
#######################################################
#                                                     #
#                        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   47 (  188),  selected   47 , name T0289AL381_5-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL381_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           -
LGA    -       -      M     225           -
LGA    I     224      E     226          0.637
LGA    M     225      K     227          0.543
LGA    E     226      V     228          3.587
LGA    K     227      D     229          1.138
LGA    V     228      Y     230          1.678
LGA    D     229      P     231          3.303
LGA    Y     230      R     232          1.724
LGA    P     231      N     233          2.349
LGA    R     232      E     234          3.315
LGA    N     233      S     235          3.827
LGA    E     234      G     236          1.143
LGA    S     235      D     237          2.089
LGA    G     236      V     238          2.894
LGA    -       -      A     239           -
LGA    D     237      A     240          3.420
LGA    V     238      V     241          1.970
LGA    A     239      I     242          0.377
LGA    -       -      H     243           -
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           -
LGA    -       -      L     254           -
LGA    -       -      H     255           -
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    A     240      V     260          4.201
LGA    V     241      F     261          3.948
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    I     242      P     270           #
LGA    H     243      L     271          1.814
LGA    -       -      G     272           -
LGA    P     244      G     273          3.779
LGA    N     245      D     274          1.179
LGA    L     246      C     275          2.920
LGA    Q     247      T     276          1.854
LGA    D     248      V     277           #
LGA    Q     249      -       -           -
LGA    D     250      Y     278           #
LGA    W     251      P     279          4.548
LGA    K     252      V     280           -
LGA    -       -      F     281           -
LGA    P     253      V     282          4.927
LGA    L     254      N     283          1.850
LGA    H     255      E     284           #
LGA    -       -      A     285           -
LGA    -       -      A     286           -
LGA    -       -      Y     287           -
LGA    P     256      Y     288          2.488
LGA    G     257      E     289           -
LGA    -       -      K     290           -
LGA    -       -      K     291           -
LGA    D     258      E     292          2.030
LGA    P     259      A     293          3.000
LGA    -       -      F     294           -
LGA    V     260      A     295          0.605
LGA    F     261      K     296          0.684
LGA    V     262      T     297          0.622
LGA    S     263      -       -           -
LGA    L     264      -       -           -
LGA    D     265      -       -           -
LGA    G     266      -       -           -
LGA    K     267      -       -           -
LGA    V     268      -       -           -
LGA    I     269      -       -           -
LGA    P     270      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   47   74    5.0     32    2.65     3.12     27.742     1.162

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.343500 * X  +  -0.848125 * Y  +   0.403351 * Z  +  70.906715
  Y_new =  -0.907476 * X  +   0.189139 * Y  +  -0.375119 * Z  +  42.691460
  Z_new =   0.241858 * X  +  -0.494884 * Y  +  -0.834622 * Z  +  40.267292 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.606377    0.535215  [ DEG:  -149.3344     30.6656 ]
  Theta =  -0.244281   -2.897312  [ DEG:   -13.9963   -166.0038 ]
  Phi   =  -1.932652    1.208941  [ DEG:  -110.7328     69.2672 ]
 
# 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: T0289AL381_5-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL381_5-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   47   74   5.0   32   2.65    3.12  27.742
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL381_5-D2
REMARK Aligment from pdb entry: 1qmuA
ATOM    737  N   ILE   224      24.223  29.664  23.733  1.00  0.00              
ATOM    738  CA  ILE   224      23.217  30.293  24.590  1.00  0.00              
ATOM    739  C   ILE   224      23.067  31.778  24.309  1.00  0.00              
ATOM    740  O   ILE   224      24.030  32.453  23.939  1.00  0.00              
ATOM    741  N   MET   225      21.861  32.287  24.535  1.00  0.00              
ATOM    742  CA  MET   225      21.566  33.703  24.331  1.00  0.00              
ATOM    743  C   MET   225      20.293  34.091  25.078  1.00  0.00              
ATOM    744  O   MET   225      19.487  33.239  25.463  1.00  0.00              
ATOM    745  N   GLU   226      20.107  35.386  25.267  1.00  0.00              
ATOM    746  CA  GLU   226      18.944  35.834  25.985  1.00  0.00              
ATOM    747  C   GLU   226      19.131  37.266  26.418  1.00  0.00              
ATOM    748  O   GLU   226      19.901  38.017  25.802  1.00  0.00              
ATOM    749  N   LYS   227      18.430  37.646  27.486  1.00  0.00              
ATOM    750  CA  LYS   227      18.494  39.012  27.993  1.00  0.00              
ATOM    751  C   LYS   227      18.677  39.068  29.491  1.00  0.00              
ATOM    752  O   LYS   227      18.290  38.154  30.226  1.00  0.00              
ATOM    753  N   VAL   228      19.246  40.191  29.915  1.00  0.00              
ATOM    754  CA  VAL   228      19.503  40.505  31.308  1.00  0.00              
ATOM    755  C   VAL   228      18.567  41.677  31.608  1.00  0.00              
ATOM    756  O   VAL   228      18.896  42.852  31.417  1.00  0.00              
ATOM    757  N   ASP   229      17.375  41.309  32.057  1.00  0.00              
ATOM    758  CA  ASP   229      16.308  42.238  32.382  1.00  0.00              
ATOM    759  C   ASP   229      16.427  42.754  33.812  1.00  0.00              
ATOM    760  O   ASP   229      16.695  41.992  34.741  1.00  0.00              
ATOM    761  N   TYR   230      16.234  44.054  33.980  1.00  0.00              
ATOM    762  CA  TYR   230      16.264  44.671  35.298  1.00  0.00              
ATOM    763  C   TYR   230      14.889  44.362  35.911  1.00  0.00              
ATOM    764  O   TYR   230      13.869  44.826  35.407  1.00  0.00              
ATOM    765  N   PRO   231      14.872  43.574  36.989  1.00  0.00              
ATOM    766  CA  PRO   231      13.636  43.164  37.665  1.00  0.00              
ATOM    767  C   PRO   231      12.626  44.269  37.999  1.00  0.00              
ATOM    768  O   PRO   231      11.422  44.022  37.902  1.00  0.00              
ATOM    769  N   ARG   232      13.082  45.465  38.400  1.00  0.00              
ATOM    770  CA  ARG   232      12.136  46.555  38.705  1.00  0.00              
ATOM    771  C   ARG   232      11.558  47.197  37.425  1.00  0.00              
ATOM    772  O   ARG   232      10.346  47.411  37.343  1.00  0.00              
ATOM    773  N   ASN   233      12.407  47.490  36.430  1.00  0.00              
ATOM    774  CA  ASN   233      11.947  48.081  35.157  1.00  0.00              
ATOM    775  C   ASN   233      11.245  47.042  34.325  1.00  0.00              
ATOM    776  O   ASN   233      10.176  47.287  33.768  1.00  0.00              
ATOM    777  N   GLU   234      11.893  45.884  34.237  1.00  0.00              
ATOM    778  CA  GLU   234      11.390  44.777  33.452  1.00  0.00              
ATOM    779  C   GLU   234      12.076  44.857  32.100  1.00  0.00              
ATOM    780  O   GLU   234      11.722  44.133  31.161  1.00  0.00              
ATOM    781  N   SER   235      13.071  45.742  32.009  1.00  0.00              
ATOM    782  CA  SER   235      13.799  45.939  30.760  1.00  0.00              
ATOM    783  C   SER   235      15.302  45.676  30.825  1.00  0.00              
ATOM    784  O   SER   235      15.916  45.697  31.895  1.00  0.00              
ATOM    785  N   GLY   236      15.878  45.445  29.649  1.00  0.00              
ATOM    786  CA  GLY   236      17.289  45.143  29.528  1.00  0.00              
ATOM    787  C   GLY   236      18.299  46.041  30.203  1.00  0.00              
ATOM    788  O   GLY   236      18.204  47.273  30.200  1.00  0.00              
ATOM    789  N   ASP   237      19.290  45.383  30.786  1.00  0.00              
ATOM    790  CA  ASP   237      20.376  46.057  31.461  1.00  0.00              
ATOM    791  C   ASP   237      21.508  46.093  30.438  1.00  0.00              
ATOM    792  O   ASP   237      21.728  45.139  29.684  1.00  0.00              
ATOM    793  N   VAL   238      22.215  47.208  30.398  1.00  0.00              
ATOM    794  CA  VAL   238      23.299  47.354  29.453  1.00  0.00              
ATOM    795  C   VAL   238      24.678  47.115  30.037  1.00  0.00              
ATOM    796  O   VAL   238      25.078  47.768  30.998  1.00  0.00              
ATOM    797  N   ALA   239      25.413  46.195  29.425  1.00  0.00              
ATOM    798  CA  ALA   239      26.773  45.895  29.836  1.00  0.00              
ATOM    799  C   ALA   239      26.818  45.031  31.075  1.00  0.00              
ATOM    800  O   ALA   239      27.698  45.171  31.927  1.00  0.00              
ATOM    801  N   ALA   240      25.843  44.141  31.174  1.00  0.00              
ATOM    802  CA  ALA   240      25.804  43.198  32.272  1.00  0.00              
ATOM    803  C   ALA   240      26.875  42.182  31.854  1.00  0.00              
ATOM    804  O   ALA   240      27.339  42.230  30.716  1.00  0.00              
ATOM    805  N   VAL   241      27.274  41.277  32.746  1.00  0.00              
ATOM    806  CA  VAL   241      28.279  40.277  32.395  1.00  0.00              
ATOM    807  C   VAL   241      27.768  38.859  32.462  1.00  0.00              
ATOM    808  O   VAL   241      27.183  38.450  33.456  1.00  0.00              
ATOM    809  N   ILE   242      28.009  38.094  31.415  1.00  0.00              
ATOM    810  CA  ILE   242      27.607  36.708  31.436  1.00  0.00              
ATOM    811  C   ILE   242      28.874  35.882  31.649  1.00  0.00              
ATOM    812  O   ILE   242      29.785  35.887  30.813  1.00  0.00              
ATOM    813  N   HIS   243      28.936  35.189  32.784  1.00  0.00              
ATOM    814  CA  HIS   243      30.092  34.366  33.110  1.00  0.00              
ATOM    815  C   HIS   243      29.716  32.894  33.051  1.00  0.00              
ATOM    816  O   HIS   243      28.627  32.517  33.484  1.00  0.00              
ATOM    817  N   PRO   244      30.603  32.059  32.513  1.00  0.00              
ATOM    818  CA  PRO   244      30.285  30.649  32.421  1.00  0.00              
ATOM    819  C   PRO   244      31.133  29.738  33.275  1.00  0.00              
ATOM    820  O   PRO   244      32.312  30.016  33.543  1.00  0.00              
ATOM    821  N   ASN   245      30.469  28.653  33.690  1.00  0.00              
ATOM    822  CA  ASN   245      31.000  27.576  34.509  1.00  0.00              
ATOM    823  C   ASN   245      32.488  27.755  34.712  1.00  0.00              
ATOM    824  O   ASN   245      32.917  28.651  35.438  1.00  0.00              
ATOM    825  N   LEU   246      33.282  26.923  34.055  1.00  0.00              
ATOM    826  CA  LEU   246      34.718  27.022  34.223  1.00  0.00              
ATOM    827  C   LEU   246      35.438  27.606  33.024  1.00  0.00              
ATOM    828  O   LEU   246      36.555  27.198  32.718  1.00  0.00              
ATOM    829  N   GLN   247      34.813  28.558  32.341  1.00  0.00              
ATOM    830  CA  GLN   247      35.468  29.171  31.191  1.00  0.00              
ATOM    831  C   GLN   247      35.786  30.604  31.539  1.00  0.00              
ATOM    832  O   GLN   247      34.877  31.407  31.795  1.00  0.00              
ATOM    833  N   ASP   248      37.075  30.925  31.542  1.00  0.00              
ATOM    834  CA  ASP   248      37.490  32.265  31.900  1.00  0.00              
ATOM    835  C   ASP   248      37.491  33.289  30.763  1.00  0.00              
ATOM    836  O   ASP   248      38.536  33.838  30.384  1.00  0.00              
ATOM    837  N   GLN   249      36.314  33.546  30.213  1.00  0.00              
ATOM    838  CA  GLN   249      36.194  34.537  29.164  1.00  0.00              
ATOM    839  C   GLN   249      34.754  34.994  29.205  1.00  0.00              
ATOM    840  O   GLN   249      33.890  34.458  28.520  1.00  0.00              
ATOM    841  N   ASP   250      34.472  35.967  30.066  1.00  0.00              
ATOM    842  CA  ASP   250      33.135  36.530  30.229  1.00  0.00              
ATOM    843  C   ASP   250      32.643  37.280  28.986  1.00  0.00              
ATOM    844  O   ASP   250      33.421  37.646  28.102  1.00  0.00              
ATOM    845  N   TRP   251      31.338  37.512  28.942  1.00  0.00              
ATOM    846  CA  TRP   251      30.695  38.202  27.835  1.00  0.00              
ATOM    847  C   TRP   251      29.787  39.307  28.381  1.00  0.00              
ATOM    848  O   TRP   251      29.210  39.158  29.454  1.00  0.00              
ATOM    849  N   LYS   252      29.675  40.415  27.653  1.00  0.00              
ATOM    850  CA  LYS   252      28.839  41.543  28.058  1.00  0.00              
ATOM    851  C   LYS   252      27.519  41.602  27.227  1.00  0.00              
ATOM    852  O   LYS   252      27.377  40.858  26.255  1.00  0.00              
ATOM    853  N   PRO   253      26.548  42.441  27.628  1.00  0.00              
ATOM    854  CA  PRO   253      25.244  42.577  26.917  1.00  0.00              
ATOM    855  C   PRO   253      25.107  43.888  26.151  1.00  0.00              
ATOM    856  O   PRO   253      25.722  44.892  26.526  1.00  0.00              
ATOM    857  N   LEU   254      24.286  43.912  25.102  1.00  0.00              
ATOM    858  CA  LEU   254      24.151  45.168  24.372  1.00  0.00              
ATOM    859  C   LEU   254      23.113  46.109  25.007  1.00  0.00              
ATOM    860  O   LEU   254      22.703  45.909  26.152  1.00  0.00              
ATOM    861  N   HIS   255      22.708  47.134  24.252  1.00  0.00              
ATOM    862  CA  HIS   255      21.732  48.156  24.673  1.00  0.00              
ATOM    863  C   HIS   255      20.352  47.631  25.134  1.00  0.00              
ATOM    864  O   HIS   255      19.712  48.242  26.004  1.00  0.00              
ATOM    865  N   PRO   256      19.900  46.511  24.562  1.00  0.00              
ATOM    866  CA  PRO   256      18.616  45.906  24.939  1.00  0.00              
ATOM    867  C   PRO   256      18.860  44.791  25.950  1.00  0.00              
ATOM    868  O   PRO   256      17.989  43.941  26.176  1.00  0.00              
ATOM    869  N   GLY   257      20.057  44.784  26.530  1.00  0.00              
ATOM    870  CA  GLY   257      20.409  43.769  27.501  1.00  0.00              
ATOM    871  C   GLY   257      20.504  42.384  26.890  1.00  0.00              
ATOM    872  O   GLY   257      20.568  41.396  27.611  1.00  0.00              
ATOM    873  N   ASP   258      20.499  42.297  25.565  1.00  0.00              
ATOM    874  CA  ASP   258      20.607  40.996  24.917  1.00  0.00              
ATOM    875  C   ASP   258      22.063  40.552  24.953  1.00  0.00              
ATOM    876  O   ASP   258      22.977  41.392  24.952  1.00  0.00              
ATOM    877  N   PRO   259      22.267  39.235  25.025  1.00  0.00              
ATOM    878  CA  PRO   259      23.609  38.651  25.054  1.00  0.00              
ATOM    879  C   PRO   259      23.624  37.374  24.228  1.00  0.00              
ATOM    880  O   PRO   259      22.581  36.740  24.011  1.00  0.00              
ATOM    881  N   VAL   260      24.811  36.998  23.770  1.00  0.00              
ATOM    882  CA  VAL   260      24.974  35.777  22.992  1.00  0.00              
ATOM    883  C   VAL   260      26.267  35.183  23.471  1.00  0.00              
ATOM    884  O   VAL   260      27.275  35.889  23.545  1.00  0.00              
ATOM    885  N   PHE   261      26.236  33.892  23.781  1.00  0.00              
ATOM    886  CA  PHE   261      27.408  33.193  24.279  1.00  0.00              
ATOM    887  C   PHE   261      27.568  31.856  23.564  1.00  0.00              
ATOM    888  O   PHE   261      26.726  30.971  23.670  1.00  0.00              
ATOM    889  N   VAL   262      28.663  31.710  22.837  1.00  0.00              
ATOM    890  CA  VAL   262      28.887  30.491  22.094  1.00  0.00              
ATOM    891  C   VAL   262      29.458  29.421  22.984  1.00  0.00              
ATOM    892  O   VAL   262      30.382  29.671  23.760  1.00  0.00              
ATOM    893  N   SER   263      28.888  28.227  22.865  1.00  0.00              
ATOM    894  CA  SER   263      29.307  27.095  23.666  1.00  0.00              
ATOM    895  C   SER   263      29.025  25.824  22.940  1.00  0.00              
ATOM    896  O   SER   263      28.270  25.783  21.967  1.00  0.00              
ATOM    897  N   LEU   264      29.614  24.773  23.474  1.00  0.00              
ATOM    898  CA  LEU   264      29.485  23.444  22.930  1.00  0.00              
ATOM    899  C   LEU   264      28.455  22.613  23.701  1.00  0.00              
ATOM    900  O   LEU   264      28.105  22.923  24.842  1.00  0.00              
ATOM    901  N   ASP   265      27.967  21.560  23.063  1.00  0.00              
ATOM    902  CA  ASP   265      27.015  20.675  23.696  1.00  0.00              
ATOM    903  C   ASP   265      27.637  20.239  25.032  1.00  0.00              
ATOM    904  O   ASP   265      28.744  19.691  25.058  1.00  0.00              
ATOM    905  N   GLY   266      26.923  20.502  26.128  1.00  0.00              
ATOM    906  CA  GLY   266      27.375  20.145  27.469  1.00  0.00              
ATOM    907  C   GLY   266      26.567  20.946  28.482  1.00  0.00              
ATOM    908  O   GLY   266      25.815  21.830  28.080  1.00  0.00              
ATOM    909  N   LYS   267      26.713  20.670  29.779  1.00  0.00              
ATOM    910  CA  LYS   267      25.958  21.410  30.805  1.00  0.00              
ATOM    911  C   LYS   267      26.795  22.499  31.502  1.00  0.00              
ATOM    912  O   LYS   267      27.880  22.208  31.983  1.00  0.00              
ATOM    913  N   VAL   268      26.301  23.735  31.581  1.00  0.00              
ATOM    914  CA  VAL   268      27.075  24.814  32.208  1.00  0.00              
ATOM    915  C   VAL   268      26.336  25.528  33.310  1.00  0.00              
ATOM    916  O   VAL   268      25.154  25.293  33.517  1.00  0.00              
ATOM    917  N   ILE   269      27.034  26.430  33.995  1.00  0.00              
ATOM    918  CA  ILE   269      26.417  27.202  35.064  1.00  0.00              
ATOM    919  C   ILE   269      26.690  28.681  34.881  1.00  0.00              
ATOM    920  O   ILE   269      27.647  29.247  35.412  1.00  0.00              
ATOM    921  N   PRO   270      25.802  29.308  34.134  1.00  0.00              
ATOM    922  CA  PRO   270      25.928  30.715  33.816  1.00  0.00              
ATOM    923  C   PRO   270      25.480  31.693  34.899  1.00  0.00              
ATOM    924  O   PRO   270      24.474  31.489  35.564  1.00  0.00              
END
