
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL044_4-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    -       -      E     226           -
LGA    -       -      K     227           -
LGA    -       -      V     228           -
LGA    -       -      D     229           -
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          5.207
LGA    N     233      V     238          1.494
LGA    E     234      A     239           #
LGA    S     235      A     240          2.929
LGA    G     236      V     241          4.086
LGA    D     237      I     242           #
LGA    V     238      H     243          2.036
LGA    A     239      P     244          2.780
LGA    A     240      N     245          2.485
LGA    V     241      -       -           -
LGA    I     242      -       -           -
LGA    H     243      -       -           -
LGA    P     244      -       -           -
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    P     259      -       -           -
LGA    V     260      -       -           -
LGA    F     261      -       -           -
LGA    V     262      -       -           -
LGA    S     263      L     246           #
LGA    -       -      Q     247           -
LGA    L     264      D     248          2.291
LGA    D     265      Q     249          2.342
LGA    -       -      D     250           -
LGA    G     266      W     251           #
LGA    K     267      K     252          4.172
LGA    V     268      P     253          2.679
LGA    I     269      L     254          1.806
LGA    -       -      H     255           -
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    P     270      D     258          3.007
LGA    L     271      P     259          3.044
LGA    G     272      V     260          3.861
LGA    -       -      F     261           -
LGA    G     273      V     262          2.602
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    D     274      G     266          2.255
LGA    C     275      K     267          1.191
LGA    T     276      V     268          3.385
LGA    V     277      I     269          2.634
LGA    Y     278      P     270          1.060
LGA    P     279      L     271          1.143
LGA    V     280      G     272          5.139
LGA    -       -      G     273           -
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    F     281      T     276          4.856
LGA    V     282      V     277          1.011
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     25    3.03     8.00     20.460     0.799

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.079787 * X  +  -0.866630 * Y  +   0.492531 * Z  +  70.962112
  Y_new =  -0.967469 * X  +   0.051679 * Y  +   0.247656 * Z  +  60.345787
  Z_new =  -0.240079 * X  +  -0.496268 * Y  +  -0.834314 * Z  +  46.823658 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.604989    0.536604  [ DEG:  -149.2549     30.7451 ]
  Theta =   0.242447    2.899145  [ DEG:    13.8912    166.1088 ]
  Phi   =  -1.488512    1.653080  [ DEG:   -85.2855     94.7145 ]
 
# 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_4-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL044_4-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   25   3.03    8.00  20.460
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL044_4-D2
REMARK Aligment from pdb entry: 1h8l_A
ATOM    785  N   ARG   232      15.770  43.852  33.125  1.00  0.00              
ATOM    786  CA  ARG   232      15.787  43.196  31.831  1.00  0.00              
ATOM    787  C   ARG   232      16.378  44.171  30.823  1.00  0.00              
ATOM    788  O   ARG   232      16.439  43.887  29.622  1.00  0.00              
ATOM    789  N   ASN   233      16.819  45.327  31.323  1.00  0.00              
ATOM    790  CA  ASN   233      17.394  46.370  30.477  1.00  0.00              
ATOM    791  C   ASN   233      18.896  46.605  30.656  1.00  0.00              
ATOM    792  O   ASN   233      19.441  46.491  31.760  1.00  0.00              
ATOM    793  N   GLU   234      19.547  46.956  29.547  1.00  0.00              
ATOM    794  CA  GLU   234      20.976  47.193  29.534  1.00  0.00              
ATOM    795  C   GLU   234      21.541  48.003  30.675  1.00  0.00              
ATOM    796  O   GLU   234      20.916  48.939  31.176  1.00  0.00              
ATOM    797  N   SER   235      22.747  47.625  31.083  1.00  0.00              
ATOM    798  CA  SER   235      23.453  48.300  32.153  1.00  0.00              
ATOM    799  C   SER   235      24.472  49.209  31.479  1.00  0.00              
ATOM    800  O   SER   235      25.245  48.772  30.629  1.00  0.00              
ATOM    801  N   GLY   236      24.454  50.482  31.848  1.00  0.00              
ATOM    802  CA  GLY   236      25.379  51.453  31.286  1.00  0.00              
ATOM    803  C   GLY   236      26.715  51.441  32.025  1.00  0.00              
ATOM    804  O   GLY   236      26.757  51.341  33.251  1.00  0.00              
ATOM    805  N   ASP   237      27.800  51.545  31.271  1.00  0.00              
ATOM    806  CA  ASP   237      29.145  51.584  31.836  1.00  0.00              
ATOM    807  C   ASP   237      29.575  50.300  32.533  1.00  0.00              
ATOM    808  O   ASP   237      30.339  50.334  33.497  1.00  0.00              
ATOM    809  N   VAL   238      29.078  49.167  32.048  1.00  0.00              
ATOM    810  CA  VAL   238      29.466  47.873  32.599  1.00  0.00              
ATOM    811  C   VAL   238      30.826  47.571  31.963  1.00  0.00              
ATOM    812  O   VAL   238      31.221  48.247  31.018  1.00  0.00              
ATOM    813  N   ALA   239      31.541  46.565  32.461  1.00  0.00              
ATOM    814  CA  ALA   239      32.852  46.236  31.906  1.00  0.00              
ATOM    815  C   ALA   239      32.950  44.860  31.255  1.00  0.00              
ATOM    816  O   ALA   239      32.405  43.877  31.753  1.00  0.00              
ATOM    817  N   ALA   240      33.657  44.802  30.134  1.00  0.00              
ATOM    818  CA  ALA   240      33.858  43.558  29.416  1.00  0.00              
ATOM    819  C   ALA   240      35.354  43.266  29.404  1.00  0.00              
ATOM    820  O   ALA   240      36.133  43.955  28.732  1.00  0.00              
ATOM    821  N   VAL   241      35.749  42.250  30.168  1.00  0.00              
ATOM    822  CA  VAL   241      37.146  41.852  30.276  1.00  0.00              
ATOM    823  C   VAL   241      37.365  40.558  29.514  1.00  0.00              
ATOM    824  O   VAL   241      36.509  39.674  29.530  1.00  0.00              
ATOM    825  N   ILE   242      38.510  40.441  28.847  1.00  0.00              
ATOM    826  CA  ILE   242      38.793  39.236  28.084  1.00  0.00              
ATOM    827  C   ILE   242      39.996  38.445  28.570  1.00  0.00              
ATOM    828  O   ILE   242      40.990  39.005  29.043  1.00  0.00              
ATOM    829  N   HIS   243      39.862  37.127  28.434  1.00  0.00              
ATOM    830  CA  HIS   243      40.864  36.140  28.801  1.00  0.00              
ATOM    831  C   HIS   243      42.168  36.760  29.277  1.00  0.00              
ATOM    832  O   HIS   243      42.285  37.186  30.427  1.00  0.00              
ATOM    833  N   PRO   244      43.148  36.824  28.390  1.00  0.00              
ATOM    834  CA  PRO   244      44.438  37.373  28.762  1.00  0.00              
ATOM    835  C   PRO   244      44.821  38.612  27.969  1.00  0.00              
ATOM    836  O   PRO   244      45.892  38.673  27.364  1.00  0.00              
ATOM    837  N   ASP   250      43.934  39.597  27.969  1.00  0.00              
ATOM    838  CA  ASP   250      44.182  40.853  27.278  1.00  0.00              
ATOM    839  C   ASP   250      43.858  41.968  28.264  1.00  0.00              
ATOM    840  O   ASP   250      42.689  42.274  28.525  1.00  0.00              
ATOM    841  N   TRP   251      44.908  42.557  28.823  1.00  0.00              
ATOM    842  CA  TRP   251      44.755  43.617  29.807  1.00  0.00              
ATOM    843  C   TRP   251      44.253  44.944  29.227  1.00  0.00              
ATOM    844  O   TRP   251      44.930  45.975  29.309  1.00  0.00              
ATOM    845  N   LYS   252      43.058  44.914  28.652  1.00  0.00              
ATOM    846  CA  LYS   252      42.449  46.101  28.060  1.00  0.00              
ATOM    847  C   LYS   252      40.942  45.888  28.048  1.00  0.00              
ATOM    848  O   LYS   252      40.384  45.343  27.100  1.00  0.00              
ATOM    849  N   PRO   253      40.266  46.301  29.122  1.00  0.00              
ATOM    850  CA  PRO   253      38.813  46.156  29.226  1.00  0.00              
ATOM    851  C   PRO   253      38.025  47.175  28.389  1.00  0.00              
ATOM    852  O   PRO   253      38.511  48.270  28.077  1.00  0.00              
ATOM    853  N   LEU   254      36.798  46.795  28.038  1.00  0.00              
ATOM    854  CA  LEU   254      35.896  47.628  27.248  1.00  0.00              
ATOM    855  C   LEU   254      34.632  47.925  28.069  1.00  0.00              
ATOM    856  O   LEU   254      34.229  47.123  28.903  1.00  0.00              
ATOM    857  N   HIS   255      34.015  49.079  27.834  1.00  0.00              
ATOM    858  CA  HIS   255      32.818  49.477  28.569  1.00  0.00              
ATOM    859  C   HIS   255      31.548  49.447  27.685  1.00  0.00              
ATOM    860  O   HIS   255      31.649  49.432  26.459  1.00  0.00              
ATOM    861  N   PRO   256      30.364  49.406  28.309  1.00  0.00              
ATOM    862  CA  PRO   256      29.071  49.360  27.587  1.00  0.00              
ATOM    863  C   PRO   256      28.443  50.747  27.423  1.00  0.00              
ATOM    864  O   PRO   256      28.724  51.657  28.212  1.00  0.00              
ATOM    865  N   GLY   257      27.582  50.920  26.420  1.00  0.00              
ATOM    866  CA  GLY   257      26.957  52.229  26.246  1.00  0.00              
ATOM    867  C   GLY   257      25.605  52.329  26.982  1.00  0.00              
ATOM    868  O   GLY   257      25.270  51.484  27.816  1.00  0.00              
ATOM    869  N   PRO   259      24.844  53.376  26.671  1.00  0.00              
ATOM    870  CA  PRO   259      23.550  53.638  27.292  1.00  0.00              
ATOM    871  C   PRO   259      22.526  52.489  27.248  1.00  0.00              
ATOM    872  O   PRO   259      21.731  52.333  28.179  1.00  0.00              
ATOM    873  N   VAL   260      22.539  51.683  26.190  1.00  0.00              
ATOM    874  CA  VAL   260      21.604  50.559  26.082  1.00  0.00              
ATOM    875  C   VAL   260      22.239  49.255  26.553  1.00  0.00              
ATOM    876  O   VAL   260      21.752  48.169  26.222  1.00  0.00              
ATOM    877  N   PHE   261      23.329  49.372  27.314  1.00  0.00              
ATOM    878  CA  PHE   261      24.036  48.208  27.825  1.00  0.00              
ATOM    879  C   PHE   261      24.748  47.407  26.750  1.00  0.00              
ATOM    880  O   PHE   261      25.168  46.275  26.982  1.00  0.00              
ATOM    881  N   VAL   262      24.892  47.992  25.567  1.00  0.00              
ATOM    882  CA  VAL   262      25.546  47.306  24.460  1.00  0.00              
ATOM    883  C   VAL   262      27.055  47.552  24.417  1.00  0.00              
ATOM    884  O   VAL   262      27.539  48.592  24.877  1.00  0.00              
ATOM    885  N   SER   263      27.789  46.579  23.872  1.00  0.00              
ATOM    886  CA  SER   263      29.241  46.664  23.772  1.00  0.00              
ATOM    887  C   SER   263      29.725  45.968  22.501  1.00  0.00              
ATOM    888  O   SER   263      28.998  45.176  21.889  1.00  0.00              
ATOM    889  N   LEU   264      30.964  46.276  22.123  1.00  0.00              
ATOM    890  CA  LEU   264      31.612  45.689  20.951  1.00  0.00              
ATOM    891  C   LEU   264      33.057  45.479  21.368  1.00  0.00              
ATOM    892  O   LEU   264      33.705  46.391  21.890  1.00  0.00              
ATOM    893  N   ASP   265      33.555  44.275  21.141  1.00  0.00              
ATOM    894  CA  ASP   265      34.910  43.935  21.521  1.00  0.00              
ATOM    895  C   ASP   265      35.592  43.237  20.353  1.00  0.00              
ATOM    896  O   ASP   265      35.276  42.098  20.021  1.00  0.00              
ATOM    897  N   GLY   266      39.474  31.401  21.061  1.00  0.00              
ATOM    898  CA  GLY   266      38.507  31.099  22.116  1.00  0.00              
ATOM    899  C   GLY   266      38.823  31.945  23.349  1.00  0.00              
ATOM    900  O   GLY   266      39.967  31.990  23.787  1.00  0.00              
ATOM    901  N   LYS   267      37.817  32.604  23.918  1.00  0.00              
ATOM    902  CA  LYS   267      38.056  33.476  25.069  1.00  0.00              
ATOM    903  C   LYS   267      37.152  33.273  26.281  1.00  0.00              
ATOM    904  O   LYS   267      36.077  32.688  26.182  1.00  0.00              
ATOM    905  N   VAL   268      37.603  33.779  27.426  1.00  0.00              
ATOM    906  CA  VAL   268      36.830  33.708  28.660  1.00  0.00              
ATOM    907  C   VAL   268      36.447  35.147  29.006  1.00  0.00              
ATOM    908  O   VAL   268      37.151  35.842  29.739  1.00  0.00              
ATOM    909  N   ILE   269      35.318  35.582  28.461  1.00  0.00              
ATOM    910  CA  ILE   269      34.822  36.933  28.658  1.00  0.00              
ATOM    911  C   ILE   269      34.030  37.111  29.952  1.00  0.00              
ATOM    912  O   ILE   269      33.166  36.297  30.274  1.00  0.00              
ATOM    913  N   PRO   270      34.319  38.186  30.683  1.00  0.00              
ATOM    914  CA  PRO   270      33.635  38.463  31.942  1.00  0.00              
ATOM    915  C   PRO   270      32.970  39.828  32.016  1.00  0.00              
ATOM    916  O   PRO   270      33.642  40.858  32.014  1.00  0.00              
ATOM    917  N   LEU   271      31.646  39.826  32.100  1.00  0.00              
ATOM    918  CA  LEU   271      30.899  41.062  32.215  1.00  0.00              
ATOM    919  C   LEU   271      30.776  41.335  33.702  1.00  0.00              
ATOM    920  O   LEU   271      30.524  40.420  34.476  1.00  0.00              
ATOM    921  N   GLY   272      30.973  42.586  34.101  1.00  0.00              
ATOM    922  CA  GLY   272      30.876  42.976  35.505  1.00  0.00              
ATOM    923  C   GLY   272      30.366  44.407  35.565  1.00  0.00              
ATOM    924  O   GLY   272      30.383  45.115  34.562  1.00  0.00              
ATOM    925  N   GLY   273      29.917  44.837  36.739  1.00  0.00              
ATOM    926  CA  GLY   273      29.405  46.195  36.895  1.00  0.00              
ATOM    927  C   GLY   273      29.210  46.549  38.359  1.00  0.00              
ATOM    928  O   GLY   273      29.001  45.670  39.196  1.00  0.00              
ATOM    929  N   ASP   274      29.281  47.843  38.661  1.00  0.00              
ATOM    930  CA  ASP   274      29.103  48.323  40.023  1.00  0.00              
ATOM    931  C   ASP   274      27.673  48.021  40.464  1.00  0.00              
ATOM    932  O   ASP   274      26.710  48.466  39.832  1.00  0.00              
ATOM    933  N   CYS   275      27.541  47.244  41.538  1.00  0.00              
ATOM    934  CA  CYS   275      26.227  46.898  42.049  1.00  0.00              
ATOM    935  C   CYS   275      25.667  45.581  41.543  1.00  0.00              
ATOM    936  O   CYS   275      24.540  45.223  41.888  1.00  0.00              
ATOM    937  N   THR   276      26.437  44.863  40.728  1.00  0.00              
ATOM    938  CA  THR   276      25.990  43.579  40.188  1.00  0.00              
ATOM    939  C   THR   276      27.016  42.479  40.408  1.00  0.00              
ATOM    940  O   THR   276      28.159  42.740  40.781  1.00  0.00              
ATOM    941  N   VAL   277      26.595  41.243  40.165  1.00  0.00              
ATOM    942  CA  VAL   277      27.467  40.095  40.324  1.00  0.00              
ATOM    943  C   VAL   277      27.942  39.648  38.949  1.00  0.00              
ATOM    944  O   VAL   277      27.133  39.348  38.066  1.00  0.00              
ATOM    945  N   TYR   278      29.270  39.601  38.754  1.00  0.00              
ATOM    946  CA  TYR   278      29.932  39.209  37.503  1.00  0.00              
ATOM    947  C   TYR   278      29.582  37.850  36.915  1.00  0.00              
ATOM    948  O   TYR   278      29.361  36.884  37.634  1.00  0.00              
ATOM    949  N   PRO   279      29.536  37.797  35.589  1.00  0.00              
ATOM    950  CA  PRO   279      29.252  36.565  34.864  1.00  0.00              
ATOM    951  C   PRO   279      30.389  36.316  33.885  1.00  0.00              
ATOM    952  O   PRO   279      30.927  37.250  33.290  1.00  0.00              
ATOM    953  N   VAL   280      30.753  35.057  33.717  1.00  0.00              
ATOM    954  CA  VAL   280      31.825  34.716  32.805  1.00  0.00              
ATOM    955  C   VAL   280      31.339  33.668  31.828  1.00  0.00              
ATOM    956  O   VAL   280      30.659  32.718  32.211  1.00  0.00              
ATOM    957  N   PHE   281      31.666  33.853  30.556  1.00  0.00              
ATOM    958  CA  PHE   281      31.259  32.911  29.527  1.00  0.00              
ATOM    959  C   PHE   281      32.438  32.599  28.632  1.00  0.00              
ATOM    960  O   PHE   281      33.290  33.449  28.396  1.00  0.00              
ATOM    961  N   VAL   282      32.485  31.370  28.138  1.00  0.00              
ATOM    962  CA  VAL   282      33.548  30.955  27.240  1.00  0.00              
ATOM    963  C   VAL   282      33.028  31.180  25.831  1.00  0.00              
ATOM    964  O   VAL   282      32.199  30.417  25.337  1.00  0.00              
END
