
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0356TS383_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS383_1-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      -       -           -
LGA    P     349      -       -           -
LGA    E     350      F     348          5.005
LGA    I     351      P     349          3.276
LGA    -       -      E     350           -
LGA    -       -      I     351           -
LGA    V     352      V     352          4.473
LGA    D     353      D     353          3.277
LGA    F     354      F     354          1.815
LGA    Y     355      Y     355          0.375
LGA    L     356      L     356          1.362
LGA    E     359      P     357          1.510
LGA    G     360      P     358          2.196
LGA    -       -      E     359           -
LGA    -       -      G     360           -
LGA    C     361      C     361          1.507
LGA    -       -      S     362           -
LGA    -       -      Y     363           -
LGA    S     362      R     364          1.635
LGA    Y     363      L     365          0.903
LGA    R     364      A     366          1.073
LGA    L     365      V     367          0.395
LGA    A     366      V     368          0.605
LGA    V     367      T     369          1.902
LGA    V     368      I     370          1.443
LGA    -       -      K     371           -
LGA    -       -      K     372           -
LGA    -       -      Q     373           -
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    -       -      H     377           -
LGA    -       -      A     378           -
LGA    -       -      K     379           -
LGA    -       -      R     380           -
LGA    -       -      V     381           -
LGA    -       -      M     382           -
LGA    -       -      M     383           -
LGA    -       -      G     384           -
LGA    -       -      V     385           -
LGA    -       -      W     386           -
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    -       -      M     393           -
LGA    -       -      Y     394           -
LGA    -       -      T     395           -
LGA    -       -      K     396           -
LGA    -       -      F     397           -
LGA    -       -      V     398           -
LGA    -       -      I     399           -
LGA    -       -      V     400           -
LGA    -       -      C     401           -
LGA    T     369      D     402          1.052
LGA    I     370      D     403          1.738
LGA    K     371      D     404          2.283
LGA    K     372      V     405           -
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           -
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    -       -      I     417           -
LGA    -       -      T     418           -
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    -       -      M     421           -
LGA    -       -      D     422           -
LGA    -       -      P     423           -
LGA    -       -      A     424           -
LGA    -       -      R     425           -
LGA    -       -      D     426           -
LGA    -       -      T     427           -
LGA    -       -      V     428           -
LGA    -       -      L     429           -
LGA    -       -      V     430           -
LGA    -       -      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    -       -      K     450           -
LGA    -       -      M     451           -
LGA    -       -      G     452           -
LGA    -       -      L     453           -
LGA    -       -      D     454           -
LGA    -       -      A     455           -
LGA    -       -      T     456           -
LGA    -       -      N     457           -
LGA    -       -      K     458           -
LGA    -       -      W     459           -
LGA    -       -      P     460           -
LGA    -       -      G     461           -
LGA    -       -      E     462           -
LGA    -       -      T     463           -
LGA    -       -      Q     464           -
LGA    -       -      R     465           -
LGA    -       -      E     466           -
LGA    -       -      W     467           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  120    5.0     20    2.25    30.00     14.150     0.851

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.737028 * X  +   0.177648 * Y  +   0.652098 * Z  +  56.034523
  Y_new =  -0.671425 * X  +  -0.082070 * Y  +  -0.736514 * Z  + 118.566505
  Z_new =  -0.077322 * X  +  -0.980666 * Y  +   0.179765 * Z  + 102.621689 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.389500    1.752093  [ DEG:   -79.6125    100.3875 ]
  Theta =   0.077399    3.064193  [ DEG:     4.4347    175.5653 ]
  Phi   =  -2.402739    0.738854  [ DEG:  -137.6668     42.3332 ]
 
# 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: T0356TS383_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_1-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  120   5.0   20   2.25   30.00  14.150
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_1-D3
PFRMAT TS
TARGET t0356
MODEL 1
PARENT 1ejeA
ATOM    645  N   PHE   348      51.985  76.025  54.929  1.00  0.00
ATOM    646  CA  PHE   348      51.708  74.725  55.519  1.00  0.00
ATOM    647  C   PHE   348      51.417  73.649  54.479  1.00  0.00
ATOM    648  O   PHE   348      51.916  72.528  54.587  1.00  0.00
ATOM    649  N   PRO   349      50.623  73.982  53.466  1.00  0.00
ATOM    650  CA  PRO   349      50.297  72.996  52.440  1.00  0.00
ATOM    651  C   PRO   349      51.555  72.381  51.840  1.00  0.00
ATOM    652  O   PRO   349      51.607  71.184  51.569  1.00  0.00
ATOM    653  N   GLU   350      52.572  73.206  51.645  1.00  0.00
ATOM    654  CA  GLU   350      53.830  72.740  51.082  1.00  0.00
ATOM    655  C   GLU   350      54.728  72.127  52.152  1.00  0.00
ATOM    656  O   GLU   350      55.202  71.001  52.021  1.00  0.00
ATOM    657  N   ILE   351      54.952  72.889  53.213  1.00  0.00
ATOM    658  CA  ILE   351      55.802  72.478  54.318  1.00  0.00
ATOM    659  C   ILE   351      55.268  71.310  55.142  1.00  0.00
ATOM    660  O   ILE   351      56.040  70.459  55.578  1.00  0.00
ATOM    661  N   VAL   352      53.955  71.278  55.358  1.00  0.00
ATOM    662  CA  VAL   352      53.330  70.221  56.153  1.00  0.00
ATOM    663  C   VAL   352      54.028  70.111  57.510  1.00  0.00
ATOM    664  O   VAL   352      54.655  69.097  57.821  1.00  0.00
ATOM    665  N   ASP   353      53.913  71.158  58.344  1.00  0.00
ATOM    666  CA  ASP   353      54.542  71.187  59.672  1.00  0.00
ATOM    667  C   ASP   353      54.092  70.038  60.552  1.00  0.00
ATOM    668  O   ASP   353      52.930  69.645  60.512  1.00  0.00
ATOM    669  N   PHE   354      55.014  69.507  61.349  1.00  0.00
ATOM    670  CA  PHE   354      54.704  68.416  62.263  1.00  0.00
ATOM    671  C   PHE   354      54.175  68.991  63.577  1.00  0.00
ATOM    672  O   PHE   354      54.781  69.890  64.157  1.00  0.00
ATOM    673  N   TYR   355      53.044  68.470  64.041  1.00  0.00
ATOM    674  CA  TYR   355      52.436  68.929  65.286  1.00  0.00
ATOM    675  C   TYR   355      52.409  67.739  66.235  1.00  0.00
ATOM    676  O   TYR   355      52.113  66.626  65.820  1.00  0.00
ATOM    677  N   LEU   356      52.731  67.975  67.503  1.00  0.00
ATOM    678  CA  LEU   356      52.755  66.909  68.493  1.00  0.00
ATOM    679  C   LEU   356      51.423  66.805  69.215  1.00  0.00
ATOM    680  O   LEU   356      50.862  67.812  69.646  1.00  0.00
ATOM    681  N   GLU   359      50.908  65.587  69.328  1.00  0.00
ATOM    682  CA  GLU   359      49.652  65.354  70.030  1.00  0.00
ATOM    683  C   GLU   359      50.054  64.899  71.427  1.00  0.00
ATOM    684  O   GLU   359      49.541  65.391  72.432  1.00  0.00
ATOM    685  N   GLY   360      51.002  63.969  71.466  1.00  0.00
ATOM    686  CA  GLY   360      51.497  63.432  72.720  1.00  0.00
ATOM    687  C   GLY   360      52.170  62.108  72.430  1.00  0.00
ATOM    688  O   GLY   360      51.752  61.408  71.512  1.00  0.00
ATOM    689  N   CYS   361      53.198  61.754  73.197  1.00  0.00
ATOM    690  CA  CYS   361      53.888  60.500  72.958  1.00  0.00
ATOM    691  C   CYS   361      54.458  60.457  71.548  1.00  0.00
ATOM    692  O   CYS   361      55.158  61.386  71.136  1.00  0.00
ATOM    693  N   SER   362      54.155  59.394  70.804  1.00  0.00
ATOM    694  CA  SER   362      54.643  59.257  69.434  1.00  0.00
ATOM    695  C   SER   362      53.542  59.510  68.408  1.00  0.00
ATOM    696  O   SER   362      53.616  59.032  67.275  1.00  0.00
ATOM    697  N   TYR   363      52.514  60.250  68.810  1.00  0.00
ATOM    698  CA  TYR   363      51.419  60.569  67.903  1.00  0.00
ATOM    699  C   TYR   363      51.577  62.007  67.442  1.00  0.00
ATOM    700  O   TYR   363      51.842  62.898  68.248  1.00  0.00
ATOM    701  N   ARG   364      51.424  62.232  66.143  1.00  0.00
ATOM    702  CA  ARG   364      51.553  63.572  65.600  1.00  0.00
ATOM    703  C   ARG   364      50.442  63.892  64.632  1.00  0.00
ATOM    704  O   ARG   364      49.631  63.037  64.275  1.00  0.00
ATOM    705  N   LEU   365      50.422  65.145  64.206  1.00  0.00
ATOM    706  CA  LEU   365      49.444  65.622  63.255  1.00  0.00
ATOM    707  C   LEU   365      50.215  66.419  62.220  1.00  0.00
ATOM    708  O   LEU   365      51.046  67.258  62.571  1.00  0.00
ATOM    709  N   ALA   366      49.974  66.129  60.947  1.00  0.00
ATOM    710  CA  ALA   366      50.638  66.857  59.877  1.00  0.00
ATOM    711  C   ALA   366      49.686  67.999  59.555  1.00  0.00
ATOM    712  O   ALA   366      48.562  67.765  59.117  1.00  0.00
ATOM    713  N   VAL   367      50.135  69.227  59.788  1.00  0.00
ATOM    714  CA  VAL   367      49.288  70.383  59.563  1.00  0.00
ATOM    715  C   VAL   367      49.221  70.958  58.165  1.00  0.00
ATOM    716  O   VAL   367      49.583  72.114  57.967  1.00  0.00
ATOM    717  N   VAL   368      48.737  70.171  57.207  1.00  0.00
ATOM    718  CA  VAL   368      48.621  70.622  55.821  1.00  0.00
ATOM    719  C   VAL   368      47.158  70.746  55.387  1.00  0.00
ATOM    720  O   VAL   368      46.836  70.625  54.208  1.00  0.00
ATOM    721  N   THR   369      46.282  71.001  56.354  1.00  0.00
ATOM    722  CA  THR   369      44.851  71.142  56.105  1.00  0.00
ATOM    723  C   THR   369      44.377  72.575  56.254  1.00  0.00
ATOM    724  O   THR   369      43.874  72.963  57.308  1.00  0.00
ATOM    725  N   ILE   370      44.520  73.357  55.190  1.00  0.00
ATOM    726  CA  ILE   370      44.113  74.749  55.228  1.00  0.00
ATOM    727  C   ILE   370      42.609  74.924  55.112  1.00  0.00
ATOM    728  O   ILE   370      41.974  74.382  54.210  1.00  0.00
ATOM    729  N   LYS   371      42.048  75.692  56.038  1.00  0.00
ATOM    730  CA  LYS   371      40.617  75.961  56.054  1.00  0.00
ATOM    731  C   LYS   371      40.453  77.434  56.412  1.00  0.00
ATOM    732  O   LYS   371      40.825  77.855  57.505  1.00  0.00
ATOM    733  N   LYS   372      39.927  78.225  55.483  1.00  0.00
ATOM    734  CA  LYS   372      39.725  79.642  55.743  1.00  0.00
ATOM    735  C   LYS   372      38.363  79.864  56.359  1.00  0.00
ATOM    736  O   LYS   372      37.430  79.106  56.114  1.00  0.00
TER
END
