
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0289TS125_5u-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS125_5u-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          1.895
LGA    M     225      M     225          1.938
LGA    E     226      E     226          1.423
LGA    K     227      K     227          0.238
LGA    V     228      V     228          1.382
LGA    N     245      D     229          1.729
LGA    L     246      Y     230          3.126
LGA    -       -      P     231           -
LGA    Q     247      R     232          4.277
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    D     248      V     238          1.673
LGA    Q     249      A     239          3.939
LGA    -       -      A     240           -
LGA    D     250      V     241          1.524
LGA    W     251      I     242          0.960
LGA    K     252      H     243          1.983
LGA    -       -      P     244           -
LGA    L     254      N     245          3.407
LGA    H     255      L     246          4.414
LGA    P     256      Q     247          3.140
LGA    G     257      D     248          2.108
LGA    D     258      Q     249          1.355
LGA    P     259      D     250          3.206
LGA    V     260      W     251          2.291
LGA    F     261      -       -           -
LGA    V     262      K     252          1.148
LGA    S     263      P     253          0.516
LGA    L     264      L     254          0.780
LGA    D     265      H     255          1.335
LGA    G     266      P     256          2.645
LGA    K     267      G     257          1.671
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    V     268      P     270          3.704
LGA    I     269      L     271          4.562
LGA    P     270      G     272           #
LGA    L     271      G     273          2.148
LGA    G     272      D     274          2.770
LGA    D     274      C     275          2.131
LGA    C     275      T     276          2.808
LGA    T     276      -       -           -
LGA    V     277      V     277          1.126
LGA    Y     278      Y     278          1.212
LGA    P     279      P     279          0.511
LGA    V     280      V     280          1.234
LGA    F     281      F     281          1.923
LGA    V     282      V     282          1.241
LGA    N     283      N     283          2.003
LGA    K     290      E     284          5.073
LGA    K     291      A     285          3.666
LGA    E     292      A     286          4.468
LGA    A     293      Y     287           #
LGA    F     294      Y     288          3.370
LGA    A     295      E     289          3.431
LGA    K     296      K     290          1.517
LGA    T     297      K     291          3.393
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    -       -      F     294           -
LGA    -       -      A     295           -
LGA    -       -      K     296           -
LGA    -       -      T     297           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   74    5.0     46    2.61    30.43     39.024     1.697

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.478623 * X  +   0.680495 * Y  +  -0.554839 * Z  + 103.295265
  Y_new =   0.176777 * X  +   0.693665 * Y  +   0.698268 * Z  + -63.866543
  Z_new =   0.860041 * X  +   0.236124 * Y  +  -0.452300 * Z  +  18.268995 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.660460   -0.481133  [ DEG:   152.4331    -27.5669 ]
  Theta =  -1.035349   -2.106243  [ DEG:   -59.3211   -120.6789 ]
  Phi   =   2.787789   -0.353804  [ DEG:   159.7285    -20.2715 ]
 
# 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: T0289TS125_5u-D2                              
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS125_5u-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   74   5.0   46   2.61   30.43  39.024
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS125_5u-D2
PFRMAT   TS
TARGET   T0289
MODEL    5  UNREFINED
PARENT   1yw4a   
ATOM     1   N   ILE   224      26.139  27.660  20.559    1.00  0.50
ATOM     1   CA  ILE   224      25.518  28.582  21.495    1.00  0.50
ATOM     1   C   ILE   224      25.180  27.826  22.773    1.00  0.50
ATOM     1   O   ILE   224      24.728  26.682  22.726    1.00  0.50
ATOM     1   N   MET   225      25.414  28.460  23.915    1.00  0.50
ATOM     1   CA  MET   225      25.104  27.850  25.201    1.00  0.50
ATOM     1   C   MET   225      23.786  28.455  25.680    1.00  0.50
ATOM     1   O   MET   225      22.870  27.736  26.074    1.00  0.50
ATOM     1   N   GLU   226      23.703  29.782  25.632    1.00  0.50
ATOM     1   CA  GLU   226      22.505  30.514  26.035    1.00  0.50
ATOM     1   C   GLU   226      22.614  31.975  25.592    1.00  0.50
ATOM     1   O   GLU   226      23.717  32.490  25.397    1.00  0.50
ATOM     1   N   LYS   227      21.472  32.640  25.437    1.00  0.50
ATOM     1   CA  LYS   227      21.467  34.037  25.020    1.00  0.50
ATOM     1   C   LYS   227      21.357  34.965  26.221    1.00  0.50
ATOM     1   O   LYS   227      20.763  34.615  27.244    1.00  0.50
ATOM     1   N   VAL   228      21.938  36.153  26.091    1.00  0.50
ATOM     1   CA  VAL   228      21.896  37.149  27.155    1.00  0.50
ATOM     1   C   VAL   228      20.637  37.983  26.983    1.00  0.50
ATOM     1   O   VAL   228      20.673  39.043  26.362    1.00  0.50
ATOM     1   N   ASN   245      19.525  37.496  27.526    1.00  0.50
ATOM     1   CA  ASN   245      18.250  38.197  27.429    1.00  0.50
ATOM     1   C   ASN   245      18.325  39.535  28.162    1.00  0.50
ATOM     1   O   ASN   245      18.670  39.587  29.341    1.00  0.50
ATOM     1   N   LEU   246      18.007  40.617  27.462    1.00  0.50
ATOM     1   CA  LEU   246      18.046  41.937  28.076    1.00  0.50
ATOM     1   C   LEU   246      16.669  42.503  28.416    1.00  0.50
ATOM     1   O   LEU   246      15.722  42.405  27.634    1.00  0.50
ATOM     1   N   GLN   247      16.579  43.089  29.605    1.00  0.50
ATOM     1   CA  GLN   247      15.355  43.705  30.096    1.00  0.50
ATOM     1   C   GLN   247      15.712  44.847  31.047    1.00  0.50
ATOM     1   O   GLN   247      16.675  44.751  31.812    1.00  0.50
ATOM     1   N   ASP   248      14.936  45.924  30.979    1.00  0.50
ATOM     1   CA  ASP   248      15.141  47.114  31.806    1.00  0.50
ATOM     1   C   ASP   248      16.490  47.758  31.503    1.00  0.50
ATOM     1   O   ASP   248      16.695  48.323  30.428    1.00  0.50
ATOM     1   N   GLN   249      20.406  46.853  33.797    1.00  0.50
ATOM     1   CA  GLN   249      21.079  46.355  32.604    1.00  0.50
ATOM     1   C   GLN   249      22.444  47.002  32.406    1.00  0.50
ATOM     1   O   GLN   249      22.555  48.225  32.306    1.00  0.50
ATOM     1   N   ASP   250      23.476  46.165  32.344    1.00  0.50
ATOM     1   CA  ASP   250      24.854  46.622  32.160    1.00  0.50
ATOM     1   C   ASP   250      25.712  45.517  31.555    1.00  0.50
ATOM     1   O   ASP   250      25.760  44.401  32.074    1.00  0.50
ATOM     1   N   TRP   251      26.390  45.842  30.458    1.00  0.50
ATOM     1   CA  TRP   251      27.261  44.895  29.765    1.00  0.50
ATOM     1   C   TRP   251      28.695  45.097  30.261    1.00  0.50
ATOM     1   O   TRP   251      29.336  46.096  29.940    1.00  0.50
ATOM     1   N   LYS   252      29.191  44.138  31.037    1.00  0.50
ATOM     1   CA  LYS   252      30.529  44.222  31.612    1.00  0.50
ATOM     1   C   LYS   252      31.698  43.974  30.658    1.00  0.50
ATOM     1   O   LYS   252      32.700  43.366  31.034    1.00  0.50
ATOM     1   N   LEU   254      31.564  44.449  29.425    1.00  0.50
ATOM     1   CA  LEU   254      32.616  44.311  28.425    1.00  0.50
ATOM     1   C   LEU   254      32.685  45.586  27.601    1.00  0.50
ATOM     1   O   LEU   254      31.661  46.223  27.342    1.00  0.50
ATOM     1   N   HIS   255      33.896  45.956  27.196    1.00  0.50
ATOM     1   CA  HIS   255      34.110  47.153  26.388    1.00  0.50
ATOM     1   C   HIS   255      33.209  47.113  25.158    1.00  0.50
ATOM     1   O   HIS   255      32.953  46.046  24.599    1.00  0.50
ATOM     1   N   PRO   256      32.737  48.281  24.734    1.00  0.50
ATOM     1   CA  PRO   256      31.852  48.374  23.578    1.00  0.50
ATOM     1   C   PRO   256      32.483  47.768  22.329    1.00  0.50
ATOM     1   O   PRO   256      31.780  47.348  21.412    1.00  0.50
ATOM     1   N   GLY   257      33.810  47.725  22.301    1.00  0.50
ATOM     1   CA  GLY   257      34.535  47.176  21.162    1.00  0.50
ATOM     1   C   GLY   257      35.055  45.763  21.415    1.00  0.50
ATOM     1   O   GLY   257      35.954  45.300  20.713    1.00  0.50
ATOM     1   N   ASP   258      34.509  45.078  22.416    1.00  0.50
ATOM     1   CA  ASP   258      34.955  43.717  22.721    1.00  0.50
ATOM     1   C   ASP   258      34.898  42.832  21.472    1.00  0.50
ATOM     1   O   ASP   258      33.903  42.831  20.748    1.00  0.50
ATOM     1   N   PRO   259      35.970  42.086  21.221    1.00  0.50
ATOM     1   CA  PRO   259      36.037  41.209  20.051    1.00  0.50
ATOM     1   C   PRO   259      35.168  39.967  20.199    1.00  0.50
ATOM     1   O   PRO   259      34.910  39.505  21.312    1.00  0.50
ATOM     1   N   VAL   260      34.719  39.425  19.069    1.00  0.50
ATOM     1   CA  VAL   260      33.908  38.218  19.096    1.00  0.50
ATOM     1   C   VAL   260      34.781  37.056  19.555    1.00  0.50
ATOM     1   O   VAL   260      35.988  37.029  19.290    1.00  0.50
ATOM     1   N   PHE   261      34.151  36.103  20.231    1.00  0.50
ATOM     1   CA  PHE   261      34.809  34.909  20.756    1.00  0.50
ATOM     1   C   PHE   261      35.736  35.222  21.919    1.00  0.50
ATOM     1   O   PHE   261      36.624  34.436  22.244    1.00  0.50
ATOM     1   N   VAL   262      35.534  36.378  22.547    1.00  0.50
ATOM     1   CA  VAL   262      36.355  36.744  23.696    1.00  0.50
ATOM     1   C   VAL   262      36.053  35.761  24.824    1.00  0.50
ATOM     1   O   VAL   262      34.894  35.571  25.190    1.00  0.50
ATOM     1   N   SER   263      37.102  35.144  25.365    1.00  0.50
ATOM     1   CA  SER   263      36.984  34.168  26.446    1.00  0.50
ATOM     1   C   SER   263      36.492  34.792  27.754    1.00  0.50
ATOM     1   O   SER   263      36.994  35.834  28.183    1.00  0.50
ATOM     1   N   LEU   264      35.511  34.150  28.383    1.00  0.50
ATOM     1   CA  LEU   264      34.959  34.632  29.647    1.00  0.50
ATOM     1   C   LEU   264      35.508  33.791  30.803    1.00  0.50
ATOM     1   O   LEU   264      35.153  32.631  30.960    1.00  0.50
ATOM     1   N   ASP   265      36.378  34.375  31.637    1.00  0.50
ATOM     1   CA  ASP   265      36.956  33.633  32.765    1.00  0.50
ATOM     1   C   ASP   265      35.943  33.157  33.795    1.00  0.50
ATOM     1   O   ASP   265      34.854  33.716  33.919    1.00  0.50
ATOM     1   N   GLY   266      36.303  32.109  34.529    1.00  0.50
ATOM     1   CA  GLY   266      35.421  31.570  35.555    1.00  0.50
ATOM     1   C   GLY   266      35.254  32.622  36.646    1.00  0.50
ATOM     1   O   GLY   266      36.226  33.026  37.284    1.00  0.50
ATOM     1   N   LYS   267      34.015  33.061  36.845    1.00  0.50
ATOM     1   CA  LYS   267      33.722  34.078  37.839    1.00  0.50
ATOM     1   C   LYS   267      32.649  35.036  37.351    1.00  0.50
ATOM     1   O   LYS   267      31.508  34.999  37.825    1.00  0.50
ATOM     1   N   VAL   268      29.716  36.394  35.350    1.00  0.50
ATOM     1   CA  VAL   268      28.623  35.752  34.624    1.00  0.50
ATOM     1   C   VAL   268      27.417  36.687  34.595    1.00  0.50
ATOM     1   O   VAL   268      27.530  37.865  34.943    1.00  0.50
ATOM     1   N   ILE   269      26.266  36.183  34.179    1.00  0.50
ATOM     1   CA  ILE   269      25.085  37.030  34.122    1.00  0.50
ATOM     1   C   ILE   269      24.179  36.814  35.332    1.00  0.50
ATOM     1   O   ILE   269      23.998  35.683  35.791    1.00  0.50
ATOM     1   N   PRO   270      23.630  37.907  35.857    1.00  0.50
ATOM     1   CA  PRO   270      22.737  37.853  37.011    1.00  0.50
ATOM     1   C   PRO   270      21.871  39.112  37.059    1.00  0.50
ATOM     1   O   PRO   270      20.683  39.045  37.386    1.00  0.50
ATOM     1   N   LEU   271      27.139  27.083  33.422    1.00  0.50
ATOM     1   CA  LEU   271      27.207  28.415  34.013    1.00  0.50
ATOM     1   C   LEU   271      28.524  29.115  33.681    1.00  0.50
ATOM     1   O   LEU   271      28.556  30.051  32.878    1.00  0.50
ATOM     1   N   GLY   272      29.608  28.659  34.301    1.00  0.50
ATOM     1   CA  GLY   272      30.925  29.247  34.073    1.00  0.50
ATOM     1   C   GLY   272      32.031  28.218  34.294    1.00  0.50
ATOM     1   O   GLY   272      31.914  27.344  35.150    1.00  0.50
ATOM     1   N   ASP   274      33.100  28.326  33.512    1.00  0.50
ATOM     1   CA  ASP   274      34.205  27.395  33.644    1.00  0.50
ATOM     1   C   ASP   274      35.434  27.827  32.865    1.00  0.50
ATOM     1   O   ASP   274      36.337  27.029  32.615    1.00  0.50
ATOM     1   N   CYS   275      35.475  29.099  32.483    1.00  0.50
ATOM     1   CA  CYS   275      36.609  29.599  31.729    1.00  0.50
ATOM     1   C   CYS   275      36.663  29.041  30.319    1.00  0.50
ATOM     1   O   CYS   275      37.682  29.154  29.633    1.00  0.50
ATOM     1   N   THR   276      35.566  28.436  29.883    1.00  0.50
ATOM     1   CA  THR   276      35.490  27.864  28.543    1.00  0.50
ATOM     1   C   THR   276      34.562  28.658  27.623    1.00  0.50
ATOM     1   O   THR   276      34.691  28.601  26.400    1.00  0.50
ATOM     1   N   VAL   277      33.630  29.399  28.214    1.00  0.50
ATOM     1   CA  VAL   277      32.686  30.174  27.428    1.00  0.50
ATOM     1   C   VAL   277      33.305  31.423  26.792    1.00  0.50
ATOM     1   O   VAL   277      34.325  31.930  27.249    1.00  0.50
ATOM     1   N   TYR   278      32.684  31.897  25.717    1.00  0.50
ATOM     1   CA  TYR   278      33.151  33.084  25.014    1.00  0.50
ATOM     1   C   TYR   278      31.924  33.882  24.589    1.00  0.50
ATOM     1   O   TYR   278      30.847  33.321  24.390    1.00  0.50
ATOM     1   N   PRO   279      32.088  35.189  24.456    1.00  0.50
ATOM     1   CA  PRO   279      30.987  36.052  24.056    1.00  0.50
ATOM     1   C   PRO   279      31.004  36.161  22.531    1.00  0.50
ATOM     1   O   PRO   279      32.070  36.191  21.910    1.00  0.50
ATOM     1   N   VAL   280      29.829  36.202  21.923    1.00  0.50
ATOM     1   CA  VAL   280      29.754  36.304  20.473    1.00  0.50
ATOM     1   C   VAL   280      28.632  37.254  20.072    1.00  0.50
ATOM     1   O   VAL   280      27.540  37.204  20.633    1.00  0.50
ATOM     1   N   PHE   281      28.923  38.132  19.117    1.00  0.50
ATOM     1   CA  PHE   281      27.957  39.107  18.613    1.00  0.50
ATOM     1   C   PHE   281      27.274  39.947  19.696    1.00  0.50
ATOM     1   O   PHE   281      26.052  40.066  19.723    1.00  0.50
ATOM     1   N   VAL   282      28.058  40.553  20.601    1.00  0.50
ATOM     1   CA  VAL   282      27.469  41.377  21.663    1.00  0.50
ATOM     1   C   VAL   282      26.794  42.638  21.109    1.00  0.50
ATOM     1   O   VAL   282      27.342  43.304  20.231    1.00  0.50
ATOM     1   N   ASN   283      25.612  42.962  21.622    1.00  0.50
ATOM     1   CA  ASN   283      24.886  44.146  21.170    1.00  0.50
ATOM     1   C   ASN   283      23.966  44.641  22.282    1.00  0.50
ATOM     1   O   ASN   283      22.756  44.404  22.254    1.00  0.50
ATOM     1   N   LYS   290      24.531  45.337  23.278    1.00  0.50
ATOM     1   CA  LYS   290      23.774  45.872  24.413    1.00  0.50
ATOM     1   C   LYS   290      22.883  47.070  24.071    1.00  0.50
ATOM     1   O   LYS   290      22.141  47.562  24.920    1.00  0.50
ATOM     1   N   LYS   291      22.958  47.529  22.825    1.00  0.50
ATOM     1   CA  LYS   291      22.170  48.673  22.378    1.00  0.50
ATOM     1   C   LYS   291      20.693  48.341  22.191    1.00  0.50
ATOM     1   O   LYS   291      19.829  49.186  22.418    1.00  0.50
ATOM     1   N   GLU   292      20.401  47.113  21.778    1.00  0.50
ATOM     1   CA  GLU   292      19.019  46.700  21.554    1.00  0.50
ATOM     1   C   GLU   292      18.134  46.913  22.779    1.00  0.50
ATOM     1   O   GLU   292      17.046  47.480  22.672    1.00  0.50
ATOM     1   N   ALA   293      18.602  46.445  23.933    1.00  0.50
ATOM     1   CA  ALA   293      17.879  46.565  25.200    1.00  0.50
ATOM     1   C   ALA   293      16.348  46.552  25.097    1.00  0.50
ATOM     1   O   ALA   293      15.676  47.426  25.655    1.00  0.50
ATOM     1   N   PHE   294      15.772  45.566  24.388    1.00  0.50
ATOM     1   CA  PHE   294      14.312  45.538  24.284    1.00  0.50
ATOM     1   C   PHE   294      13.743  44.436  25.179    1.00  0.50
ATOM     1   O   PHE   294      13.520  44.633  26.373    1.00  0.50
ATOM     1   N   ALA   295      13.514  43.277  24.575    1.00  0.50
ATOM     1   CA  ALA   295      13.005  42.121  25.283    1.00  0.50
ATOM     1   C   ALA   295      13.684  40.945  24.615    1.00  0.50
ATOM     1   O   ALA   295      13.409  39.782  24.905    1.00  0.50
ATOM     1   N   LYS   296      14.588  41.282  23.699    1.00  0.50
ATOM     1   CA  LYS   296      15.355  40.306  22.937    1.00  0.50
ATOM     1   C   LYS   296      16.708  40.094  23.604    1.00  0.50
ATOM     1   O   LYS   296      16.926  40.520  24.739    1.00  0.50
ATOM     1   N   THR   297      17.618  39.444  22.885    1.00  0.50
ATOM     1   CA  THR   297      18.949  39.171  23.402    1.00  0.50
ATOM     1   C   THR   297      19.940  40.238  22.950    1.00  0.50
ATOM     1   O   THR   297      19.768  40.853  21.897    1.00  0.50
TER
END
