
#######################################################
#                                                     #
#                        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   51 (  204),  selected   51 , name T0289AL044_5-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL044_5-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          3.117
LGA    M     225      M     225          3.304
LGA    E     226      E     226          2.767
LGA    K     227      K     227          1.253
LGA    D     229      V     228          0.710
LGA    Y     230      D     229          1.225
LGA    P     231      Y     230          2.410
LGA    R     232      P     231          4.087
LGA    N     233      R     232          2.936
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    E     234      V     238          2.438
LGA    S     235      A     239          3.488
LGA    G     236      A     240          2.586
LGA    D     237      V     241          1.903
LGA    V     238      I     242          2.246
LGA    -       -      H     243           -
LGA    -       -      P     244           -
LGA    A     239      N     245          1.892
LGA    A     240      L     246           #
LGA    V     241      Q     247          3.995
LGA    I     242      D     248          3.113
LGA    H     243      Q     249          1.773
LGA    P     244      D     250          3.311
LGA    D     250      W     251          2.224
LGA    W     251      -       -           -
LGA    K     252      K     252          1.103
LGA    P     253      P     253          0.795
LGA    L     254      L     254          1.870
LGA    H     255      H     255          2.098
LGA    P     256      P     256          2.573
LGA    G     257      -       -           -
LGA    D     258      G     257          1.513
LGA    P     259      D     258          3.242
LGA    V     260      P     259          2.205
LGA    F     261      V     260          2.200
LGA    V     262      F     261          2.134
LGA    S     263      V     262           #
LGA    L     264      S     263          5.479
LGA    D     265      L     264           #
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    K     267      K     267           #
LGA    V     268      V     268          5.135
LGA    I     269      I     269          4.073
LGA    P     270      P     270          2.819
LGA    L     271      L     271          3.001
LGA    -       -      G     272           -
LGA    -       -      G     273           -
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    -       -      T     276           -
LGA    -       -      V     277           -
LGA    -       -      Y     278           -
LGA    -       -      P     279           -
LGA    -       -      V     280           -
LGA    -       -      F     281           -
LGA    G     272      V     282          0.642
LGA    G     273      N     283          1.076
LGA    D     274      E     284           #
LGA    C     275      A     285          4.099
LGA    T     276      A     286          5.151
LGA    V     277      Y     287           #
LGA    Y     278      Y     288          4.449
LGA    P     279      E     289          4.522
LGA    V     280      K     290          2.284
LGA    F     281      K     291          3.478
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)   51   74    5.0     43    2.97    32.56     35.731     1.398

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.548624 * X  +  -0.105042 * Y  +  -0.829444 * Z  +  40.645679
  Y_new =  -0.140708 * X  +  -0.966325 * Y  +   0.215447 * Z  +  65.723755
  Z_new =  -0.824143 * X  +   0.234909 * Y  +   0.515369 * Z  +  -1.795293 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.427673   -2.713920  [ DEG:    24.5039   -155.4961 ]
  Theta =   0.968688    2.172904  [ DEG:    55.5017    124.4983 ]
  Phi   =  -2.890529    0.251063  [ DEG:  -165.6151     14.3849 ]
 
# 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: T0289AL044_5-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL044_5-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   51   74   5.0   43   2.97   32.56  35.731
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL044_5-D2
REMARK Aligment from pdb entry: 2bco_A
ATOM    801  N   ILE   224      25.985  26.945  21.777  1.00  0.00              
ATOM    802  CA  ILE   224      25.582  28.038  22.649  1.00  0.00              
ATOM    803  C   ILE   224      25.468  27.615  24.119  1.00  0.00              
ATOM    804  O   ILE   224      24.556  26.882  24.493  1.00  0.00              
ATOM    805  N   MET   225      26.409  28.068  24.944  1.00  0.00              
ATOM    806  CA  MET   225      26.388  27.749  26.369  1.00  0.00              
ATOM    807  C   MET   225      25.098  28.308  26.930  1.00  0.00              
ATOM    808  O   MET   225      24.312  27.588  27.537  1.00  0.00              
ATOM    809  N   GLU   226      24.889  29.604  26.726  1.00  0.00              
ATOM    810  CA  GLU   226      23.673  30.262  27.173  1.00  0.00              
ATOM    811  C   GLU   226      23.445  31.568  26.432  1.00  0.00              
ATOM    812  O   GLU   226      24.368  32.147  25.853  1.00  0.00              
ATOM    813  N   LYS   227      22.194  32.012  26.438  1.00  0.00              
ATOM    814  CA  LYS   227      21.807  33.239  25.763  1.00  0.00              
ATOM    815  C   LYS   227      21.492  34.317  26.803  1.00  0.00              
ATOM    816  O   LYS   227      20.734  34.078  27.740  1.00  0.00              
ATOM    817  N   ASP   229      22.091  35.495  26.640  1.00  0.00              
ATOM    818  CA  ASP   229      21.892  36.610  27.563  1.00  0.00              
ATOM    819  C   ASP   229      20.743  37.516  27.111  1.00  0.00              
ATOM    820  O   ASP   229      20.741  38.011  25.985  1.00  0.00              
ATOM    821  N   TYR   230      19.779  37.742  27.996  1.00  0.00              
ATOM    822  CA  TYR   230      18.634  38.591  27.678  1.00  0.00              
ATOM    823  C   TYR   230      18.540  39.798  28.615  1.00  0.00              
ATOM    824  O   TYR   230      18.586  39.645  29.835  1.00  0.00              
ATOM    825  N   PRO   231      18.404  40.992  28.040  1.00  0.00              
ATOM    826  CA  PRO   231      18.297  42.224  28.827  1.00  0.00              
ATOM    827  C   PRO   231      16.955  42.304  29.557  1.00  0.00              
ATOM    828  O   PRO   231      15.893  42.362  28.932  1.00  0.00              
ATOM    829  N   ARG   232      17.021  42.312  30.886  1.00  0.00              
ATOM    830  CA  ARG   232      15.833  42.372  31.727  1.00  0.00              
ATOM    831  C   ARG   232      15.479  43.773  32.217  1.00  0.00              
ATOM    832  O   ARG   232      14.300  44.111  32.325  1.00  0.00              
ATOM    833  N   ASN   233      16.489  44.584  32.515  1.00  0.00              
ATOM    834  CA  ASN   233      16.245  45.934  33.012  1.00  0.00              
ATOM    835  C   ASN   233      16.860  47.024  32.144  1.00  0.00              
ATOM    836  O   ASN   233      17.645  46.750  31.237  1.00  0.00              
ATOM    837  N   GLU   234      16.495  48.266  32.442  1.00  0.00              
ATOM    838  CA  GLU   234      16.988  49.425  31.706  1.00  0.00              
ATOM    839  C   GLU   234      18.462  49.673  32.028  1.00  0.00              
ATOM    840  O   GLU   234      19.237  50.094  31.166  1.00  0.00              
ATOM    841  N   SER   235      18.838  49.408  33.276  1.00  0.00              
ATOM    842  CA  SER   235      20.212  49.581  33.739  1.00  0.00              
ATOM    843  C   SER   235      20.990  48.302  33.451  1.00  0.00              
ATOM    844  O   SER   235      21.149  47.438  34.313  1.00  0.00              
ATOM    845  N   GLY   236      21.473  48.200  32.221  1.00  0.00              
ATOM    846  CA  GLY   236      22.212  47.037  31.750  1.00  0.00              
ATOM    847  C   GLY   236      23.499  47.514  31.078  1.00  0.00              
ATOM    848  O   GLY   236      23.499  48.543  30.405  1.00  0.00              
ATOM    849  N   ASP   237      24.594  46.784  31.258  1.00  0.00              
ATOM    850  CA  ASP   237      25.848  47.167  30.613  1.00  0.00              
ATOM    851  C   ASP   237      26.922  46.100  30.793  1.00  0.00              
ATOM    852  O   ASP   237      26.748  45.145  31.547  1.00  0.00              
ATOM    853  N   VAL   238      28.032  46.272  30.086  1.00  0.00              
ATOM    854  CA  VAL   238      29.150  45.343  30.157  1.00  0.00              
ATOM    855  C   VAL   238      30.352  46.103  30.694  1.00  0.00              
ATOM    856  O   VAL   238      30.384  47.325  30.628  1.00  0.00              
ATOM    857  N   ALA   239      33.564  45.459  29.626  1.00  0.00              
ATOM    858  CA  ALA   239      34.501  45.614  28.516  1.00  0.00              
ATOM    859  C   ALA   239      34.082  46.768  27.611  1.00  0.00              
ATOM    860  O   ALA   239      32.934  47.208  27.645  1.00  0.00              
ATOM    861  N   ALA   240      35.021  47.251  26.805  1.00  0.00              
ATOM    862  CA  ALA   240      34.769  48.357  25.889  1.00  0.00              
ATOM    863  C   ALA   240      33.946  47.930  24.687  1.00  0.00              
ATOM    864  O   ALA   240      33.791  46.739  24.417  1.00  0.00              
ATOM    865  N   VAL   241      33.429  48.916  23.961  1.00  0.00              
ATOM    866  CA  VAL   241      32.616  48.645  22.784  1.00  0.00              
ATOM    867  C   VAL   241      33.382  47.935  21.668  1.00  0.00              
ATOM    868  O   VAL   241      32.771  47.276  20.831  1.00  0.00              
ATOM    869  N   ILE   242      34.706  48.067  21.649  1.00  0.00              
ATOM    870  CA  ILE   242      35.508  47.396  20.630  1.00  0.00              
ATOM    871  C   ILE   242      35.855  45.974  21.083  1.00  0.00              
ATOM    872  O   ILE   242      36.819  45.367  20.609  1.00  0.00              
ATOM    873  N   HIS   243      35.059  45.458  22.014  1.00  0.00              
ATOM    874  CA  HIS   243      35.247  44.110  22.538  1.00  0.00              
ATOM    875  C   HIS   243      35.212  43.104  21.380  1.00  0.00              
ATOM    876  O   HIS   243      34.331  43.161  20.527  1.00  0.00              
ATOM    877  N   PRO   244      36.165  42.182  21.357  1.00  0.00              
ATOM    878  CA  PRO   244      36.244  41.188  20.290  1.00  0.00              
ATOM    879  C   PRO   244      35.241  40.048  20.434  1.00  0.00              
ATOM    880  O   PRO   244      34.831  39.702  21.546  1.00  0.00              
ATOM    881  N   ASP   250      34.829  39.481  19.301  1.00  0.00              
ATOM    882  CA  ASP   250      33.928  38.340  19.322  1.00  0.00              
ATOM    883  C   ASP   250      34.773  37.183  19.839  1.00  0.00              
ATOM    884  O   ASP   250      35.986  37.134  19.609  1.00  0.00              
ATOM    885  N   TRP   251      34.132  36.258  20.538  1.00  0.00              
ATOM    886  CA  TRP   251      34.814  35.107  21.122  1.00  0.00              
ATOM    887  C   TRP   251      35.838  35.501  22.170  1.00  0.00              
ATOM    888  O   TRP   251      36.897  34.886  22.268  1.00  0.00              
ATOM    889  N   LYS   252      35.534  36.541  22.939  1.00  0.00              
ATOM    890  CA  LYS   252      36.419  36.959  24.018  1.00  0.00              
ATOM    891  C   LYS   252      36.033  36.026  25.165  1.00  0.00              
ATOM    892  O   LYS   252      34.878  36.000  25.593  1.00  0.00              
ATOM    893  N   PRO   253      37.000  35.257  25.653  1.00  0.00              
ATOM    894  CA  PRO   253      36.739  34.297  26.721  1.00  0.00              
ATOM    895  C   PRO   253      36.804  34.868  28.125  1.00  0.00              
ATOM    896  O   PRO   253      37.308  35.967  28.347  1.00  0.00              
ATOM    897  N   LEU   254      36.284  34.101  29.075  1.00  0.00              
ATOM    898  CA  LEU   254      36.278  34.502  30.473  1.00  0.00              
ATOM    899  C   LEU   254      36.630  33.293  31.319  1.00  0.00              
ATOM    900  O   LEU   254      36.625  32.166  30.834  1.00  0.00              
ATOM    901  N   HIS   255      36.948  33.533  32.585  1.00  0.00              
ATOM    902  CA  HIS   255      37.276  32.454  33.501  1.00  0.00              
ATOM    903  C   HIS   255      36.027  32.245  34.338  1.00  0.00              
ATOM    904  O   HIS   255      35.217  33.157  34.460  1.00  0.00              
ATOM    905  N   PRO   256      35.856  31.053  34.897  1.00  0.00              
ATOM    906  CA  PRO   256      34.672  30.784  35.700  1.00  0.00              
ATOM    907  C   PRO   256      34.469  31.810  36.810  1.00  0.00              
ATOM    908  O   PRO   256      35.398  32.143  37.546  1.00  0.00              
ATOM    909  N   GLY   257      33.245  32.323  36.904  1.00  0.00              
ATOM    910  CA  GLY   257      32.917  33.293  37.933  1.00  0.00              
ATOM    911  C   GLY   257      33.366  34.714  37.662  1.00  0.00              
ATOM    912  O   GLY   257      33.185  35.590  38.508  1.00  0.00              
ATOM    913  N   ASP   258      33.962  34.957  36.499  1.00  0.00              
ATOM    914  CA  ASP   258      34.404  36.309  36.176  1.00  0.00              
ATOM    915  C   ASP   258      33.198  37.171  35.808  1.00  0.00              
ATOM    916  O   ASP   258      32.343  36.750  35.023  1.00  0.00              
ATOM    917  N   PRO   259      33.121  38.365  36.386  1.00  0.00              
ATOM    918  CA  PRO   259      32.017  39.268  36.088  1.00  0.00              
ATOM    919  C   PRO   259      32.418  40.108  34.886  1.00  0.00              
ATOM    920  O   PRO   259      33.550  40.578  34.804  1.00  0.00              
ATOM    921  N   VAL   260      31.500  40.286  33.945  1.00  0.00              
ATOM    922  CA  VAL   260      31.808  41.068  32.754  1.00  0.00              
ATOM    923  C   VAL   260      30.705  42.064  32.433  1.00  0.00              
ATOM    924  O   VAL   260      30.750  42.749  31.412  1.00  0.00              
ATOM    925  N   PHE   261      29.710  42.138  33.306  1.00  0.00              
ATOM    926  CA  PHE   261      28.620  43.066  33.092  1.00  0.00              
ATOM    927  C   PHE   261      27.608  42.966  34.210  1.00  0.00              
ATOM    928  O   PHE   261      27.877  42.362  35.250  1.00  0.00              
ATOM    929  N   VAL   262      26.440  43.555  33.999  1.00  0.00              
ATOM    930  CA  VAL   262      25.399  43.515  35.006  1.00  0.00              
ATOM    931  C   VAL   262      24.050  43.862  34.386  1.00  0.00              
ATOM    932  O   VAL   262      23.963  44.640  33.430  1.00  0.00              
ATOM    933  N   SER   263      22.999  43.259  34.924  1.00  0.00              
ATOM    934  CA  SER   263      21.644  43.489  34.451  1.00  0.00              
ATOM    935  C   SER   263      20.856  43.888  35.694  1.00  0.00              
ATOM    936  O   SER   263      20.486  43.034  36.512  1.00  0.00              
ATOM    937  N   LEU   264      20.607  45.186  35.841  1.00  0.00              
ATOM    938  CA  LEU   264      19.897  45.658  37.012  1.00  0.00              
ATOM    939  C   LEU   264      20.826  45.507  38.200  1.00  0.00              
ATOM    940  O   LEU   264      21.841  46.198  38.288  1.00  0.00              
ATOM    941  N   ASP   265      20.497  44.592  39.106  1.00  0.00              
ATOM    942  CA  ASP   265      21.324  44.358  40.288  1.00  0.00              
ATOM    943  C   ASP   265      22.154  43.094  40.102  1.00  0.00              
ATOM    944  O   ASP   265      23.321  43.039  40.487  1.00  0.00              
ATOM    945  N   LYS   267      21.528  42.079  39.513  1.00  0.00              
ATOM    946  CA  LYS   267      22.170  40.790  39.271  1.00  0.00              
ATOM    947  C   LYS   267      23.263  40.930  38.213  1.00  0.00              
ATOM    948  O   LYS   267      22.981  41.244  37.057  1.00  0.00              
ATOM    949  N   VAL   268      24.528  40.692  38.597  1.00  0.00              
ATOM    950  CA  VAL   268      25.657  40.799  37.668  1.00  0.00              
ATOM    951  C   VAL   268      25.762  39.652  36.662  1.00  0.00              
ATOM    952  O   VAL   268      25.140  38.604  36.827  1.00  0.00              
ATOM    953  N   ILE   269      26.554  39.872  35.618  1.00  0.00              
ATOM    954  CA  ILE   269      26.768  38.870  34.578  1.00  0.00              
ATOM    955  C   ILE   269      28.146  38.248  34.782  1.00  0.00              
ATOM    956  O   ILE   269      29.148  38.963  34.831  1.00  0.00              
ATOM    957  N   PRO   270      28.194  36.925  34.922  1.00  0.00              
ATOM    958  CA  PRO   270      29.468  36.231  35.105  1.00  0.00              
ATOM    959  C   PRO   270      29.470  34.896  34.387  1.00  0.00              
ATOM    960  O   PRO   270      28.428  34.259  34.247  1.00  0.00              
ATOM    961  N   LEU   271      30.644  34.475  33.934  1.00  0.00              
ATOM    962  CA  LEU   271      30.772  33.206  33.231  1.00  0.00              
ATOM    963  C   LEU   271      30.356  32.053  34.140  1.00  0.00              
ATOM    964  O   LEU   271      30.620  32.075  35.341  1.00  0.00              
ATOM    965  N   GLY   272      28.082  40.815  21.110  1.00  0.00              
ATOM    966  CA  GLY   272      27.594  41.600  22.253  1.00  0.00              
ATOM    967  C   GLY   272      26.927  42.879  21.750  1.00  0.00              
ATOM    968  O   GLY   272      27.393  43.484  20.792  1.00  0.00              
ATOM    969  N   GLY   273      25.841  43.288  22.395  1.00  0.00              
ATOM    970  CA  GLY   273      25.141  44.510  21.997  1.00  0.00              
ATOM    971  C   GLY   273      24.363  45.068  23.186  1.00  0.00              
ATOM    972  O   GLY   273      23.307  44.547  23.543  1.00  0.00              
ATOM    973  N   ASP   274      24.893  46.128  23.788  1.00  0.00              
ATOM    974  CA  ASP   274      24.274  46.758  24.953  1.00  0.00              
ATOM    975  C   ASP   274      23.100  47.679  24.609  1.00  0.00              
ATOM    976  O   ASP   274      22.344  48.083  25.493  1.00  0.00              
ATOM    977  N   CYS   275      22.946  48.006  23.329  1.00  0.00              
ATOM    978  CA  CYS   275      21.865  48.882  22.899  1.00  0.00              
ATOM    979  C   CYS   275      20.577  48.108  22.643  1.00  0.00              
ATOM    980  O   CYS   275      19.504  48.695  22.499  1.00  0.00              
ATOM    981  N   THR   276      20.702  46.788  22.591  1.00  0.00              
ATOM    982  CA  THR   276      19.571  45.904  22.363  1.00  0.00              
ATOM    983  C   THR   276      18.387  46.286  23.246  1.00  0.00              
ATOM    984  O   THR   276      18.523  46.423  24.459  1.00  0.00              
ATOM    985  N   VAL   277      17.225  46.457  22.627  1.00  0.00              
ATOM    986  CA  VAL   277      16.023  46.829  23.361  1.00  0.00              
ATOM    987  C   VAL   277      15.712  45.829  24.468  1.00  0.00              
ATOM    988  O   VAL   277      16.194  44.697  24.456  1.00  0.00              
ATOM    989  N   TYR   278      14.897  46.262  25.422  1.00  0.00              
ATOM    990  CA  TYR   278      14.499  45.430  26.551  1.00  0.00              
ATOM    991  C   TYR   278      13.838  44.126  26.091  1.00  0.00              
ATOM    992  O   TYR   278      13.051  44.119  25.150  1.00  0.00              
ATOM    993  N   PRO   279      14.171  43.022  26.754  1.00  0.00              
ATOM    994  CA  PRO   279      13.576  41.745  26.404  1.00  0.00              
ATOM    995  C   PRO   279      14.226  40.972  25.271  1.00  0.00              
ATOM    996  O   PRO   279      13.926  39.795  25.086  1.00  0.00              
ATOM    997  N   VAL   280      15.094  41.622  24.500  1.00  0.00              
ATOM    998  CA  VAL   280      15.786  40.961  23.392  1.00  0.00              
ATOM    999  C   VAL   280      17.128  40.421  23.896  1.00  0.00              
ATOM   1000  O   VAL   280      17.528  40.710  25.025  1.00  0.00              
ATOM   1001  N   PHE   281      17.830  39.645  23.076  1.00  0.00              
ATOM   1002  CA  PHE   281      19.107  39.100  23.522  1.00  0.00              
ATOM   1003  C   PHE   281      20.233  40.099  23.335  1.00  0.00              
ATOM   1004  O   PHE   281      20.326  40.765  22.302  1.00  0.00              
END
