
#######################################################
#                                                     #
#                        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   38 (  152),  selected   38 , name T0316AL381_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL381_5-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220           -
LGA    R     221      R     221           -
LGA    M     222      M     222           -
LGA    M     223      M     223           -
LGA    T     224      T     224           -
LGA    I     249      V     225           -
LGA    G     250      D     226           -
LGA    G     251      G     227           -
LGA    Q     252      R     228           -
LGA    H     253      D     229           -
LGA    G     254      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    G     255      D     256           #
LGA    D     256      -       -           -
LGA    N     257      -       -           -
LGA    A     258      -       -           -
LGA    P     259      N     257          3.436
LGA    W     260      A     258          2.192
LGA    F     261      P     259          1.253
LGA    V     262      W     260          1.521
LGA    V     263      F     261          1.179
LGA    G     264      V     262          2.590
LGA    K     265      V     263          2.426
LGA    D     266      G     264          3.407
LGA    L     267      K     265          1.727
LGA    S     268      D     266          3.080
LGA    K     269      L     267          3.308
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    N     270      I     271          1.922
LGA    I     271      L     272          3.045
LGA    L     272      Y     273          3.755
LGA    Y     273      V     274          4.949
LGA    V     274      G     275          1.505
LGA    G     275      Q     276          3.083
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    Q     276      H     280          2.019
LGA    G     277      D     281          3.050
LGA    F     278      S     282          3.050
LGA    Y     279      L     283           -
LGA    H     280      -       -           -
LGA    D     281      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   38   60    5.0     20    2.79     0.00     23.124     0.692

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.897957 * X  +  -0.131874 * Y  +  -0.419861 * Z  +  83.626648
  Y_new =  -0.385858 * X  +  -0.694711 * Y  +  -0.607034 * Z  +  97.203423
  Z_new =  -0.211630 * X  +   0.707097 * Y  +  -0.674705 * Z  + -39.973682 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.332757   -0.808836  [ DEG:   133.6571    -46.3429 ]
  Theta =   0.213243    2.928350  [ DEG:    12.2179    167.7821 ]
  Phi   =  -0.405851    2.735742  [ DEG:   -23.2535    156.7465 ]
 
# 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: T0316AL381_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL381_5-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38   60   5.0   20   2.79    0.00  23.124
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL381_5-D2
REMARK Aligment from pdb entry: 1korA
ATOM    697  N   GLY   220      34.581  31.444 -48.597  1.00  0.00              
ATOM    698  CA  GLY   220      34.321  30.050 -48.892  1.00  0.00              
ATOM    699  C   GLY   220      35.443  29.068 -48.619  1.00  0.00              
ATOM    700  O   GLY   220      35.254  27.860 -48.754  1.00  0.00              
ATOM    701  N   ARG   221      36.612  29.556 -48.231  1.00  0.00              
ATOM    702  CA  ARG   221      37.723  28.648 -47.959  1.00  0.00              
ATOM    703  C   ARG   221      37.440  27.694 -46.807  1.00  0.00              
ATOM    704  O   ARG   221      37.726  26.506 -46.894  1.00  0.00              
ATOM    705  N   MET   222      36.880  28.211 -45.720  1.00  0.00              
ATOM    706  CA  MET   222      36.608  27.370 -44.562  1.00  0.00              
ATOM    707  C   MET   222      35.613  26.261 -44.856  1.00  0.00              
ATOM    708  O   MET   222      34.651  26.450 -45.598  1.00  0.00              
ATOM    709  N   MET   223      35.852  25.104 -44.253  1.00  0.00              
ATOM    710  CA  MET   223      35.006  23.946 -44.468  1.00  0.00              
ATOM    711  C   MET   223      34.468  23.340 -43.178  1.00  0.00              
ATOM    712  O   MET   223      33.370  22.778 -43.155  1.00  0.00              
ATOM    713  N   THR   224      35.236  23.459 -42.098  1.00  0.00              
ATOM    714  CA  THR   224      34.824  22.891 -40.828  1.00  0.00              
ATOM    715  C   THR   224      33.917  23.804 -40.018  1.00  0.00              
ATOM    716  O   THR   224      33.127  23.335 -39.203  1.00  0.00              
ATOM    717  N   ILE   249      34.033  25.107 -40.224  1.00  0.00              
ATOM    718  CA  ILE   249      33.193  26.038 -39.493  1.00  0.00              
ATOM    719  C   ILE   249      32.340  26.843 -40.455  1.00  0.00              
ATOM    720  O   ILE   249      32.755  27.137 -41.574  1.00  0.00              
ATOM    721  N   GLY   250      31.140  27.174 -40.001  1.00  0.00              
ATOM    722  CA  GLY   250      30.188  27.971 -40.763  1.00  0.00              
ATOM    723  C   GLY   250      30.677  29.410 -40.730  1.00  0.00              
ATOM    724  O   GLY   250      31.240  29.844 -39.730  1.00  0.00              
ATOM    725  N   GLY   251      30.471  30.146 -41.816  1.00  0.00              
ATOM    726  CA  GLY   251      30.856  31.558 -41.868  1.00  0.00              
ATOM    727  C   GLY   251      30.038  32.276 -40.786  1.00  0.00              
ATOM    728  O   GLY   251      28.816  32.146 -40.740  1.00  0.00              
ATOM    729  N   GLN   252      30.703  33.029 -39.893  1.00  0.00              
ATOM    730  CA  GLN   252      30.010  33.751 -38.821  1.00  0.00              
ATOM    731  C   GLN   252      28.833  34.591 -39.317  1.00  0.00              
ATOM    732  O   GLN   252      27.845  34.775 -38.607  1.00  0.00              
ATOM    733  N   HIS   253      28.944  35.100 -40.538  1.00  0.00              
ATOM    734  CA  HIS   253      27.877  35.915 -41.096  1.00  0.00              
ATOM    735  C   HIS   253      26.680  35.056 -41.478  1.00  0.00              
ATOM    736  O   HIS   253      25.608  35.582 -41.766  1.00  0.00              
ATOM    737  N   GLY   254      26.870  33.737 -41.460  1.00  0.00              
ATOM    738  CA  GLY   254      25.817  32.780 -41.801  1.00  0.00              
ATOM    739  C   GLY   254      25.437  31.894 -40.607  1.00  0.00              
ATOM    740  O   GLY   254      24.665  30.943 -40.745  1.00  0.00              
ATOM    741  N   GLY   255      25.987  32.196 -39.440  1.00  0.00              
ATOM    742  CA  GLY   255      25.699  31.415 -38.237  1.00  0.00              
ATOM    743  C   GLY   255      24.284  31.696 -37.718  1.00  0.00              
ATOM    744  O   GLY   255      23.673  32.706 -38.069  1.00  0.00              
ATOM    745  N   ASP   256      23.747  30.795 -36.874  1.00  0.00              
ATOM    746  CA  ASP   256      22.400  30.968 -36.323  1.00  0.00              
ATOM    747  C   ASP   256      22.183  32.353 -35.716  1.00  0.00              
ATOM    748  O   ASP   256      23.106  32.952 -35.145  1.00  0.00              
ATOM    749  N   ASN   257      20.957  32.854 -35.842  1.00  0.00              
ATOM    750  CA  ASN   257      20.609  34.161 -35.306  1.00  0.00              
ATOM    751  C   ASN   257      20.402  34.155 -33.798  1.00  0.00              
ATOM    752  O   ASN   257      20.304  35.211 -33.179  1.00  0.00              
ATOM    753  N   ALA   258      20.327  32.972 -33.202  1.00  0.00              
ATOM    754  CA  ALA   258      20.149  32.870 -31.760  1.00  0.00              
ATOM    755  C   ALA   258      21.396  32.233 -31.162  1.00  0.00              
ATOM    756  O   ALA   258      22.001  31.359 -31.772  1.00  0.00              
ATOM    757  N   PRO   259      21.802  32.674 -29.967  1.00  0.00              
ATOM    758  CA  PRO   259      22.993  32.078 -29.356  1.00  0.00              
ATOM    759  C   PRO   259      22.650  30.686 -28.838  1.00  0.00              
ATOM    760  O   PRO   259      21.481  30.387 -28.584  1.00  0.00              
ATOM    761  N   TRP   260      23.659  29.834 -28.691  1.00  0.00              
ATOM    762  CA  TRP   260      23.448  28.487 -28.182  1.00  0.00              
ATOM    763  C   TRP   260      24.319  28.266 -26.958  1.00  0.00              
ATOM    764  O   TRP   260      25.504  28.617 -26.956  1.00  0.00              
ATOM    765  N   PHE   261      23.719  27.698 -25.916  1.00  0.00              
ATOM    766  CA  PHE   261      24.434  27.398 -24.685  1.00  0.00              
ATOM    767  C   PHE   261      24.906  25.955 -24.715  1.00  0.00              
ATOM    768  O   PHE   261      24.213  25.072 -25.219  1.00  0.00              
ATOM    769  N   VAL   262      26.088  25.714 -24.163  1.00  0.00              
ATOM    770  CA  VAL   262      26.642  24.372 -24.109  1.00  0.00              
ATOM    771  C   VAL   262      27.360  24.227 -22.780  1.00  0.00              
ATOM    772  O   VAL   262      27.950  25.181 -22.286  1.00  0.00              
ATOM    773  N   VAL   263      27.281  23.042 -22.194  1.00  0.00              
ATOM    774  CA  VAL   263      27.971  22.780 -20.941  1.00  0.00              
ATOM    775  C   VAL   263      28.979  21.673 -21.183  1.00  0.00              
ATOM    776  O   VAL   263      28.703  20.724 -21.908  1.00  0.00              
ATOM    777  N   GLY   264      30.156  21.805 -20.584  1.00  0.00              
ATOM    778  CA  GLY   264      31.188  20.793 -20.738  1.00  0.00              
ATOM    779  C   GLY   264      31.697  20.399 -19.368  1.00  0.00              
ATOM    780  O   GLY   264      32.121  21.257 -18.588  1.00  0.00              
ATOM    781  N   LYS   265      31.639  19.104 -19.078  1.00  0.00              
ATOM    782  CA  LYS   265      32.097  18.580 -17.797  1.00  0.00              
ATOM    783  C   LYS   265      33.508  18.016 -17.910  1.00  0.00              
ATOM    784  O   LYS   265      33.824  17.307 -18.865  1.00  0.00              
ATOM    785  N   ASP   266      34.339  18.336 -16.922  1.00  0.00              
ATOM    786  CA  ASP   266      35.711  17.853 -16.854  1.00  0.00              
ATOM    787  C   ASP   266      35.816  16.978 -15.619  1.00  0.00              
ATOM    788  O   ASP   266      35.205  17.286 -14.592  1.00  0.00              
ATOM    789  N   LEU   267      36.567  15.886 -15.699  1.00  0.00              
ATOM    790  CA  LEU   267      36.713  15.064 -14.513  1.00  0.00              
ATOM    791  C   LEU   267      38.182  14.685 -14.505  1.00  0.00              
ATOM    792  O   LEU   267      38.599  13.821 -15.266  1.00  0.00              
ATOM    793  N   SER   268      38.989  15.288 -13.654  1.00  0.00              
ATOM    794  CA  SER   268      40.401  14.908 -13.672  1.00  0.00              
ATOM    795  C   SER   268      41.347  15.489 -14.698  1.00  0.00              
ATOM    796  O   SER   268      42.380  14.909 -15.001  1.00  0.00              
ATOM    797  N   LYS   269      40.964  16.642 -15.243  1.00  0.00              
ATOM    798  CA  LYS   269      41.772  17.302 -16.247  1.00  0.00              
ATOM    799  C   LYS   269      41.283  17.088 -17.672  1.00  0.00              
ATOM    800  O   LYS   269      41.697  17.800 -18.580  1.00  0.00              
ATOM    801  N   ASN   270      40.398  16.115 -17.873  1.00  0.00              
ATOM    802  CA  ASN   270      39.881  15.834 -19.213  1.00  0.00              
ATOM    803  C   ASN   270      38.370  15.999 -19.312  1.00  0.00              
ATOM    804  O   ASN   270      37.649  15.717 -18.355  1.00  0.00              
ATOM    805  N   ILE   271      37.872  16.459 -20.477  1.00  0.00              
ATOM    806  CA  ILE   271      36.429  16.647 -20.680  1.00  0.00              
ATOM    807  C   ILE   271      35.781  15.272 -20.847  1.00  0.00              
ATOM    808  O   ILE   271      36.254  14.451 -21.634  1.00  0.00              
ATOM    809  N   LEU   272      34.714  15.013 -20.097  1.00  0.00              
ATOM    810  CA  LEU   272      34.054  13.715 -20.158  1.00  0.00              
ATOM    811  C   LEU   272      32.591  13.724 -20.572  1.00  0.00              
ATOM    812  O   LEU   272      32.020  12.668 -20.813  1.00  0.00              
ATOM    813  N   TYR   273      31.985  14.904 -20.648  1.00  0.00              
ATOM    814  CA  TYR   273      30.581  15.005 -21.025  1.00  0.00              
ATOM    815  C   TYR   273      30.253  16.341 -21.676  1.00  0.00              
ATOM    816  O   TYR   273      30.913  17.347 -21.422  1.00  0.00              
ATOM    817  N   VAL   274      29.227  16.334 -22.524  1.00  0.00              
ATOM    818  CA  VAL   274      28.769  17.540 -23.203  1.00  0.00              
ATOM    819  C   VAL   274      27.253  17.582 -23.042  1.00  0.00              
ATOM    820  O   VAL   274      26.552  16.652 -23.433  1.00  0.00              
ATOM    821  N   GLY   275      26.759  18.663 -22.452  1.00  0.00              
ATOM    822  CA  GLY   275      25.331  18.831 -22.209  1.00  0.00              
ATOM    823  C   GLY   275      24.767  17.664 -21.416  1.00  0.00              
ATOM    824  O   GLY   275      23.654  17.213 -21.666  1.00  0.00              
ATOM    825  N   GLN   276      25.548  17.172 -20.461  1.00  0.00              
ATOM    826  CA  GLN   276      25.096  16.069 -19.636  1.00  0.00              
ATOM    827  C   GLN   276      25.266  14.685 -20.238  1.00  0.00              
ATOM    828  O   GLN   276      25.001  13.684 -19.573  1.00  0.00              
ATOM    829  N   GLY   277      25.700  14.602 -21.490  1.00  0.00              
ATOM    830  CA  GLY   277      25.887  13.293 -22.105  1.00  0.00              
ATOM    831  C   GLY   277      27.350  12.856 -22.044  1.00  0.00              
ATOM    832  O   GLY   277      28.236  13.551 -22.555  1.00  0.00              
ATOM    833  N   PHE   278      27.610  11.720 -21.404  1.00  0.00              
ATOM    834  CA  PHE   278      28.975  11.223 -21.328  1.00  0.00              
ATOM    835  C   PHE   278      29.410  10.753 -22.719  1.00  0.00              
ATOM    836  O   PHE   278      28.686  10.025 -23.396  1.00  0.00              
ATOM    837  N   TYR   279      30.591  11.195 -23.147  1.00  0.00              
ATOM    838  CA  TYR   279      31.116  10.852 -24.471  1.00  0.00              
ATOM    839  C   TYR   279      32.595  10.473 -24.452  1.00  0.00              
ATOM    840  O   TYR   279      33.386  11.067 -23.718  1.00  0.00              
ATOM    841  N   HIS   280      32.962   9.489 -25.272  1.00  0.00              
ATOM    842  CA  HIS   280      34.349   9.050 -25.369  1.00  0.00              
ATOM    843  C   HIS   280      35.150  10.219 -25.941  1.00  0.00              
ATOM    844  O   HIS   280      34.584  11.121 -26.569  1.00  0.00              
ATOM    845  N   ASP   281      36.477  10.219 -25.728  1.00  0.00              
ATOM    846  CA  ASP   281      37.345  11.288 -26.227  1.00  0.00              
ATOM    847  C   ASP   281      37.058  11.745 -27.659  1.00  0.00              
ATOM    848  O   ASP   281      36.771  12.920 -27.886  1.00  0.00              
END
