
#######################################################
#                                                     #
#                        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   49 (  195),  selected   49 , name T0386AL333_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL333_1-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    P     220      L     226          3.965
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    E     221      F     229          2.005
LGA    K     222      M     230          2.157
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    I     223      V     240          1.928
LGA    R     224      N     241          1.184
LGA    L     225      D     242          2.645
LGA    L     226      R     243          2.335
LGA    K     227      P     244          4.128
LGA    E     228      V     245          2.539
LGA    F     229      -       -           -
LGA    M     230      -       -           -
LGA    H     231      M     246          2.504
LGA    T     232      V     247          2.329
LGA    M     233      A     248          2.540
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    K     234      I     275           #
LGA    N     235      I     276           #
LGA    T     236      G     277          3.307
LGA    G     237      N     278          4.012
LGA    R     238      I     279          2.499
LGA    N     239      D     280          3.920
LGA    V     240      H     281          3.200
LGA    N     241      L     282          3.778
LGA    D     242      -       -           -
LGA    R     243      P     283          3.503
LGA    P     244      P     284          0.792
LGA    V     245      -       -           -
LGA    M     246      E     285           #
LGA    L     268      Q     286           -
LGA    N     269      L     287           -
LGA    V     270      K     288           -
LGA    K     271      I     289           -
LGA    Y     274      L     290           -
LGA    I     275      K     291           -
LGA    I     276      P     292           -
LGA    G     277      G     293           -
LGA    N     278      D     294           -
LGA    I     279      K     295           -
LGA    D     280      I     296           -
LGA    H     281      T     297           -
LGA    L     282      F     298           -
LGA    P     283      T     299           -
LGA    P     284      -       -           -
LGA    E     285      -       -           -
LGA    Q     286      -       -           -
LGA    L     287      -       -           -
LGA    K     288      -       -           -
LGA    F     298      -       -           -
LGA    T     299      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   49   81    5.0     20    2.91     5.00     15.735     0.664

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.961094 * X  +  -0.234573 * Y  +  -0.145858 * Z  + -19.506086
  Y_new =  -0.233721 * X  +  -0.972027 * Y  +   0.023197 * Z  +  65.967461
  Z_new =  -0.147220 * X  +   0.011795 * Y  +  -0.989034 * Z  + 118.201218 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.129667   -0.011926  [ DEG:   179.3167     -0.6833 ]
  Theta =   0.147757    2.993836  [ DEG:     8.4658    171.5342 ]
  Phi   =  -0.238552    2.903041  [ DEG:   -13.6680    166.3320 ]
 
# 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: T0386AL333_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL333_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   49   81   5.0   20   2.91    5.00  15.735
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL333_1-D2
REMARK Aligment from pdb entry: 1nf1_A
ATOM    609  N   ASN   219      13.586  67.040  82.239  1.00  0.00              
ATOM    610  CA  ASN   219      12.661  68.079  81.814  1.00  0.00              
ATOM    611  C   ASN   219      11.568  67.588  80.887  1.00  0.00              
ATOM    612  O   ASN   219      10.561  68.271  80.723  1.00  0.00              
ATOM    613  N   PRO   220      11.724  66.375  80.357  1.00  0.00              
ATOM    614  CA  PRO   220      10.810  65.840  79.338  1.00  0.00              
ATOM    615  C   PRO   220      10.752  66.787  78.135  1.00  0.00              
ATOM    616  O   PRO   220       9.678  67.251  77.733  1.00  0.00              
ATOM    617  N   GLU   221      11.932  67.041  77.568  1.00  0.00              
ATOM    618  CA  GLU   221      12.148  68.060  76.541  1.00  0.00              
ATOM    619  C   GLU   221      13.308  67.623  75.629  1.00  0.00              
ATOM    620  O   GLU   221      14.376  67.225  76.116  1.00  0.00              
ATOM    621  N   LYS   222      13.091  67.671  74.314  1.00  0.00              
ATOM    622  CA  LYS   222      14.114  67.246  73.353  1.00  0.00              
ATOM    623  C   LYS   222      14.949  68.404  72.788  1.00  0.00              
ATOM    624  O   LYS   222      14.558  69.576  72.871  1.00  0.00              
ATOM    625  N   ILE   223      23.501  68.197  69.608  1.00  0.00              
ATOM    626  CA  ILE   223      22.990  67.308  70.646  1.00  0.00              
ATOM    627  C   ILE   223      21.723  66.588  70.163  1.00  0.00              
ATOM    628  O   ILE   223      21.186  65.724  70.861  1.00  0.00              
ATOM    629  N   ARG   224      21.280  66.931  68.951  1.00  0.00              
ATOM    630  CA  ARG   224      20.239  66.190  68.236  1.00  0.00              
ATOM    631  C   ARG   224      20.398  64.659  68.306  1.00  0.00              
ATOM    632  O   ARG   224      19.407  63.941  68.432  1.00  0.00              
ATOM    633  N   LEU   225      21.644  64.139  68.217  1.00  0.00              
ATOM    634  CA  LEU   225      21.856  62.680  68.217  1.00  0.00              
ATOM    635  C   LEU   225      21.462  61.915  69.479  1.00  0.00              
ATOM    636  O   LEU   225      21.139  60.725  69.403  1.00  0.00              
ATOM    637  N   LEU   226      21.572  62.570  70.638  1.00  0.00              
ATOM    638  CA  LEU   226      21.335  61.916  71.934  1.00  0.00              
ATOM    639  C   LEU   226      19.853  61.936  72.284  1.00  0.00              
ATOM    640  O   LEU   226      19.423  61.300  73.247  1.00  0.00              
ATOM    641  N   LYS   227      19.063  62.532  71.401  1.00  0.00              
ATOM    642  CA  LYS   227      17.634  62.664  71.611  1.00  0.00              
ATOM    643  C   LYS   227      16.916  61.330  71.679  1.00  0.00              
ATOM    644  O   LYS   227      15.705  61.289  71.857  1.00  0.00              
ATOM    645  N   GLU   228      17.643  60.243  71.464  1.00  0.00              
ATOM    646  CA  GLU   228      17.048  58.922  71.570  1.00  0.00              
ATOM    647  C   GLU   228      17.522  58.208  72.823  1.00  0.00              
ATOM    648  O   GLU   228      16.842  57.310  73.321  1.00  0.00              
ATOM    649  N   PHE   229      18.700  58.588  73.313  1.00  0.00              
ATOM    650  CA  PHE   229      19.151  58.160  74.639  1.00  0.00              
ATOM    651  C   PHE   229      18.276  58.826  75.698  1.00  0.00              
ATOM    652  O   PHE   229      17.775  58.167  76.608  1.00  0.00              
ATOM    653  N   MET   230      18.007  60.111  75.491  1.00  0.00              
ATOM    654  CA  MET   230      17.169  60.880  76.391  1.00  0.00              
ATOM    655  C   MET   230      15.807  60.217  76.592  1.00  0.00              
ATOM    656  O   MET   230      15.524  59.725  77.680  1.00  0.00              
ATOM    657  N   HIS   231      15.079  59.994  75.504  1.00  0.00              
ATOM    658  CA  HIS   231      13.701  59.519  75.599  1.00  0.00              
ATOM    659  C   HIS   231      13.531  58.041  75.946  1.00  0.00              
ATOM    660  O   HIS   231      12.416  57.597  76.248  1.00  0.00              
ATOM    661  N   THR   232      14.635  57.298  75.962  1.00  0.00              
ATOM    662  CA  THR   232      14.597  55.881  76.316  1.00  0.00              
ATOM    663  C   THR   232      14.518  55.627  77.825  1.00  0.00              
ATOM    664  O   THR   232      14.062  54.560  78.251  1.00  0.00              
ATOM    665  N   MET   233      14.928  56.612  78.630  1.00  0.00              
ATOM    666  CA  MET   233      14.867  56.487  80.089  1.00  0.00              
ATOM    667  C   MET   233      14.234  57.689  80.812  1.00  0.00              
ATOM    668  O   MET   233      14.616  58.027  81.939  1.00  0.00              
ATOM    669  N   LYS   234      13.153  58.209  80.231  1.00  0.00              
ATOM    670  CA  LYS   234      12.321  59.229  80.872  1.00  0.00              
ATOM    671  C   LYS   234      11.317  58.606  81.848  1.00  0.00              
ATOM    672  O   LYS   234      10.918  59.233  82.824  1.00  0.00              
ATOM    673  N   ASN   235      10.873  57.390  81.544  1.00  0.00              
ATOM    674  CA  ASN   235       9.979  56.642  82.422  1.00  0.00              
ATOM    675  C   ASN   235      10.800  56.027  83.540  1.00  0.00              
ATOM    676  O   ASN   235      10.297  55.800  84.634  1.00  0.00              
ATOM    677  N   THR   236      12.065  55.742  83.242  1.00  0.00              
ATOM    678  CA  THR   236      13.003  55.212  84.223  1.00  0.00              
ATOM    679  C   THR   236      13.370  56.277  85.244  1.00  0.00              
ATOM    680  O   THR   236      13.644  55.973  86.398  1.00  0.00              
ATOM    681  N   GLY   237      13.392  57.529  84.803  1.00  0.00              
ATOM    682  CA  GLY   237      13.729  58.635  85.684  1.00  0.00              
ATOM    683  C   GLY   237      12.560  59.050  86.577  1.00  0.00              
ATOM    684  O   GLY   237      12.781  59.570  87.655  1.00  0.00              
ATOM    685  N   ARG   238      11.330  58.801  86.134  1.00  0.00              
ATOM    686  CA  ARG   238      10.122  59.036  86.935  1.00  0.00              
ATOM    687  C   ARG   238       9.977  58.068  88.110  1.00  0.00              
ATOM    688  O   ARG   238       9.448  58.438  89.154  1.00  0.00              
ATOM    689  N   ASN   239      10.299  56.795  87.880  1.00  0.00              
ATOM    690  CA  ASN   239      10.220  55.760  88.912  1.00  0.00              
ATOM    691  C   ASN   239      10.948  56.201  90.173  1.00  0.00              
ATOM    692  O   ASN   239      10.403  56.130  91.268  1.00  0.00              
ATOM    693  N   VAL   240      12.209  56.593  89.993  1.00  0.00              
ATOM    694  CA  VAL   240      13.088  57.088  91.048  1.00  0.00              
ATOM    695  C   VAL   240      12.619  58.417  91.663  1.00  0.00              
ATOM    696  O   VAL   240      12.742  58.604  92.877  1.00  0.00              
ATOM    697  N   ASN   241      12.073  59.323  90.846  1.00  0.00              
ATOM    698  CA  ASN   241      11.511  60.576  91.360  1.00  0.00              
ATOM    699  C   ASN   241      10.321  60.229  92.235  1.00  0.00              
ATOM    700  O   ASN   241      10.133  60.804  93.307  1.00  0.00              
ATOM    701  N   ASP   242       9.582  59.207  91.814  1.00  0.00              
ATOM    702  CA  ASP   242       8.332  58.830  92.467  1.00  0.00              
ATOM    703  C   ASP   242       8.623  58.076  93.751  1.00  0.00              
ATOM    704  O   ASP   242       7.887  58.203  94.727  1.00  0.00              
ATOM    705  N   ARG   243       9.705  57.297  93.733  1.00  0.00              
ATOM    706  CA  ARG   243      10.181  56.562  94.899  1.00  0.00              
ATOM    707  C   ARG   243      10.693  57.531  95.977  1.00  0.00              
ATOM    708  O   ARG   243      10.281  57.443  97.134  1.00  0.00              
ATOM    709  N   PRO   244      11.471  58.537  95.571  1.00  0.00              
ATOM    710  CA  PRO   244      12.095  59.464  96.527  1.00  0.00              
ATOM    711  C   PRO   244      11.177  60.612  96.982  1.00  0.00              
ATOM    712  O   PRO   244      11.603  61.519  97.698  1.00  0.00              
ATOM    713  N   VAL   245       9.910  60.546  96.590  1.00  0.00              
ATOM    714  CA  VAL   245       8.914  61.516  97.030  1.00  0.00              
ATOM    715  C   VAL   245       7.759  60.824  97.751  1.00  0.00              
ATOM    716  O   VAL   245       6.721  61.434  98.014  1.00  0.00              
ATOM    717  N   MET   246       7.953  59.550  98.081  1.00  0.00              
ATOM    718  CA  MET   246       6.923  58.745  98.733  1.00  0.00              
ATOM    719  C   MET   246       7.562  57.782  99.749  1.00  0.00              
ATOM    720  O   MET   246       7.032  56.665  99.961  1.00  0.00              
ATOM    721  N   LEU   268      21.562  83.374 113.317  1.00  0.00              
ATOM    722  CA  LEU   268      20.747  84.293 114.170  1.00  0.00              
ATOM    723  C   LEU   268      21.149  85.754 113.957  1.00  0.00              
ATOM    724  O   LEU   268      21.772  86.371 114.835  1.00  0.00              
ATOM    725  N   ASN   269      20.823  86.289 112.777  1.00  0.00              
ATOM    726  CA  ASN   269      21.112  87.684 112.439  1.00  0.00              
ATOM    727  C   ASN   269      19.852  88.549 112.559  1.00  0.00              
ATOM    728  O   ASN   269      18.881  88.367 111.825  1.00  0.00              
ATOM    729  CA  VAL   270      18.768  90.387 113.780  1.00  0.00              
ATOM    730  C   VAL   270      19.130  91.746 113.170  1.00  0.00              
ATOM    731  O   VAL   270      18.514  92.769 113.496  1.00  0.00              
ATOM    732  N   LYS   271      20.180  91.750 112.346  1.00  0.00              
ATOM    733  CA  LYS   271      20.537  92.906 111.532  1.00  0.00              
ATOM    734  C   LYS   271      19.437  93.189 110.518  1.00  0.00              
ATOM    735  O   LYS   271      19.119  94.348 110.237  1.00  0.00              
ATOM    736  N   TYR   274      18.749  92.131 110.105  1.00  0.00              
ATOM    737  CA  TYR   274      17.600  92.267 109.228  1.00  0.00              
ATOM    738  C   TYR   274      16.441  92.984 109.918  1.00  0.00              
ATOM    739  O   TYR   274      16.033  94.056 109.495  1.00  0.00              
ATOM    740  N   ILE   275      15.995  92.450 111.046  1.00  0.00              
ATOM    741  CA  ILE   275      14.879  93.040 111.786  1.00  0.00              
ATOM    742  C   ILE   275      15.119  94.510 112.146  1.00  0.00              
ATOM    743  O   ILE   275      14.330  95.379 111.776  1.00  0.00              
ATOM    744  N   ILE   276      16.238  94.779 112.818  1.00  0.00              
ATOM    745  CA  ILE   276      16.567  96.122 113.285  1.00  0.00              
ATOM    746  C   ILE   276      16.636  97.108 112.122  1.00  0.00              
ATOM    747  O   ILE   276      16.106  98.214 112.215  1.00  0.00              
ATOM    748  N   GLY   277      17.186  96.666 110.993  1.00  0.00              
ATOM    749  CA  GLY   277      17.383  97.556 109.849  1.00  0.00              
ATOM    750  C   GLY   277      16.144  97.760 108.985  1.00  0.00              
ATOM    751  O   GLY   277      16.153  98.594 108.075  1.00  0.00              
ATOM    752  N   ASN   278      15.070  97.034 109.300  1.00  0.00              
ATOM    753  CA  ASN   278      13.847  97.076 108.501  1.00  0.00              
ATOM    754  C   ASN   278      12.586  97.187 109.359  1.00  0.00              
ATOM    755  O   ASN   278      11.479  96.996 108.859  1.00  0.00              
ATOM    756  N   ILE   279      12.742  97.698 110.576  1.00  0.00              
ATOM    757  CA  ILE   279      11.685  97.635 111.590  1.00  0.00              
ATOM    758  C   ILE   279      10.449  98.535 111.421  1.00  0.00              
ATOM    759  O   ILE   279       9.389  98.255 111.990  1.00  0.00              
ATOM    760  N   ASP   280      10.588  99.649 110.714  1.00  0.00              
ATOM    761  CA  ASP   280       9.453 100.557 110.553  1.00  0.00              
ATOM    762  C   ASP   280       8.637 100.154 109.336  1.00  0.00              
ATOM    763  O   ASP   280       7.458 100.506 109.207  1.00  0.00              
ATOM    764  N   HIS   281       9.239  99.280 108.536  1.00  0.00              
ATOM    765  CA  HIS   281       8.635  98.792 107.313  1.00  0.00              
ATOM    766  C   HIS   281       8.078  97.379 107.490  1.00  0.00              
ATOM    767  O   HIS   281       7.085  97.028 106.846  1.00  0.00              
ATOM    768  N   LEU   282       8.686  96.589 108.383  1.00  0.00              
ATOM    769  CA  LEU   282       8.115  95.291 108.771  1.00  0.00              
ATOM    770  C   LEU   282       7.167  95.467 109.945  1.00  0.00              
ATOM    771  O   LEU   282       6.909  94.524 110.695  1.00  0.00              
ATOM    772  N   PRO   283       6.682  96.697 110.106  1.00  0.00              
ATOM    773  CA  PRO   283       5.650  96.991 111.080  1.00  0.00              
ATOM    774  C   PRO   283       4.526  97.779 110.442  1.00  0.00              
ATOM    775  O   PRO   283       3.377  97.702 110.867  1.00  0.00              
ATOM    776  N   PRO   284       4.863  98.588 109.449  1.00  0.00              
ATOM    777  CA  PRO   284       3.834  99.227 108.649  1.00  0.00              
ATOM    778  C   PRO   284       3.177  98.140 107.799  1.00  0.00              
ATOM    779  O   PRO   284       1.985  98.215 107.486  1.00  0.00              
ATOM    780  N   GLU   285       3.948  97.088 107.516  1.00  0.00              
ATOM    781  CA  GLU   285       3.452  95.896 106.835  1.00  0.00              
ATOM    782  C   GLU   285       2.482  95.162 107.745  1.00  0.00              
ATOM    783  O   GLU   285       1.350  94.858 107.355  1.00  0.00              
ATOM    784  N   GLN   286       2.930  94.906 108.970  1.00  0.00              
ATOM    785  CA  GLN   286       2.144  94.171 109.949  1.00  0.00              
ATOM    786  C   GLN   286       0.812  94.850 110.284  1.00  0.00              
ATOM    787  O   GLN   286      -0.042  94.248 110.917  1.00  0.00              
ATOM    788  N   LEU   287       0.618  96.081 109.814  1.00  0.00              
ATOM    789  CA  LEU   287      -0.663  96.773 109.972  1.00  0.00              
ATOM    790  C   LEU   287      -1.681  96.410 108.876  1.00  0.00              
ATOM    791  O   LEU   287      -2.621  97.166 108.597  1.00  0.00              
ATOM    792  N   LYS   288      -1.467  95.255 108.249  1.00  0.00              
ATOM    793  CA  LYS   288      -2.517  94.558 107.513  1.00  0.00              
ATOM    794  C   LYS   288      -2.248  93.051 107.546  1.00  0.00              
ATOM    795  O   LYS   288      -3.094  92.327 108.115  1.00  0.00              
ATOM    796  N   PHE   298      -0.787  90.757 119.217  1.00  0.00              
ATOM    797  CA  PHE   298       0.253  91.821 119.321  1.00  0.00              
ATOM    798  C   PHE   298       1.639  91.395 118.802  1.00  0.00              
ATOM    799  O   PHE   298       2.650  91.669 119.454  1.00  0.00              
ATOM    800  N   THR   299       1.716  90.800 117.591  1.00  0.00              
ATOM    801  CA  THR   299       3.000  90.294 117.071  1.00  0.00              
ATOM    802  C   THR   299       4.071  91.376 116.846  1.00  0.00              
ATOM    803  O   THR   299       5.264  91.142 117.074  1.00  0.00              
END
