATOM    443  CA  PRO   443      46.748  43.728  43.455  1.00 25.00           C
ATOM    444  CA  VAL   444      47.750  42.208  46.775  1.00 25.00           C
ATOM    445  CA  SER   445      47.691  40.549  50.209  1.00 25.00           C
ATOM    446  CA  GLY   446      50.211  41.327  52.933  1.00 25.00           C
ATOM    447  CA  LEU   447      50.335  45.013  53.758  1.00 25.00           C
ATOM    448  CA  GLY   448      51.472  48.484  54.877  1.00 25.00           C
ATOM    449  CA  SER   449      53.421  51.723  55.352  1.00 25.00           C
ATOM    450  CA  LYS   450      51.045  54.668  55.333  1.00 25.00           C
ATOM    451  CA  MET   451      51.790  55.152  59.029  1.00 25.00           C
ATOM    452  CA  GLY   452      49.781  57.437  61.413  1.00 25.00           C
ATOM    453  CA  LEU   453      48.017  58.726  64.561  1.00 25.00           C
ATOM    454  CA  ASP   454      45.285  58.435  67.174  1.00 25.00           C
ATOM    455  CA  ALA   455      42.684  55.735  66.424  1.00 25.00           C
ATOM    456  CA  THR   456      39.404  54.570  67.859  1.00 25.00           C
ATOM    457  CA  ASN   457      36.421  52.819  69.351  1.00 25.00           C
ATOM    458  CA  LYS   458      33.075  51.909  70.953  1.00 25.00           C
ATOM    459  CA  TRP   459      29.579  53.350  70.457  1.00 25.00           C
ATOM    460  CA  PRO   460      26.229  55.137  70.197  1.00 25.00           C
ATOM    461  CA  GLY   461      23.993  57.633  68.357  1.00 25.00           C
ATOM    462  CA  GLU   462      21.853  60.187  70.045  1.00 25.00           C
ATOM    463  CA  THR   463      20.039  62.777  67.870  1.00 25.00           C
ATOM    464  CA  GLN   464      20.791  66.131  69.421  1.00 25.00           C
ATOM    465  CA  ARG   465      17.774  68.272  68.606  1.00 25.00           C
ATOM    466  CA  GLU   466      19.414  71.615  68.954  1.00 25.00           C
ATOM    467  CA  TRP   467      19.470  75.018  70.713  1.00 25.00           C
TER
END
