
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0289AL243_3-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL243_3-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          4.529
LGA    M     225      M     225          4.445
LGA    E     226      E     226          4.247
LGA    K     227      K     227          2.643
LGA    V     228      V     228          3.132
LGA    D     229      D     229          2.922
LGA    -       -      Y     230           -
LGA    -       -      P     231           -
LGA    -       -      R     232           -
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    R     232      D     237           #
LGA    Q     247      V     238          1.418
LGA    D     248      A     239          3.027
LGA    Q     249      A     240           #
LGA    D     250      V     241           #
LGA    W     251      I     242          5.008
LGA    K     252      H     243          3.975
LGA    -       -      P     244           -
LGA    -       -      N     245           -
LGA    -       -      L     246           -
LGA    -       -      Q     247           -
LGA    -       -      D     248           -
LGA    -       -      Q     249           -
LGA    -       -      D     250           -
LGA    -       -      W     251           -
LGA    -       -      K     252           -
LGA    P     253      P     253          1.094
LGA    L     254      L     254          1.348
LGA    H     255      H     255          1.621
LGA    P     256      P     256          1.782
LGA    G     257      G     257          1.339
LGA    D     258      D     258          1.395
LGA    P     259      P     259          1.305
LGA    V     260      V     260          3.691
LGA    F     261      F     261          3.496
LGA    V     262      V     262          1.479
LGA    S     263      S     263          3.770
LGA    D     265      L     264          4.066
LGA    G     266      D     265          4.844
LGA    -       -      G     266           -
LGA    K     267      K     267          4.526
LGA    V     268      V     268          2.431
LGA    I     269      I     269          3.319
LGA    P     270      P     270          1.751
LGA    L     271      L     271          1.891
LGA    G     272      G     272          2.041
LGA    D     274      G     273          3.049
LGA    -       -      D     274           -
LGA    C     275      C     275          2.019
LGA    T     276      T     276          1.988
LGA    V     277      V     277          1.446
LGA    Y     278      Y     278          1.620
LGA    P     279      P     279          0.846
LGA    V     280      V     280          0.463
LGA    F     281      F     281          0.693
LGA    V     282      V     282          0.884
LGA    N     283      N     283          1.534
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      A     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      E     289           -
LGA    -       -      K     290           -
LGA    -       -      K     291           -
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)   42   74    5.0     39    2.81    82.05     35.467     1.342

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.646881 * X  +  -0.231600 * Y  +  -0.726572 * Z  +  41.996433
  Y_new =  -0.098536 * X  +  -0.919396 * Y  +   0.380792 * Z  +  62.865513
  Z_new =  -0.756198 * X  +   0.317920 * Y  +   0.571919 * Z  +  -4.853380 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.507349   -2.634244  [ DEG:    29.0689   -150.9311 ]
  Theta =   0.857483    2.284109  [ DEG:    49.1302    130.8698 ]
  Phi   =  -2.990431    0.151162  [ DEG:  -171.3391      8.6609 ]
 
# 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: T0289AL243_3-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL243_3-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   74   5.0   39   2.81   82.05  35.467
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL243_3-D2
REMARK Aligment from pdb entry: 2bcoA
ATOM    805  N   ILE   224      23.921  28.566  22.916  1.00  0.00              
ATOM    806  CA  ILE   224      23.790  29.762  23.735  1.00  0.00              
ATOM    807  C   ILE   224      23.764  29.454  25.237  1.00  0.00              
ATOM    808  O   ILE   224      22.791  28.907  25.751  1.00  0.00              
ATOM    809  N   MET   225      24.846  29.796  25.933  1.00  0.00              
ATOM    810  CA  MET   225      24.923  29.572  27.375  1.00  0.00              
ATOM    811  C   MET   225      23.803  30.370  28.008  1.00  0.00              
ATOM    812  O   MET   225      22.981  29.829  28.740  1.00  0.00              
ATOM    813  N   GLU   226      23.782  31.668  27.724  1.00  0.00              
ATOM    814  CA  GLU   226      22.739  32.544  28.230  1.00  0.00              
ATOM    815  C   GLU   226      22.644  33.822  27.415  1.00  0.00              
ATOM    816  O   GLU   226      23.582  34.203  26.709  1.00  0.00              
ATOM    817  N   LYS   227      21.487  34.466  27.502  1.00  0.00              
ATOM    818  CA  LYS   227      21.231  35.697  26.773  1.00  0.00              
ATOM    819  C   LYS   227      21.201  36.873  27.751  1.00  0.00              
ATOM    820  O   LYS   227      20.517  36.821  28.770  1.00  0.00              
ATOM    821  N   VAL   228      21.958  37.923  27.442  1.00  0.00              
ATOM    822  CA  VAL   228      22.035  39.111  28.290  1.00  0.00              
ATOM    823  C   VAL   228      21.004  40.165  27.878  1.00  0.00              
ATOM    824  O   VAL   228      20.963  40.583  26.722  1.00  0.00              
ATOM    825  N   ASP   229      20.185  40.601  28.829  1.00  0.00              
ATOM    826  CA  ASP   229      19.162  41.606  28.553  1.00  0.00              
ATOM    827  C   ASP   229      19.359  42.868  29.398  1.00  0.00              
ATOM    828  O   ASP   229      19.507  42.784  30.617  1.00  0.00              
ATOM    829  N   ARG   232      19.354  44.030  28.748  1.00  0.00              
ATOM    830  CA  ARG   232      19.526  45.309  29.443  1.00  0.00              
ATOM    831  C   ARG   232      18.297  45.654  30.286  1.00  0.00              
ATOM    832  O   ARG   232      17.198  45.849  29.761  1.00  0.00              
ATOM    833  N   GLN   247      18.502  45.733  31.599  1.00  0.00              
ATOM    834  CA  GLN   247      17.433  46.039  32.540  1.00  0.00              
ATOM    835  C   GLN   247      17.358  47.507  32.950  1.00  0.00              
ATOM    836  O   GLN   247      16.265  48.042  33.140  1.00  0.00              
ATOM    837  N   ASP   248      18.509  48.157  33.089  1.00  0.00              
ATOM    838  CA  ASP   248      18.535  49.557  33.501  1.00  0.00              
ATOM    839  C   ASP   248      19.221  50.475  32.497  1.00  0.00              
ATOM    840  O   ASP   248      19.853  50.019  31.545  1.00  0.00              
ATOM    841  N   GLN   249      19.090  51.776  32.730  1.00  0.00              
ATOM    842  CA  GLN   249      19.680  52.790  31.864  1.00  0.00              
ATOM    843  C   GLN   249      21.201  52.810  32.027  1.00  0.00              
ATOM    844  O   GLN   249      21.939  53.044  31.067  1.00  0.00              
ATOM    845  N   ASP   250      21.658  52.564  33.252  1.00  0.00              
ATOM    846  CA  ASP   250      23.083  52.536  33.571  1.00  0.00              
ATOM    847  C   ASP   250      23.614  51.131  33.312  1.00  0.00              
ATOM    848  O   ASP   250      23.724  50.307  34.219  1.00  0.00              
ATOM    849  N   TRP   251      23.944  50.875  32.054  1.00  0.00              
ATOM    850  CA  TRP   251      24.437  49.579  31.608  1.00  0.00              
ATOM    851  C   TRP   251      25.706  49.795  30.784  1.00  0.00              
ATOM    852  O   TRP   251      25.798  50.767  30.036  1.00  0.00              
ATOM    853  N   LYS   252      26.684  48.907  30.917  1.00  0.00              
ATOM    854  CA  LYS   252      27.909  49.037  30.131  1.00  0.00              
ATOM    855  C   LYS   252      28.813  47.820  30.293  1.00  0.00              
ATOM    856  O   LYS   252      28.570  46.955  31.132  1.00  0.00              
ATOM    857  N   PRO   253      36.456  35.165  25.096  1.00  0.00              
ATOM    858  CA  PRO   253      36.159  34.329  26.255  1.00  0.00              
ATOM    859  C   PRO   253      36.460  34.967  27.598  1.00  0.00              
ATOM    860  O   PRO   253      37.152  35.979  27.686  1.00  0.00              
ATOM    861  N   LEU   254      35.927  34.356  28.649  1.00  0.00              
ATOM    862  CA  LEU   254      36.130  34.838  30.006  1.00  0.00              
ATOM    863  C   LEU   254      36.373  33.642  30.907  1.00  0.00              
ATOM    864  O   LEU   254      36.139  32.503  30.513  1.00  0.00              
ATOM    865  N   HIS   255      36.855  33.904  32.115  1.00  0.00              
ATOM    866  CA  HIS   255      37.102  32.843  33.078  1.00  0.00              
ATOM    867  C   HIS   255      35.929  32.895  34.041  1.00  0.00              
ATOM    868  O   HIS   255      35.292  33.935  34.167  1.00  0.00              
ATOM    869  N   PRO   256      35.632  31.785  34.705  1.00  0.00              
ATOM    870  CA  PRO   256      34.510  31.765  35.632  1.00  0.00              
ATOM    871  C   PRO   256      34.589  32.877  36.674  1.00  0.00              
ATOM    872  O   PRO   256      35.631  33.096  37.292  1.00  0.00              
ATOM    873  N   GLY   257      33.478  33.590  36.841  1.00  0.00              
ATOM    874  CA  GLY   257      33.417  34.662  37.818  1.00  0.00              
ATOM    875  C   GLY   257      34.054  35.970  37.396  1.00  0.00              
ATOM    876  O   GLY   257      34.104  36.914  38.185  1.00  0.00              
ATOM    877  N   ASP   258      34.557  36.040  36.167  1.00  0.00              
ATOM    878  CA  ASP   258      35.171  37.277  35.701  1.00  0.00              
ATOM    879  C   ASP   258      34.085  38.302  35.381  1.00  0.00              
ATOM    880  O   ASP   258      33.098  37.981  34.714  1.00  0.00              
ATOM    881  N   PRO   259      34.259  39.526  35.869  1.00  0.00              
ATOM    882  CA  PRO   259      33.287  40.579  35.606  1.00  0.00              
ATOM    883  C   PRO   259      33.688  41.266  34.311  1.00  0.00              
ATOM    884  O   PRO   259      34.865  41.536  34.087  1.00  0.00              
ATOM    885  N   VAL   260      32.716  41.534  33.448  1.00  0.00              
ATOM    886  CA  VAL   260      33.019  42.180  32.176  1.00  0.00              
ATOM    887  C   VAL   260      32.060  43.323  31.882  1.00  0.00              
ATOM    888  O   VAL   260      32.106  43.927  30.812  1.00  0.00              
ATOM    889  N   PHE   261      31.186  43.614  32.836  1.00  0.00              
ATOM    890  CA  PHE   261      30.240  44.695  32.652  1.00  0.00              
ATOM    891  C   PHE   261      29.347  44.832  33.865  1.00  0.00              
ATOM    892  O   PHE   261      29.623  44.256  34.919  1.00  0.00              
ATOM    893  N   VAL   262      28.271  45.591  33.718  1.00  0.00              
ATOM    894  CA  VAL   262      27.348  45.787  34.817  1.00  0.00              
ATOM    895  C   VAL   262      26.013  46.312  34.299  1.00  0.00              
ATOM    896  O   VAL   262      25.952  47.034  33.299  1.00  0.00              
ATOM    897  N   SER   263      24.943  45.925  34.979  1.00  0.00              
ATOM    898  CA  SER   263      23.599  46.346  34.617  1.00  0.00              
ATOM    899  C   SER   263      23.018  46.946  35.893  1.00  0.00              
ATOM    900  O   SER   263      22.605  46.217  36.806  1.00  0.00              
ATOM    901  N   ASP   265      22.994  48.274  35.961  1.00  0.00              
ATOM    902  CA  ASP   265      22.494  48.928  37.153  1.00  0.00              
ATOM    903  C   ASP   265      23.506  48.699  38.258  1.00  0.00              
ATOM    904  O   ASP   265      24.622  49.217  38.197  1.00  0.00              
ATOM    905  N   GLY   266      23.132  47.908  39.259  1.00  0.00              
ATOM    906  CA  GLY   266      24.031  47.614  40.373  1.00  0.00              
ATOM    907  C   GLY   266      24.626  46.221  40.210  1.00  0.00              
ATOM    908  O   GLY   266      25.804  45.998  40.487  1.00  0.00              
ATOM    909  N   LYS   267      23.790  45.290  39.762  1.00  0.00              
ATOM    910  CA  LYS   267      24.191  43.899  39.562  1.00  0.00              
ATOM    911  C   LYS   267      25.176  43.792  38.399  1.00  0.00              
ATOM    912  O   LYS   267      24.828  44.076  37.254  1.00  0.00              
ATOM    913  N   VAL   268      26.420  43.372  38.681  1.00  0.00              
ATOM    914  CA  VAL   268      27.448  43.234  37.646  1.00  0.00              
ATOM    915  C   VAL   268      27.265  42.026  36.727  1.00  0.00              
ATOM    916  O   VAL   268      26.506  41.107  37.030  1.00  0.00              
ATOM    917  N   ILE   269      27.969  42.047  35.599  1.00  0.00              
ATOM    918  CA  ILE   269      27.912  40.961  34.626  1.00  0.00              
ATOM    919  C   ILE   269      29.188  40.134  34.748  1.00  0.00              
ATOM    920  O   ILE   269      30.290  40.675  34.648  1.00  0.00              
ATOM    921  N   PRO   270      29.041  38.832  34.985  1.00  0.00              
ATOM    922  CA  PRO   270      30.200  37.950  35.103  1.00  0.00              
ATOM    923  C   PRO   270      29.916  36.591  34.493  1.00  0.00              
ATOM    924  O   PRO   270      28.778  36.128  34.501  1.00  0.00              
ATOM    925  N   LEU   271      30.955  35.955  33.967  1.00  0.00              
ATOM    926  CA  LEU   271      30.807  34.641  33.355  1.00  0.00              
ATOM    927  C   LEU   271      30.310  33.632  34.387  1.00  0.00              
ATOM    928  O   LEU   271      30.699  33.684  35.552  1.00  0.00              
ATOM    929  N   GLY   272      29.448  32.720  33.946  1.00  0.00              
ATOM    930  CA  GLY   272      28.887  31.694  34.817  1.00  0.00              
ATOM    931  C   GLY   272      29.781  30.458  34.787  1.00  0.00              
ATOM    932  O   GLY   272      30.328  30.048  35.812  1.00  0.00              
ATOM    933  N   ASP   274      29.929  29.867  33.606  1.00  0.00              
ATOM    934  CA  ASP   274      30.773  28.689  33.441  1.00  0.00              
ATOM    935  C   ASP   274      32.211  29.154  33.291  1.00  0.00              
ATOM    936  O   ASP   274      32.547  30.280  33.650  1.00  0.00              
ATOM    937  N   CYS   275      33.061  28.287  32.757  1.00  0.00              
ATOM    938  CA  CYS   275      34.459  28.631  32.564  1.00  0.00              
ATOM    939  C   CYS   275      34.746  28.624  31.065  1.00  0.00              
ATOM    940  O   CYS   275      35.828  29.019  30.620  1.00  0.00              
ATOM    941  N   THR   276      33.757  28.188  30.288  1.00  0.00              
ATOM    942  CA  THR   276      33.900  28.107  28.841  1.00  0.00              
ATOM    943  C   THR   276      32.995  29.062  28.050  1.00  0.00              
ATOM    944  O   THR   276      32.700  28.813  26.883  1.00  0.00              
ATOM    945  N   VAL   277      32.566  30.151  28.680  1.00  0.00              
ATOM    946  CA  VAL   277      31.706  31.118  28.010  1.00  0.00              
ATOM    947  C   VAL   277      32.491  32.161  27.224  1.00  0.00              
ATOM    948  O   VAL   277      33.611  32.532  27.584  1.00  0.00              
ATOM    949  N   TYR   278      31.887  32.622  26.137  1.00  0.00              
ATOM    950  CA  TYR   278      32.484  33.640  25.291  1.00  0.00              
ATOM    951  C   TYR   278      31.346  34.569  24.935  1.00  0.00              
ATOM    952  O   TYR   278      30.198  34.147  24.866  1.00  0.00              
ATOM    953  N   PRO   279      31.651  35.836  24.711  1.00  0.00              
ATOM    954  CA  PRO   279      30.605  36.778  24.371  1.00  0.00              
ATOM    955  C   PRO   279      30.518  36.955  22.860  1.00  0.00              
ATOM    956  O   PRO   279      31.541  37.000  22.183  1.00  0.00              
ATOM    957  N   VAL   280      29.296  37.040  22.337  1.00  0.00              
ATOM    958  CA  VAL   280      29.068  37.217  20.900  1.00  0.00              
ATOM    959  C   VAL   280      28.025  38.312  20.635  1.00  0.00              
ATOM    960  O   VAL   280      27.013  38.390  21.331  1.00  0.00              
ATOM    961  N   PHE   281      28.265  39.152  19.630  1.00  0.00              
ATOM    962  CA  PHE   281      27.323  40.230  19.289  1.00  0.00              
ATOM    963  C   PHE   281      27.062  41.182  20.457  1.00  0.00              
ATOM    964  O   PHE   281      25.925  41.332  20.900  1.00  0.00              
ATOM    965  N   VAL   282      28.106  41.831  20.984  1.00  0.00              
ATOM    966  CA  VAL   282      27.870  42.755  22.102  1.00  0.00              
ATOM    967  C   VAL   282      27.365  44.092  21.566  1.00  0.00              
ATOM    968  O   VAL   282      27.819  44.552  20.524  1.00  0.00              
ATOM    969  N   ASN   283      26.431  44.714  22.275  1.00  0.00              
ATOM    970  CA  ASN   283      25.895  46.008  21.851  1.00  0.00              
ATOM    971  C   ASN   283      25.344  46.759  23.060  1.00  0.00              
ATOM    972  O   ASN   283      24.262  46.443  23.553  1.00  0.00              
END
