
#######################################################
#                                                     #
#                        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   41 (  202),  selected   41 , name T0386TS239_3_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS239_3_2-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      -       -           -
LGA    H     231      -       -           -
LGA    T     232      -       -           -
LGA    M     233      -       -           -
LGA    K     234      -       -           -
LGA    N     235      -       -           -
LGA    T     236      N     219          1.078
LGA    G     237      P     220          0.980
LGA    R     238      E     221          1.393
LGA    N     239      K     222          0.666
LGA    V     240      I     223          0.785
LGA    N     241      R     224          1.020
LGA    D     242      L     225          1.063
LGA    R     243      L     226          0.684
LGA    P     244      K     227          0.913
LGA    V     245      E     228          0.843
LGA    M     246      F     229          1.130
LGA    V     247      M     230          1.302
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    A     248      M     233          1.877
LGA    K     249      K     234          1.747
LGA    E     250      N     235          3.118
LGA    G     251      T     236          1.689
LGA    E     252      G     237          3.189
LGA    T     253      R     238          5.233
LGA    Y     254      N     239           -
LGA    T     255      V     240           -
LGA    G     256      N     241           -
LGA    T     257      D     242           -
LGA    Y     258      R     243           -
LGA    R     259      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)   41   81    5.0     18    1.96     5.56     20.923     0.875

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.158181 * X  +   0.100099 * Y  +  -0.982323 * Z  +  11.047829
  Y_new =   0.395648 * X  +  -0.917918 * Y  +  -0.029826 * Z  +  54.315292
  Z_new =  -0.904678 * X  +  -0.383937 * Y  +  -0.184801 * Z  + 173.563171 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.019398    1.122195  [ DEG:  -115.7030     64.2970 ]
  Theta =   1.130622    2.010970  [ DEG:    64.7799    115.2201 ]
  Phi   =   1.190462   -1.951131  [ DEG:    68.2084   -111.7916 ]
 
# 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_3_2-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS239_3_2-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   81   5.0   18   1.96    5.56  20.923
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS239_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 1a17
ATOM    474  N   ASN   219     -24.090  30.041  69.003  1.00  9.99
ATOM    475  CA  ASN   219     -23.916  29.818  70.394  1.00  9.99
ATOM    476  C   ASN   219     -23.513  31.150  70.907  1.00  9.99
ATOM    477  O   ASN   219     -22.471  31.650  70.548  1.00  9.99
ATOM    478  CB  ASN   219     -22.828  28.807  70.651  1.00  9.99
ATOM    479  N   PRO   220     -24.433  31.782  71.609  1.00  9.99
ATOM    480  CA  PRO   220     -24.229  33.086  72.233  1.00  9.99
ATOM    481  C   PRO   220     -22.998  33.032  73.152  1.00  9.99
ATOM    482  O   PRO   220     -22.300  34.030  73.364  1.00  9.99
ATOM    483  CB  PRO   220     -25.480  33.462  73.039  1.00  9.99
ATOM    484  N   GLU   221     -22.741  31.840  73.672  1.00  9.99
ATOM    485  CA  GLU   221     -21.618  31.548  74.557  1.00  9.99
ATOM    486  C   GLU   221     -20.310  31.858  73.805  1.00  9.99
ATOM    487  O   GLU   221     -19.515  32.699  74.234  1.00  9.99
ATOM    488  CB  GLU   221     -21.685  30.057  74.891  1.00  9.99
ATOM    489  N   LYS   222     -20.100  31.181  72.674  1.00  9.99
ATOM    490  CA  LYS   222     -18.911  31.380  71.851  1.00  9.99
ATOM    491  C   LYS   222     -18.681  32.872  71.585  1.00  9.99
ATOM    492  O   LYS   222     -17.563  33.382  71.773  1.00  9.99
ATOM    493  CB  LYS   222     -19.044  30.621  70.548  1.00  9.99
ATOM    494  N   ILE   223     -19.761  33.567  71.209  1.00  9.99
ATOM    495  CA  ILE   223     -19.736  35.008  70.924  1.00  9.99
ATOM    496  C   ILE   223     -19.259  35.798  72.107  1.00  9.99
ATOM    497  O   ILE   223     -18.386  36.617  71.970  1.00  9.99
ATOM    498  CB  ILE   223     -21.118  35.506  70.524  1.00  9.99
ATOM    499  N   ARG   224     -19.825  35.525  73.269  1.00  9.99
ATOM    500  CA  ARG   224     -19.453  36.216  74.485  1.00  9.99
ATOM    501  C   ARG   224     -17.948  36.072  74.767  1.00  9.99
ATOM    502  O   ARG   224     -17.259  37.066  74.964  1.00  9.99
ATOM    503  CB  ARG   224     -20.265  35.658  75.657  1.00  9.99
ATOM    504  N   LEU   225     -17.433  34.845  74.751  1.00  9.99
ATOM    505  CA  LEU   225     -16.006  34.591  75.029  1.00  9.99
ATOM    506  C   LEU   225     -15.060  35.306  74.086  1.00  9.99
ATOM    507  O   LEU   225     -14.093  35.941  74.503  1.00  9.99
ATOM    508  CB  LEU   225     -15.719  33.099  74.985  1.00  9.99
ATOM    509  N   LEU   226     -15.348  35.158  72.803  1.00  9.99
ATOM    510  CA  LEU   226     -14.585  35.784  71.754  1.00  9.99
ATOM    511  C   LEU   226     -14.625  37.324  71.890  1.00  9.99
ATOM    512  O   LEU   226     -13.653  37.996  71.548  1.00  9.99
ATOM    513  CB  LEU   226     -15.159  35.312  70.428  1.00  9.99
ATOM    514  N   LYS   227     -15.739  37.879  72.381  1.00  9.99
ATOM    515  CA  LYS   227     -15.881  39.328  72.593  1.00  9.99
ATOM    516  C   LYS   227     -14.987  39.755  73.735  1.00  9.99
ATOM    517  O   LYS   227     -14.228  40.701  73.595  1.00  9.99
ATOM    518  CB  LYS   227     -17.320  39.732  72.934  1.00  9.99
ATOM    519  N   GLU   228     -15.105  39.079  74.873  1.00  9.99
ATOM    520  CA  GLU   228     -14.270  39.369  76.034  1.00  9.99
ATOM    521  C   GLU   228     -12.819  39.437  75.552  1.00  9.99
ATOM    522  O   GLU   228     -12.099  40.405  75.806  1.00  9.99
ATOM    523  CB  GLU   228     -14.403  38.236  77.092  1.00  9.99
ATOM    524  N   PHE   229     -12.429  38.423  74.792  1.00  9.99
ATOM    525  CA  PHE   229     -11.072  38.302  74.314  1.00  9.99
ATOM    526  C   PHE   229     -10.623  39.350  73.315  1.00  9.99
ATOM    527  O   PHE   229      -9.555  39.925  73.487  1.00  9.99
ATOM    528  CB  PHE   229     -10.809  36.877  73.824  1.00  9.99
ATOM    529  N   MET   230     -11.411  39.617  72.283  1.00  9.99
ATOM    530  CA  MET   230     -10.999  40.638  71.322  1.00  9.99
ATOM    531  C   MET   230     -10.870  41.952  72.066  1.00  9.99
ATOM    532  O   MET   230      -9.997  42.757  71.777  1.00  9.99
ATOM    533  CB  MET   230     -11.994  40.785  70.178  1.00  9.99
ATOM    534  N   HIS   231     -11.689  42.113  73.097  1.00  9.99
ATOM    535  CA  HIS   231     -11.678  43.311  73.933  1.00  9.99
ATOM    536  C   HIS   231     -10.333  43.402  74.656  1.00  9.99
ATOM    537  O   HIS   231      -9.623  44.404  74.544  1.00  9.99
ATOM    538  CB  HIS   231     -12.828  43.235  74.944  1.00  9.99
ATOM    539  N   THR   232      -9.943  42.327  75.330  1.00  9.99
ATOM    540  CA  THR   232      -8.680  42.296  76.060  1.00  9.99
ATOM    541  C   THR   232      -7.471  42.537  75.150  1.00  9.99
ATOM    542  O   THR   232      -6.444  43.038  75.598  1.00  9.99
ATOM    543  CB  THR   232      -8.556  40.972  76.856  1.00  9.99
ATOM    544  N   MET   233      -7.602  42.191  73.876  1.00  9.99
ATOM    545  CA  MET   233      -6.538  42.389  72.895  1.00  9.99
ATOM    546  C   MET   233      -6.454  43.881  72.547  1.00  9.99
ATOM    547  O   MET   233      -5.355  44.423  72.331  1.00  9.99
ATOM    548  CB  MET   233      -6.822  41.608  71.603  1.00  9.99
ATOM    549  N   LYS   234      -7.616  44.538  72.510  1.00  9.99
ATOM    550  CA  LYS   234      -7.695  45.956  72.203  1.00  9.99
ATOM    551  C   LYS   234      -7.319  46.834  73.392  1.00  9.99
ATOM    552  O   LYS   234      -6.696  47.870  73.184  1.00  9.99
ATOM    553  CB  LYS   234      -9.064  46.314  71.627  1.00  9.99
ATOM    554  N   ASN   235       0.828  54.705  77.653  1.00  9.99
ATOM    555  CA  ASN   235       2.166  54.712  78.241  1.00  9.99
ATOM    556  C   ASN   235       3.147  55.391  77.294  1.00  9.99
ATOM    557  O   ASN   235       4.061  56.092  77.724  1.00  9.99
ATOM    558  CB  ASN   235       2.607  53.290  78.542  1.00  9.99
ATOM    559  N   THR   236       2.962  55.164  76.005  1.00  9.99
ATOM    560  CA  THR   236       3.814  55.791  75.011  1.00  9.99
ATOM    561  C   THR   236       3.497  57.280  74.910  1.00  9.99
ATOM    562  O   THR   236       4.374  58.086  74.585  1.00  9.99
ATOM    563  CB  THR   236       3.627  55.082  73.658  1.00  9.99
ATOM    564  N   GLY   237       2.247  57.641  75.193  1.00  9.99
ATOM    565  CA  GLY   237       1.800  59.022  75.158  1.00  9.99
ATOM    566  C   GLY   237       2.368  59.750  76.356  1.00  9.99
ATOM    567  O   GLY   237       2.850  60.880  76.252  1.00  9.99
ATOM    568  N   ARG   238       2.320  59.071  77.499  1.00  9.99
ATOM    569  CA  ARG   238       2.792  59.611  78.760  1.00  9.99
ATOM    570  C   ARG   238       4.278  59.840  78.718  1.00  9.99
ATOM    571  O   ARG   238       4.791  60.826  79.219  1.00  9.99
ATOM    572  CB  ARG   238       2.430  58.666  79.900  1.00  9.99
ATOM    573  N   ASN   239       4.978  58.909  78.115  1.00  9.99
ATOM    574  CA  ASN   239       6.409  59.038  77.984  1.00  9.99
ATOM    575  C   ASN   239       6.792  60.180  77.027  1.00  9.99
ATOM    576  O   ASN   239       7.795  60.844  77.238  1.00  9.99
ATOM    577  CB  ASN   239       6.995  57.718  77.475  1.00  9.99
ATOM    578  N   VAL   240       6.028  60.376  75.955  1.00  9.99
ATOM    579  CA  VAL   240       6.349  61.424  74.997  1.00  9.99
ATOM    580  C   VAL   240       6.223  62.779  75.646  1.00  9.99
ATOM    581  O   VAL   240       7.061  63.650  75.442  1.00  9.99
ATOM    582  CB  VAL   240       5.431  61.378  73.780  1.00  9.99
ATOM    583  N   ASN   241       5.163  62.955  76.422  1.00  9.99
ATOM    584  CA  ASN   241       4.935  64.219  77.090  1.00  9.99
ATOM    585  C   ASN   241       6.124  64.550  77.961  1.00  9.99
ATOM    586  O   ASN   241       6.583  65.689  78.000  1.00  9.99
ATOM    587  CB  ASN   241       3.648  64.188  77.925  1.00  9.99
ATOM    588  N   ASP   242       6.648  63.548  78.640  1.00  9.99
ATOM    589  CA  ASP   242       7.793  63.776  79.491  1.00  9.99
ATOM    590  C   ASP   242       9.069  64.099  78.695  1.00  9.99
ATOM    591  O   ASP   242       9.852  64.922  79.150  1.00  9.99
ATOM    592  CB  ASP   242       7.997  62.591  80.436  1.00  9.99
ATOM    593  N   ARG   243       9.286  63.481  77.520  1.00  9.99
ATOM    594  CA  ARG   243      10.494  63.774  76.717  1.00  9.99
ATOM    595  C   ARG   243      10.400  65.196  76.202  1.00  9.99
ATOM    596  O   ARG   243      11.299  66.003  76.390  1.00  9.99
ATOM    597  CB  ARG   243      10.672  62.835  75.495  1.00  9.99
ATOM    598  N   PRO   244       9.268  65.516  75.612  1.00  9.99
ATOM    599  CA  PRO   244       9.061  66.828  75.052  1.00  9.99
ATOM    600  C   PRO   244       9.255  67.904  76.110  1.00  9.99
ATOM    601  O   PRO   244       9.985  68.868  75.881  1.00  9.99
ATOM    602  CB  PRO   244       7.719  66.863  74.325  1.00  9.99
ATOM    603  N   VAL   245       8.718  67.684  77.302  1.00  9.99
ATOM    604  CA  VAL   245       8.885  68.638  78.405  1.00  9.99
ATOM    605  C   VAL   245      10.359  68.797  78.812  1.00  9.99
ATOM    606  O   VAL   245      10.755  69.840  79.306  1.00  9.99
ATOM    607  CB  VAL   245       8.126  68.171  79.655  1.00  9.99
ATOM    608  N   MET   246      11.154  67.753  78.640  1.00  9.99
ATOM    609  CA  MET   246      12.556  67.790  79.039  1.00  9.99
ATOM    610  C   MET   246      13.535  68.183  77.939  1.00  9.99
ATOM    611  O   MET   246      14.743  68.259  78.192  1.00  9.99
ATOM    612  CB  MET   246      12.971  66.417  79.603  1.00  9.99
ATOM    613  N   VAL   247      13.028  68.417  76.729  1.00  9.99
ATOM    614  CA  VAL   247      13.886  68.775  75.597  1.00  9.99
ATOM    615  C   VAL   247      14.654  70.076  75.823  1.00  9.99
ATOM    616  O   VAL   247      14.063  71.134  76.047  1.00  9.99
ATOM    617  CB  VAL   247      13.071  68.864  74.296  1.00  9.99
ATOM    618  N   ALA   248      15.975  70.001  75.723  1.00  9.99
ATOM    619  CA  ALA   248      16.815  71.170  75.928  1.00  9.99
ATOM    620  C   ALA   248      16.908  72.055  74.691  1.00  9.99
ATOM    621  O   ALA   248      17.877  72.020  73.930  1.00  9.99
ATOM    622  CB  ALA   248      18.206  70.756  76.406  1.00  9.99
ATOM    623  N   LYS   249      15.859  72.834  74.496  1.00  9.99
ATOM    624  CA  LYS   249      15.789  73.764  73.391  1.00  9.99
ATOM    625  C   LYS   249      16.610  74.996  73.756  1.00  9.99
ATOM    626  O   LYS   249      17.420  75.449  72.965  1.00  9.99
ATOM    627  CB  LYS   249      14.322  74.056  73.054  1.00  9.99
ATOM    628  N   GLU   250      16.545  75.394  75.021  1.00  9.99
ATOM    629  CA  GLU   250      17.294  76.548  75.531  1.00  9.99
ATOM    630  C   GLU   250      18.803  76.579  75.243  1.00  9.99
ATOM    631  O   GLU   250      19.373  77.639  75.075  1.00  9.99
ATOM    632  CB  GLU   250      17.040  76.708  77.034  1.00  9.99
ATOM    633  N   GLY   251      19.454  75.428  75.200  1.00  9.99
ATOM    634  CA  GLY   251      20.885  75.395  74.931  1.00  9.99
ATOM    635  C   GLY   251      21.180  75.361  73.457  1.00  9.99
ATOM    636  O   GLY   251      22.344  75.284  73.060  1.00  9.99
ATOM    637  N   GLU   252      20.137  75.307  72.639  1.00  9.99
ATOM    638  CA  GLU   252      20.361  75.299  71.203  1.00  9.99
ATOM    639  C   GLU   252      20.795  76.708  70.821  1.00  9.99
ATOM    640  O   GLU   252      20.446  77.668  71.513  1.00  9.99
ATOM    641  CB  GLU   252      19.094  74.877  70.468  1.00  9.99
ATOM    642  N   THR   253      21.565  76.832  69.743  1.00  9.99
ATOM    643  CA  THR   253      22.056  78.137  69.299  1.00  9.99
ATOM    644  C   THR   253      21.807  78.524  67.858  1.00  9.99
ATOM    645  O   THR   253      21.936  77.735  66.915  1.00  9.99
ATOM    646  CB  THR   253      23.555  78.314  69.540  1.00  9.99
ATOM    647  N   TYR   254      21.491  79.801  67.717  1.00  9.99
ATOM    648  CA  TYR   254      21.228  80.413  66.438  1.00  9.99
ATOM    649  C   TYR   254      22.601  80.471  65.790  1.00  9.99
ATOM    650  O   TYR   254      23.634  80.422  66.478  1.00  9.99
ATOM    651  CB  TYR   254      20.578  81.805  66.676  1.00  9.99
ATOM    652  N   THR   255      22.640  80.453  64.471  1.00  9.99
ATOM    653  CA  THR   255      23.940  80.501  63.837  1.00  9.99
ATOM    654  C   THR   255      24.571  81.871  64.058  1.00  9.99
ATOM    655  O   THR   255      24.150  82.852  63.452  1.00  9.99
ATOM    656  CB  THR   255      23.848  80.192  62.341  1.00  9.99
ATOM    657  N   GLY   256      25.521  81.961  64.984  1.00  9.99
ATOM    658  CA  GLY   256      26.192  83.237  65.225  1.00  9.99
ATOM    659  C   GLY   256      27.533  83.249  64.489  1.00  9.99
ATOM    660  O   GLY   256      28.608  83.134  65.092  1.00  9.99
ATOM    661  N   THR   257      27.420  83.328  63.163  1.00  9.99
ATOM    662  CA  THR   257      28.528  83.366  62.202  1.00  9.99
ATOM    663  C   THR   257      27.908  83.937  60.910  1.00  9.99
ATOM    664  O   THR   257      26.698  83.777  60.704  1.00  9.99
ATOM    665  CB  THR   257      29.080  81.950  61.966  1.00  9.99
ATOM    666  N   TYR   258      28.691  84.649  60.090  1.00  9.99
ATOM    667  CA  TYR   258      28.180  85.249  58.829  1.00  9.99
ATOM    668  C   TYR   258      27.451  84.215  57.925  1.00  9.99
ATOM    669  O   TYR   258      27.794  83.019  57.928  1.00  9.99
ATOM    670  CB  TYR   258      29.325  85.986  58.066  1.00  9.99
ATOM    671  N   ARG   259      26.417  84.678  57.211  1.00  9.99
ATOM    672  CA  ARG   259      25.631  83.828  56.310  1.00  9.99
ATOM    673  C   ARG   259      25.027  84.617  55.142  1.00  9.99
ATOM    674  O   ARG   259      25.586  85.622  54.674  1.00  9.99
ATOM    675  CB  ARG   259      24.513  83.120  57.082  1.00  9.99
TER
END
