
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0289AL044_3-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL044_3-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R     232      I     224           -
LGA    N     233      M     225           -
LGA    -       -      E     226           -
LGA    -       -      K     227           -
LGA    -       -      V     228           -
LGA    -       -      D     229           -
LGA    -       -      Y     230           -
LGA    E     234      P     231          4.493
LGA    S     235      R     232          1.775
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    G     236      V     238          0.655
LGA    D     237      A     239          4.679
LGA    V     238      A     240          1.425
LGA    A     239      V     241          1.223
LGA    A     240      I     242          2.103
LGA    V     241      H     243          4.002
LGA    -       -      P     244           -
LGA    I     242      N     245          4.771
LGA    H     243      L     246          3.999
LGA    P     244      -       -           -
LGA    D     250      -       -           -
LGA    W     251      Q     247          3.429
LGA    K     252      D     248           -
LGA    P     253      Q     249           -
LGA    L     254      -       -           -
LGA    H     255      -       -           -
LGA    P     256      -       -           -
LGA    G     257      -       -           -
LGA    P     259      -       -           -
LGA    V     260      -       -           -
LGA    F     261      -       -           -
LGA    V     262      -       -           -
LGA    S     263      -       -           -
LGA    L     264      -       -           -
LGA    D     265      D     250           #
LGA    -       -      W     251           -
LGA    -       -      K     252           -
LGA    G     266      P     253          2.804
LGA    K     267      L     254          0.475
LGA    V     268      H     255          4.267
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    I     269      D     258          4.791
LGA    P     270      P     259          2.145
LGA    -       -      V     260           -
LGA    L     271      F     261          1.611
LGA    G     272      V     262          0.730
LGA    G     273      S     263          1.417
LGA    D     274      L     264          1.598
LGA    C     275      D     265          0.391
LGA    T     276      G     266          3.055
LGA    V     277      K     267          2.756
LGA    Y     278      V     268          1.474
LGA    P     279      I     269          2.096
LGA    V     280      P     270          1.858
LGA    F     281      L     271          1.855
LGA    V     282      G     272          4.590
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    -       -      V     282           -
LGA    -       -      N     283           -
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)   45   74    5.0     28    2.89     3.57     25.355     0.938

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.891468 * X  +  -0.202906 * Y  +   0.405109 * Z  +  76.569939
  Y_new =   0.443955 * X  +  -0.212614 * Y  +   0.870459 * Z  +  14.016497
  Z_new =  -0.090490 * X  +   0.955837 * Y  +   0.279619 * Z  +  -9.477050 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.286199   -1.855394  [ DEG:    73.6938   -106.3062 ]
  Theta =   0.090614    3.050979  [ DEG:     5.1918    174.8082 ]
  Phi   =   2.679543   -0.462050  [ DEG:   153.5265    -26.4735 ]
 
# 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_3-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL044_3-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   74   5.0   28   2.89    3.57  25.355
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL044_3-D2
REMARK Aligment from pdb entry: 1uwy_A
ATOM    785  N   ARG   232      13.815  37.724  40.857  1.00  0.00              
ATOM    786  CA  ARG   232      13.618  37.239  39.503  1.00  0.00              
ATOM    787  C   ARG   232      12.915  38.270  38.652  1.00  0.00              
ATOM    788  O   ARG   232      11.879  37.995  38.014  1.00  0.00              
ATOM    789  N   ASN   233      13.463  39.475  38.642  1.00  0.00              
ATOM    790  CA  ASN   233      12.856  40.525  37.846  1.00  0.00              
ATOM    791  C   ASN   233      13.846  41.079  36.852  1.00  0.00              
ATOM    792  O   ASN   233      14.854  41.646  37.223  1.00  0.00              
ATOM    793  N   GLU   234      13.582  40.895  35.560  1.00  0.00              
ATOM    794  CA  GLU   234      14.527  41.421  34.578  1.00  0.00              
ATOM    795  C   GLU   234      14.817  42.894  34.824  1.00  0.00              
ATOM    796  O   GLU   234      13.896  43.717  34.781  1.00  0.00              
ATOM    797  N   SER   235      16.082  43.218  35.096  1.00  0.00              
ATOM    798  CA  SER   235      16.463  44.597  35.308  1.00  0.00              
ATOM    799  C   SER   235      16.860  45.057  33.932  1.00  0.00              
ATOM    800  O   SER   235      17.776  44.521  33.327  1.00  0.00              
ATOM    801  N   GLY   236      16.163  46.049  33.400  1.00  0.00              
ATOM    802  CA  GLY   236      16.518  46.538  32.071  1.00  0.00              
ATOM    803  C   GLY   236      17.617  47.592  32.223  1.00  0.00              
ATOM    804  O   GLY   236      18.160  47.782  33.300  1.00  0.00              
ATOM    805  N   ASP   237      17.949  48.266  31.139  1.00  0.00              
ATOM    806  CA  ASP   237      18.945  49.310  31.191  1.00  0.00              
ATOM    807  C   ASP   237      20.255  49.061  31.958  1.00  0.00              
ATOM    808  O   ASP   237      21.005  49.984  32.234  1.00  0.00              
ATOM    809  N   VAL   238      20.535  47.825  32.310  1.00  0.00              
ATOM    810  CA  VAL   238      21.761  47.536  33.033  1.00  0.00              
ATOM    811  C   VAL   238      22.874  47.397  32.010  1.00  0.00              
ATOM    812  O   VAL   238      22.594  47.190  30.831  1.00  0.00              
ATOM    813  N   ALA   239      24.128  47.513  32.449  1.00  0.00              
ATOM    814  CA  ALA   239      25.265  47.359  31.539  1.00  0.00              
ATOM    815  C   ALA   239      25.794  45.936  31.583  1.00  0.00              
ATOM    816  O   ALA   239      26.111  45.410  32.645  1.00  0.00              
ATOM    817  N   ALA   240      25.886  45.299  30.430  1.00  0.00              
ATOM    818  CA  ALA   240      26.451  43.965  30.406  1.00  0.00              
ATOM    819  C   ALA   240      27.471  43.869  29.284  1.00  0.00              
ATOM    820  O   ALA   240      27.100  43.815  28.121  1.00  0.00              
ATOM    821  N   VAL   241      28.752  43.908  29.612  1.00  0.00              
ATOM    822  CA  VAL   241      29.735  43.736  28.572  1.00  0.00              
ATOM    823  C   VAL   241      30.919  42.994  29.082  1.00  0.00              
ATOM    824  O   VAL   241      31.080  42.866  30.284  1.00  0.00              
ATOM    825  N   ILE   242      31.713  42.456  28.161  1.00  0.00              
ATOM    826  CA  ILE   242      32.880  41.674  28.519  1.00  0.00              
ATOM    827  C   ILE   242      33.917  42.532  29.215  1.00  0.00              
ATOM    828  O   ILE   242      34.015  43.724  28.949  1.00  0.00              
ATOM    829  N   HIS   243      34.701  41.923  30.101  1.00  0.00              
ATOM    830  CA  HIS   243      35.694  42.655  30.891  1.00  0.00              
ATOM    831  C   HIS   243      36.484  43.739  30.170  1.00  0.00              
ATOM    832  O   HIS   243      36.436  44.899  30.575  1.00  0.00              
ATOM    833  N   PRO   244      37.195  43.371  29.106  1.00  0.00              
ATOM    834  CA  PRO   244      38.041  44.319  28.353  1.00  0.00              
ATOM    835  C   PRO   244      37.472  44.928  27.044  1.00  0.00              
ATOM    836  O   PRO   244      38.227  45.481  26.226  1.00  0.00              
ATOM    837  N   ASP   250      36.153  44.829  26.862  1.00  0.00              
ATOM    838  CA  ASP   250      35.469  45.334  25.672  1.00  0.00              
ATOM    839  C   ASP   250      34.461  46.422  25.988  1.00  0.00              
ATOM    840  O   ASP   250      33.299  46.343  25.566  1.00  0.00              
ATOM    841  N   TRP   251      34.885  47.436  26.731  1.00  0.00              
ATOM    842  CA  TRP   251      33.965  48.516  27.056  1.00  0.00              
ATOM    843  C   TRP   251      33.789  49.379  25.807  1.00  0.00              
ATOM    844  O   TRP   251      34.751  49.720  25.114  1.00  0.00              
ATOM    845  N   LYS   252      29.844  54.170  24.096  1.00  0.00              
ATOM    846  CA  LYS   252      28.537  54.296  24.750  1.00  0.00              
ATOM    847  C   LYS   252      28.371  52.838  25.091  1.00  0.00              
ATOM    848  O   LYS   252      28.251  52.008  24.175  1.00  0.00              
ATOM    849  N   PRO   253      28.408  52.507  26.406  1.00  0.00              
ATOM    850  CA  PRO   253      28.295  51.173  27.019  1.00  0.00              
ATOM    851  C   PRO   253      27.011  50.427  26.712  1.00  0.00              
ATOM    852  O   PRO   253      25.929  51.009  26.768  1.00  0.00              
ATOM    853  N   LEU   254      27.154  49.135  26.393  1.00  0.00              
ATOM    854  CA  LEU   254      26.037  48.241  26.043  1.00  0.00              
ATOM    855  C   LEU   254      25.168  47.835  27.225  1.00  0.00              
ATOM    856  O   LEU   254      25.611  47.183  28.166  1.00  0.00              
ATOM    857  N   HIS   255      23.909  48.220  27.167  1.00  0.00              
ATOM    858  CA  HIS   255      23.000  47.907  28.249  1.00  0.00              
ATOM    859  C   HIS   255      21.967  46.850  27.843  1.00  0.00              
ATOM    860  O   HIS   255      21.823  46.536  26.656  1.00  0.00              
ATOM    861  N   PRO   256      21.257  46.299  28.824  1.00  0.00              
ATOM    862  CA  PRO   256      20.231  45.323  28.522  1.00  0.00              
ATOM    863  C   PRO   256      19.001  46.015  27.899  1.00  0.00              
ATOM    864  O   PRO   256      18.872  47.236  27.922  1.00  0.00              
ATOM    865  N   GLY   257      18.101  45.238  27.319  1.00  0.00              
ATOM    866  CA  GLY   257      16.910  45.830  26.735  1.00  0.00              
ATOM    867  C   GLY   257      15.733  45.888  27.740  1.00  0.00              
ATOM    868  O   GLY   257      15.876  45.569  28.928  1.00  0.00              
ATOM    869  N   PRO   259      14.566  46.312  27.266  1.00  0.00              
ATOM    870  CA  PRO   259      13.431  46.409  28.159  1.00  0.00              
ATOM    871  C   PRO   259      13.140  45.056  28.780  1.00  0.00              
ATOM    872  O   PRO   259      12.591  44.978  29.864  1.00  0.00              
ATOM    873  N   VAL   260      13.518  43.984  28.109  1.00  0.00              
ATOM    874  CA  VAL   260      13.267  42.667  28.672  1.00  0.00              
ATOM    875  C   VAL   260      14.459  42.203  29.478  1.00  0.00              
ATOM    876  O   VAL   260      14.575  41.040  29.837  1.00  0.00              
ATOM    877  N   PHE   261      15.350  43.133  29.772  1.00  0.00              
ATOM    878  CA  PHE   261      16.507  42.798  30.581  1.00  0.00              
ATOM    879  C   PHE   261      17.456  41.791  29.985  1.00  0.00              
ATOM    880  O   PHE   261      18.418  41.363  30.636  1.00  0.00              
ATOM    881  N   VAL   262      17.189  41.404  28.749  1.00  0.00              
ATOM    882  CA  VAL   262      18.073  40.453  28.091  1.00  0.00              
ATOM    883  C   VAL   262      19.290  41.185  27.515  1.00  0.00              
ATOM    884  O   VAL   262      19.272  42.417  27.335  1.00  0.00              
ATOM    885  N   SER   263      20.347  40.418  27.246  1.00  0.00              
ATOM    886  CA  SER   263      21.570  40.979  26.699  1.00  0.00              
ATOM    887  C   SER   263      22.118  40.086  25.591  1.00  0.00              
ATOM    888  O   SER   263      22.007  38.865  25.659  1.00  0.00              
ATOM    889  N   LEU   264      22.672  40.691  24.552  1.00  0.00              
ATOM    890  CA  LEU   264      23.261  39.907  23.475  1.00  0.00              
ATOM    891  C   LEU   264      24.673  40.417  23.203  1.00  0.00              
ATOM    892  O   LEU   264      24.895  41.619  23.053  1.00  0.00              
ATOM    893  N   ASP   265      25.630  39.510  23.128  1.00  0.00              
ATOM    894  CA  ASP   265      26.996  39.916  22.854  1.00  0.00              
ATOM    895  C   ASP   265      27.685  39.022  21.808  1.00  0.00              
ATOM    896  O   ASP   265      28.123  37.905  22.150  1.00  0.00              
ATOM    897  N   GLY   266      37.106  31.962  26.156  1.00  0.00              
ATOM    898  CA  GLY   266      36.618  32.135  27.519  1.00  0.00              
ATOM    899  C   GLY   266      36.554  33.605  27.915  1.00  0.00              
ATOM    900  O   GLY   266      37.544  34.341  27.847  1.00  0.00              
ATOM    901  N   LYS   267      35.374  34.029  28.342  1.00  0.00              
ATOM    902  CA  LYS   267      35.183  35.411  28.746  1.00  0.00              
ATOM    903  C   LYS   267      34.760  35.621  30.201  1.00  0.00              
ATOM    904  O   LYS   267      34.548  34.675  30.965  1.00  0.00              
ATOM    905  N   VAL   268      34.642  36.891  30.560  1.00  0.00              
ATOM    906  CA  VAL   268      34.262  37.319  31.889  1.00  0.00              
ATOM    907  C   VAL   268      33.387  38.509  31.605  1.00  0.00              
ATOM    908  O   VAL   268      33.836  39.485  30.999  1.00  0.00              
ATOM    909  N   ILE   269      32.136  38.444  32.022  1.00  0.00              
ATOM    910  CA  ILE   269      31.252  39.560  31.751  1.00  0.00              
ATOM    911  C   ILE   269      31.088  40.366  33.034  1.00  0.00              
ATOM    912  O   ILE   269      31.014  39.795  34.106  1.00  0.00              
ATOM    913  N   PRO   270      31.090  41.690  32.932  1.00  0.00              
ATOM    914  CA  PRO   270      30.929  42.541  34.106  1.00  0.00              
ATOM    915  C   PRO   270      29.538  43.124  34.073  1.00  0.00              
ATOM    916  O   PRO   270      29.241  44.035  33.271  1.00  0.00              
ATOM    917  N   LEU   271      28.681  42.585  34.934  1.00  0.00              
ATOM    918  CA  LEU   271      27.308  43.055  35.022  1.00  0.00              
ATOM    919  C   LEU   271      27.297  44.194  36.025  1.00  0.00              
ATOM    920  O   LEU   271      27.455  44.009  37.230  1.00  0.00              
ATOM    921  N   GLY   272      27.123  45.394  35.506  1.00  0.00              
ATOM    922  CA  GLY   272      27.134  46.563  36.347  1.00  0.00              
ATOM    923  C   GLY   272      25.779  47.233  36.328  1.00  0.00              
ATOM    924  O   GLY   272      25.411  47.902  35.352  1.00  0.00              
ATOM    925  N   GLY   273      25.037  47.006  37.417  1.00  0.00              
ATOM    926  CA  GLY   273      23.707  47.578  37.594  1.00  0.00              
ATOM    927  C   GLY   273      23.898  48.890  38.315  1.00  0.00              
ATOM    928  O   GLY   273      24.591  48.953  39.334  1.00  0.00              
ATOM    929  N   ASP   274      23.274  49.959  37.801  1.00  0.00              
ATOM    930  CA  ASP   274      23.403  51.280  38.406  1.00  0.00              
ATOM    931  C   ASP   274      23.553  51.321  39.911  1.00  0.00              
ATOM    932  O   ASP   274      22.782  50.715  40.659  1.00  0.00              
ATOM    933  N   CYS   275      24.596  52.031  40.327  1.00  0.00              
ATOM    934  CA  CYS   275      24.881  52.198  41.729  1.00  0.00              
ATOM    935  C   CYS   275      25.233  50.888  42.369  1.00  0.00              
ATOM    936  O   CYS   275      24.767  50.584  43.467  1.00  0.00              
ATOM    937  N   THR   276      26.054  50.105  41.684  1.00  0.00              
ATOM    938  CA  THR   276      26.468  48.823  42.227  1.00  0.00              
ATOM    939  C   THR   276      27.862  48.414  41.793  1.00  0.00              
ATOM    940  O   THR   276      28.405  48.932  40.809  1.00  0.00              
ATOM    941  N   VAL   277      28.447  47.495  42.552  1.00  0.00              
ATOM    942  CA  VAL   277      29.756  46.992  42.215  1.00  0.00              
ATOM    943  C   VAL   277      29.499  46.125  41.007  1.00  0.00              
ATOM    944  O   VAL   277      28.511  45.386  40.952  1.00  0.00              
ATOM    945  N   TYR   278      30.355  46.240  39.990  1.00  0.00              
ATOM    946  CA  TYR   278      30.112  45.399  38.823  1.00  0.00              
ATOM    947  C   TYR   278      30.104  43.930  39.241  1.00  0.00              
ATOM    948  O   TYR   278      30.944  43.479  40.023  1.00  0.00              
ATOM    949  N   PRO   279      29.134  43.190  38.734  1.00  0.00              
ATOM    950  CA  PRO   279      29.034  41.791  39.061  1.00  0.00              
ATOM    951  C   PRO   279      29.765  40.936  38.051  1.00  0.00              
ATOM    952  O   PRO   279      29.498  41.008  36.858  1.00  0.00              
ATOM    953  N   VAL   280      30.698  40.131  38.534  1.00  0.00              
ATOM    954  CA  VAL   280      31.418  39.225  37.661  1.00  0.00              
ATOM    955  C   VAL   280      30.527  38.000  37.415  1.00  0.00              
ATOM    956  O   VAL   280      29.763  37.570  38.290  1.00  0.00              
ATOM    957  N   PHE   281      30.639  37.449  36.213  1.00  0.00              
ATOM    958  CA  PHE   281      29.919  36.251  35.799  1.00  0.00              
ATOM    959  C   PHE   281      30.720  35.749  34.603  1.00  0.00              
ATOM    960  O   PHE   281      30.798  36.418  33.564  1.00  0.00              
ATOM    961  N   VAL   282      31.353  34.589  34.782  1.00  0.00              
ATOM    962  CA  VAL   282      32.209  34.005  33.753  1.00  0.00              
ATOM    963  C   VAL   282      31.516  33.042  32.794  1.00  0.00              
ATOM    964  O   VAL   282      30.601  32.296  33.178  1.00  0.00              
END
