
#######################################################
#                                                     #
#                        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   34 (  168),  selected   34 , name T0386TS239_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS239_4-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      -       -           -
LGA    P     220      -       -           -
LGA    E     221      -       -           -
LGA    K     222      -       -           -
LGA    I     223      -       -           -
LGA    R     224      -       -           -
LGA    L     225      -       -           -
LGA    L     226      -       -           -
LGA    K     227      -       -           -
LGA    E     228      -       -           -
LGA    F     229      -       -           -
LGA    M     230      N     219          1.722
LGA    H     231      P     220          1.498
LGA    T     232      E     221          1.671
LGA    M     233      K     222          0.523
LGA    K     234      I     223          0.209
LGA    N     235      R     224          0.807
LGA    T     236      L     225          0.824
LGA    G     237      L     226          0.843
LGA    R     238      K     227          0.845
LGA    N     239      E     228          1.148
LGA    V     240      F     229          1.121
LGA    N     241      M     230          1.107
LGA    D     242      H     231          1.464
LGA    R     243      T     232          0.762
LGA    P     244      M     233          1.963
LGA    V     245      K     234          2.362
LGA    M     246      N     235          3.532
LGA    V     247      T     236          2.388
LGA    A     248      G     237          3.160
LGA    K     249      -       -           -
LGA    E     250      R     238          4.962
LGA    G     251      N     239           -
LGA    E     252      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34   81    5.0     20    2.00     0.00     22.775     0.953

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.959608 * X  +   0.243648 * Y  +  -0.140671 * Z  +  10.389760
  Y_new =   0.228693 * X  +   0.966754 * Y  +   0.114394 * Z  + -32.952789
  Z_new =   0.163866 * X  +   0.077603 * Y  +  -0.983426 * Z  +  44.027954 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.062845   -0.078748  [ DEG:   175.4881     -4.5119 ]
  Theta =  -0.164608   -2.976985  [ DEG:    -9.4313   -170.5686 ]
  Phi   =   2.907638   -0.233955  [ DEG:   166.5954    -13.4046 ]
 
# 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: T0386TS239_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS239_4-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   81   5.0   20   2.00    0.00  22.775
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS239_4-D2
PFRMAT TS
TARGET T0386
MODEL 4
PARENT 1p5q_A
ATOM    775  N   ASN   219      -8.182  35.149  70.040  1.00  9.99
ATOM    776  CA  ASN   219      -8.245  34.584  68.687  1.00  9.99
ATOM    777  C   ASN   219      -8.599  33.127  68.768  1.00  9.99
ATOM    778  O   ASN   219      -9.502  32.648  68.079  1.00  9.99
ATOM    779  CB  ASN   219      -6.901  34.699  67.973  1.00  9.99
ATOM    780  N   PRO   220      -8.101  44.454  78.339  1.00  9.99
ATOM    781  CA  PRO   220      -8.507  45.842  78.593  1.00  9.99
ATOM    782  C   PRO   220      -7.473  46.542  79.468  1.00  9.99
ATOM    783  O   PRO   220      -6.912  47.586  79.090  1.00  9.99
ATOM    784  CB  PRO   220      -9.866  45.876  79.275  1.00  9.99
ATOM    785  N   GLU   221      -7.229  45.952  80.638  1.00  9.99
ATOM    786  CA  GLU   221      -6.260  46.481  81.601  1.00  9.99
ATOM    787  C   GLU   221      -4.993  46.890  80.857  1.00  9.99
ATOM    788  O   GLU   221      -4.542  48.036  80.977  1.00  9.99
ATOM    789  CB  GLU   221      -5.880  45.421  82.643  1.00  9.99
ATOM    790  N   LYS   222      -4.434  45.941  80.092  1.00  9.99
ATOM    791  CA  LYS   222      -3.232  46.173  79.289  1.00  9.99
ATOM    792  C   LYS   222      -3.380  47.412  78.396  1.00  9.99
ATOM    793  O   LYS   222      -2.491  48.270  78.371  1.00  9.99
ATOM    794  CB  LYS   222      -2.923  44.947  78.435  1.00  9.99
ATOM    795  N   ILE   223      -4.493  47.529  77.677  1.00  9.99
ATOM    796  CA  ILE   223      -4.673  48.704  76.830  1.00  9.99
ATOM    797  C   ILE   223      -4.653  49.990  77.663  1.00  9.99
ATOM    798  O   ILE   223      -3.965  50.953  77.320  1.00  9.99
ATOM    799  CB  ILE   223      -5.995  48.635  76.077  1.00  9.99
ATOM    800  N   ARG   224      -5.400  50.023  78.760  1.00  9.99
ATOM    801  CA  ARG   224      -5.424  51.238  79.584  1.00  9.99
ATOM    802  C   ARG   224      -4.033  51.629  80.060  1.00  9.99
ATOM    803  O   ARG   224      -3.615  52.763  79.857  1.00  9.99
ATOM    804  CB  ARG   224      -6.348  51.069  80.801  1.00  9.99
ATOM    805  N   LEU   225      -3.312  50.693  80.674  1.00  9.99
ATOM    806  CA  LEU   225      -1.976  50.989  81.191  1.00  9.99
ATOM    807  C   LEU   225      -1.026  51.401  80.073  1.00  9.99
ATOM    808  O   LEU   225      -0.271  52.377  80.219  1.00  9.99
ATOM    809  CB  LEU   225      -1.413  49.777  81.962  1.00  9.99
ATOM    810  N   LEU   226      -1.060  50.655  78.967  1.00  9.99
ATOM    811  CA  LEU   226      -0.212  50.952  77.809  1.00  9.99
ATOM    812  C   LEU   226      -0.587  52.315  77.237  1.00  9.99
ATOM    813  O   LEU   226       0.262  53.053  76.698  1.00  9.99
ATOM    814  CB  LEU   226      -0.398  49.908  76.701  1.00  9.99
ATOM    815  N   LYS   227      -1.876  52.626  77.340  1.00  9.99
ATOM    816  CA  LYS   227      -2.418  53.899  76.874  1.00  9.99
ATOM    817  C   LYS   227      -1.762  54.984  77.746  1.00  9.99
ATOM    818  O   LYS   227      -1.136  55.906  77.222  1.00  9.99
ATOM    819  CB  LYS   227      -3.952  53.877  77.025  1.00  9.99
ATOM    820  N   GLU   228      -1.870  54.857  79.071  1.00  9.99
ATOM    821  CA  GLU   228      -1.260  55.833  79.983  1.00  9.99
ATOM    822  C   GLU   228       0.242  55.915  79.731  1.00  9.99
ATOM    823  O   GLU   228       0.786  56.990  79.490  1.00  9.99
ATOM    824  CB  GLU   228      -1.510  55.465  81.469  1.00  9.99
ATOM    825  N   PHE   229       0.902  54.763  79.776  1.00  9.99
ATOM    826  CA  PHE   229       2.339  54.695  79.576  1.00  9.99
ATOM    827  C   PHE   229       2.827  55.605  78.427  1.00  9.99
ATOM    828  O   PHE   229       3.805  56.354  78.589  1.00  9.99
ATOM    829  CB  PHE   229       2.751  53.230  79.332  1.00  9.99
ATOM    830  N   MET   230       2.153  55.550  77.277  1.00  9.99
ATOM    831  CA  MET   230       2.548  56.382  76.140  1.00  9.99
ATOM    832  C   MET   230       2.365  57.871  76.420  1.00  9.99
ATOM    833  O   MET   230       3.237  58.697  76.093  1.00  9.99
ATOM    834  CB  MET   230       1.746  55.986  74.919  1.00  9.99
ATOM    835  N   HIS   231       1.234  58.224  77.026  1.00  9.99
ATOM    836  CA  HIS   231       0.989  59.616  77.374  1.00  9.99
ATOM    837  C   HIS   231       2.131  60.131  78.279  1.00  9.99
ATOM    838  O   HIS   231       2.628  61.241  78.077  1.00  9.99
ATOM    839  CB  HIS   231      -0.347  59.748  78.065  1.00  9.99
ATOM    840  N   THR   232       2.549  59.342  79.273  1.00  9.99
ATOM    841  CA  THR   232       3.656  59.764  80.132  1.00  9.99
ATOM    842  C   THR   232       4.881  59.978  79.235  1.00  9.99
ATOM    843  O   THR   232       5.301  61.120  79.034  1.00  9.99
ATOM    844  CB  THR   232       3.980  58.706  81.192  1.00  9.99
ATOM    845  N   MET   233       5.427  58.886  78.678  1.00  9.99
ATOM    846  CA  MET   233       6.610  58.949  77.808  1.00  9.99
ATOM    847  C   MET   233       6.569  60.115  76.843  1.00  9.99
ATOM    848  O   MET   233       7.509  60.900  76.774  1.00  9.99
ATOM    849  CB  MET   233       6.773  57.670  76.997  1.00  9.99
ATOM    850  N   LYS   234       5.484  60.238  76.093  1.00  9.99
ATOM    851  CA  LYS   234       5.384  61.338  75.149  1.00  9.99
ATOM    852  C   LYS   234       5.660  62.721  75.755  1.00  9.99
ATOM    853  O   LYS   234       6.462  63.490  75.207  1.00  9.99
ATOM    854  CB  LYS   234       4.013  61.355  74.492  1.00  9.99
ATOM    855  N   ASN   235       5.004  63.055  76.871  1.00  9.99
ATOM    856  CA  ASN   235       5.219  64.375  77.475  1.00  9.99
ATOM    857  C   ASN   235       6.683  64.483  77.858  1.00  9.99
ATOM    858  O   ASN   235       7.302  65.559  77.765  1.00  9.99
ATOM    859  CB  ASN   235       4.344  64.597  78.729  1.00  9.99
ATOM    860  N   THR   236       7.239  63.353  78.271  1.00  9.99
ATOM    861  CA  THR   236       8.623  63.323  78.683  1.00  9.99
ATOM    862  C   THR   236       9.537  63.799  77.567  1.00  9.99
ATOM    863  O   THR   236      10.369  64.692  77.783  1.00  9.99
ATOM    864  CB  THR   236       9.017  61.919  79.100  1.00  9.99
ATOM    865  N   GLY   237       9.392  63.210  76.379  1.00  9.99
ATOM    866  CA  GLY   237      10.240  63.618  75.259  1.00  9.99
ATOM    867  C   GLY   237       9.942  65.049  74.891  1.00  9.99
ATOM    868  O   GLY   237      10.861  65.839  74.620  1.00  9.99
ATOM    869  N   ARG   238       8.658  65.400  74.902  1.00  9.99
ATOM    870  CA  ARG   238       8.285  66.777  74.605  1.00  9.99
ATOM    871  C   ARG   238       9.094  67.714  75.529  1.00  9.99
ATOM    872  O   ARG   238       9.798  68.610  75.035  1.00  9.99
ATOM    873  CB  ARG   238       6.809  66.971  74.817  1.00  9.99
ATOM    874  N   ASN   239       9.039  67.496  76.851  1.00  9.99
ATOM    875  CA  ASN   239       9.787  68.360  77.779  1.00  9.99
ATOM    876  C   ASN   239      11.292  68.279  77.608  1.00  9.99
ATOM    877  O   ASN   239      11.990  69.271  77.799  1.00  9.99
ATOM    878  CB  ASN   239       9.486  68.018  79.227  1.00  9.99
ATOM    879  N   VAL   240      11.799  67.092  77.288  1.00  9.99
ATOM    880  CA  VAL   240      13.236  66.921  77.110  1.00  9.99
ATOM    881  C   VAL   240      13.617  67.681  75.853  1.00  9.99
ATOM    882  O   VAL   240      14.654  68.350  75.804  1.00  9.99
ATOM    883  CB  VAL   240      13.586  65.434  76.963  1.00  9.99
ATOM    884  N   ASN   241      12.759  67.581  74.840  1.00  9.99
ATOM    885  CA  ASN   241      12.990  68.258  73.570  1.00  9.99
ATOM    886  C   ASN   241      13.142  69.750  73.817  1.00  9.99
ATOM    887  O   ASN   241      14.199  70.348  73.546  1.00  9.99
ATOM    888  CB  ASN   241      11.806  68.044  72.630  1.00  9.99
ATOM    889  N   ASP   242      12.062  70.339  74.329  1.00  9.99
ATOM    890  CA  ASP   242      12.024  71.761  74.626  1.00  9.99
ATOM    891  C   ASP   242      13.196  72.165  75.507  1.00  9.99
ATOM    892  O   ASP   242      13.932  73.088  75.153  1.00  9.99
ATOM    893  CB  ASP   242      10.697  72.114  75.300  1.00  9.99
ATOM    894  N   ARG   243      13.392  71.481  76.635  1.00  9.99
ATOM    895  CA  ARG   243      14.500  71.828  77.526  1.00  9.99
ATOM    896  C   ARG   243      15.807  71.759  76.733  1.00  9.99
ATOM    897  O   ARG   243      16.705  72.565  76.934  1.00  9.99
ATOM    898  CB  ARG   243      14.509  70.905  78.757  1.00  9.99
ATOM    899  N   PRO   244      15.891  70.824  75.793  1.00  9.99
ATOM    900  CA  PRO   244      17.079  70.715  74.943  1.00  9.99
ATOM    901  C   PRO   244      17.249  71.933  74.037  1.00  9.99
ATOM    902  O   PRO   244      18.350  72.489  73.919  1.00  9.99
ATOM    903  CB  PRO   244      17.006  69.474  74.064  1.00  9.99
ATOM    904  N   VAL   245      16.167  72.333  73.373  1.00  9.99
ATOM    905  CA  VAL   245      16.221  73.498  72.491  1.00  9.99
ATOM    906  C   VAL   245      16.710  74.711  73.289  1.00  9.99
ATOM    907  O   VAL   245      17.467  75.547  72.780  1.00  9.99
ATOM    908  CB  VAL   245      14.837  73.776  71.889  1.00  9.99
ATOM    909  N   MET   246      16.284  74.793  74.547  1.00  9.99
ATOM    910  CA  MET   246      16.669  75.906  75.418  1.00  9.99
ATOM    911  C   MET   246      18.186  75.998  75.512  1.00  9.99
ATOM    912  O   MET   246      18.777  76.964  75.058  1.00  9.99
ATOM    913  CB  MET   246      16.064  75.713  76.811  1.00  9.99
ATOM    914  N   VAL   247      18.806  74.980  76.101  1.00  9.99
ATOM    915  CA  VAL   247      20.257  74.931  76.244  1.00  9.99
ATOM    916  C   VAL   247      20.903  75.352  74.928  1.00  9.99
ATOM    917  O   VAL   247      21.912  76.058  74.910  1.00  9.99
ATOM    918  CB  VAL   247      20.699  73.501  76.598  1.00  9.99
ATOM    919  N   ALA   248      19.727  77.403  72.230  1.00  9.99
ATOM    920  CA  ALA   248      19.706  78.839  71.935  1.00  9.99
ATOM    921  C   ALA   248      20.733  79.584  72.774  1.00  9.99
ATOM    922  O   ALA   248      21.574  80.308  72.236  1.00  9.99
ATOM    923  CB  ALA   248      18.314  79.410  72.178  1.00  9.99
ATOM    924  N   LYS   249      20.669  79.405  74.089  1.00  9.99
ATOM    925  CA  LYS   249      21.631  80.040  74.980  1.00  9.99
ATOM    926  C   LYS   249      23.028  79.758  74.403  1.00  9.99
ATOM    927  O   LYS   249      23.942  80.587  74.487  1.00  9.99
ATOM    928  CB  LYS   249      21.529  79.431  76.382  1.00  9.99
ATOM    929  N   GLU   250      23.177  78.577  73.806  1.00  9.99
ATOM    930  CA  GLU   250      24.447  78.170  73.223  1.00  9.99
ATOM    931  C   GLU   250      24.810  79.064  72.044  1.00  9.99
ATOM    932  O   GLU   250      25.660  78.707  71.218  1.00  9.99
ATOM    933  CB  GLU   250      24.383  76.699  72.788  1.00  9.99
ATOM    934  N   GLY   251      24.160  80.223  71.962  1.00  9.99
ATOM    935  CA  GLY   251      24.431  81.173  70.890  1.00  9.99
ATOM    936  C   GLY   251      25.036  82.462  71.442  1.00  9.99
ATOM    937  O   GLY   251      24.447  83.549  71.358  1.00  9.99
ATOM    938  N   GLU   252      26.224  82.305  72.025  1.00  9.99
ATOM    939  CA  GLU   252      26.980  83.409  72.591  1.00  9.99
ATOM    940  C   GLU   252      27.807  84.007  71.447  1.00  9.99
ATOM    941  O   GLU   252      27.862  85.255  71.332  1.00  9.99
ATOM    942  CB  GLU   252      27.894  82.897  73.719  1.00  9.99
TER
END
