
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0299AL381_4-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299AL381_4-D2.T0299_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    -       -      L      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      F      82           -
LGA    -       -      E      83           -
LGA    -       -      A      84           -
LGA    -       -      E      85           -
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    -       -      N      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      A      91           -
LGA    -       -      W      92           -
LGA    -       -      W      93           -
LGA    -       -      S      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      R      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    -       -      F     102           -
LGA    L      79      L     103          4.490
LGA    E      80      F     104          3.110
LGA    D      81      Y     105          2.630
LGA    F      82      T     106          2.667
LGA    E      83      -       -           -
LGA    A      84      -       -           -
LGA    E      85      E     107          1.649
LGA    L      86      G     108          1.690
LGA    E      87      -       -           -
LGA    N      88      -       -           -
LGA    L      89      -       -           -
LGA    A      98      -       -           -
LGA    R      99      L     109           #
LGA    K     100      D     110          4.172
LGA    D     101      V     111          3.298
LGA    F     102      D     112          1.936
LGA    -       -      Q     113           -
LGA    L     103      V     114          1.920
LGA    F     104      I     115          2.989
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    Y     105      V     118          0.378
LGA    T     106      E     119          3.639
LGA    -       -      S     120           -
LGA    -       -      L     121           -
LGA    E     107      E     122          4.225
LGA    G     108      L     123          1.884
LGA    L     109      K     124          3.309
LGA    -       -      D     125           -
LGA    D     110      E     126          3.372
LGA    V     111      V     127          3.166
LGA    D     112      L     128           -
LGA    Q     113      Y     129           -
LGA    V     114      F     130           -
LGA    -       -      G     131           -
LGA    -       -      K     132           -
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      W     137           -
LGA    -       -      G     138           -
LGA    I     115      K     139          3.431
LGA    A     116      F     140          4.947
LGA    -       -      S     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    T     117      S     144          0.957
LGA    -       -      Y     145           -
LGA    -       -      S     146           -
LGA    -       -      K     147           -
LGA    -       -      T     148           -
LGA    -       -      A     149           -
LGA    -       -      Y     150           -
LGA    -       -      H     151           -
LGA    -       -      K     152           -
LGA    -       -      Y     153           -
LGA    -       -      L     154           -
LGA    -       -      L     155           -
LGA    -       -      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    -       -      F     159           -
LGA    -       -      Y     160           -
LGA    -       -      R     161           -
LGA    -       -      H     162           -
LGA    -       -      I     163           -
LGA    -       -      T     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      N     167           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   31   89    5.0     21    3.07    19.05     13.715     0.662

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.189887 * X  +  -0.710791 * Y  +  -0.677288 * Z  +  69.963654
  Y_new =  -0.254511 * X  +   0.630621 * Y  +  -0.733172 * Z  +  36.084469
  Z_new =   0.948244 * X  +   0.311597 * Y  +  -0.061158 * Z  + -80.080933 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.764604   -1.376989  [ DEG:   101.1044    -78.8956 ]
  Theta =  -1.247660   -1.893933  [ DEG:   -71.4856   -108.5144 ]
  Phi   =  -0.929806    2.211787  [ DEG:   -53.2739    126.7261 ]
 
# 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: T0299AL381_4-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_4-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31   89   5.0   21   3.07   19.05  13.715
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_4-D2
REMARK Aligment from pdb entry: 1z5oA
ATOM    185  N   LEU    79       6.440  53.895   1.081  1.00  0.00              
ATOM    186  CA  LEU    79       5.845  54.740   2.102  1.00  0.00              
ATOM    187  C   LEU    79       4.326  54.825   2.126  1.00  0.00              
ATOM    188  O   LEU    79       3.724  54.548   3.161  1.00  0.00              
ATOM    189  N   GLU    80       3.696  55.214   1.017  1.00  0.00              
ATOM    190  CA  GLU    80       2.238  55.346   1.017  1.00  0.00              
ATOM    191  C   GLU    80       1.478  54.034   1.274  1.00  0.00              
ATOM    192  O   GLU    80       0.378  54.063   1.794  1.00  0.00              
ATOM    193  N   ASP    81       2.060  52.891   0.905  1.00  0.00              
ATOM    194  CA  ASP    81       1.413  51.597   1.133  1.00  0.00              
ATOM    195  C   ASP    81       1.468  51.292   2.634  1.00  0.00              
ATOM    196  O   ASP    81       0.509  50.771   3.219  1.00  0.00              
ATOM    197  N   PHE    82       2.594  51.647   3.248  1.00  0.00              
ATOM    198  CA  PHE    82       2.797  51.453   4.673  1.00  0.00              
ATOM    199  C   PHE    82       1.858  52.389   5.454  1.00  0.00              
ATOM    200  O   PHE    82       1.217  51.978   6.431  1.00  0.00              
ATOM    201  N   GLU    83       1.780  53.644   5.024  1.00  0.00              
ATOM    202  CA  GLU    83       0.907  54.615   5.676  1.00  0.00              
ATOM    203  C   GLU    83      -0.557  54.178   5.525  1.00  0.00              
ATOM    204  O   GLU    83      -1.352  54.352   6.435  1.00  0.00              
ATOM    205  N   ALA    84      -0.893  53.598   4.375  1.00  0.00              
ATOM    206  CA  ALA    84      -2.253  53.134   4.067  1.00  0.00              
ATOM    207  C   ALA    84      -2.624  52.008   5.041  1.00  0.00              
ATOM    208  O   ALA    84      -3.681  52.026   5.683  1.00  0.00              
ATOM    209  N   GLU    85      -1.737  51.035   5.169  1.00  0.00              
ATOM    210  CA  GLU    85      -1.975  49.941   6.095  1.00  0.00              
ATOM    211  C   GLU    85      -2.102  50.491   7.525  1.00  0.00              
ATOM    212  O   GLU    85      -3.022  50.125   8.242  1.00  0.00              
ATOM    213  N   LEU    86      -1.180  51.374   7.923  1.00  0.00              
ATOM    214  CA  LEU    86      -1.186  51.950   9.272  1.00  0.00              
ATOM    215  C   LEU    86      -2.468  52.706   9.565  1.00  0.00              
ATOM    216  O   LEU    86      -3.003  52.640  10.673  1.00  0.00              
ATOM    217  N   GLU    87      -2.944  53.438   8.567  1.00  0.00              
ATOM    218  CA  GLU    87      -4.180  54.204   8.674  1.00  0.00              
ATOM    219  C   GLU    87      -5.345  53.257   8.983  1.00  0.00              
ATOM    220  O   GLU    87      -6.163  53.524   9.863  1.00  0.00              
ATOM    221  N   ASN    88      -5.405  52.142   8.259  1.00  0.00              
ATOM    222  CA  ASN    88      -6.488  51.185   8.455  1.00  0.00              
ATOM    223  C   ASN    88      -6.476  50.491   9.812  1.00  0.00              
ATOM    224  O   ASN    88      -7.499  49.960  10.245  1.00  0.00              
ATOM    225  N   LEU    89      -5.326  50.504  10.477  1.00  0.00              
ATOM    226  CA  LEU    89      -5.180  49.887  11.793  1.00  0.00              
ATOM    227  C   LEU    89      -5.000  50.941  12.878  1.00  0.00              
ATOM    228  O   LEU    89      -4.798  50.623  14.055  1.00  0.00              
ATOM    229  N   ALA    98      -5.054  52.199  12.466  1.00  0.00              
ATOM    230  CA  ALA    98      -4.898  53.310  13.383  1.00  0.00              
ATOM    231  C   ALA    98      -3.569  53.306  14.129  1.00  0.00              
ATOM    232  O   ALA    98      -3.533  53.497  15.348  1.00  0.00              
ATOM    233  N   ARG    99      -2.485  53.071  13.393  1.00  0.00              
ATOM    234  CA  ARG    99      -1.138  53.064  13.965  1.00  0.00              
ATOM    235  C   ARG    99      -0.360  54.291  13.460  1.00  0.00              
ATOM    236  O   ARG    99      -0.311  54.561  12.247  1.00  0.00              
ATOM    237  N   LYS   100       0.230  55.071  14.382  1.00  0.00              
ATOM    238  CA  LYS   100       1.004  56.260  14.002  1.00  0.00              
ATOM    239  C   LYS   100       2.216  55.820  13.180  1.00  0.00              
ATOM    240  O   LYS   100       2.845  54.800  13.508  1.00  0.00              
ATOM    241  N   ASP   101       2.547  56.589  12.140  1.00  0.00              
ATOM    242  CA  ASP   101       3.694  56.291  11.285  1.00  0.00              
ATOM    243  C   ASP   101       4.401  57.577  10.884  1.00  0.00              
ATOM    244  O   ASP   101       3.831  58.667  10.943  1.00  0.00              
ATOM    245  N   PHE   102       5.643  57.432  10.444  1.00  0.00              
ATOM    246  CA  PHE   102       6.422  58.555   9.958  1.00  0.00              
ATOM    247  C   PHE   102       7.458  57.943   9.015  1.00  0.00              
ATOM    248  O   PHE   102       7.946  56.837   9.251  1.00  0.00              
ATOM    249  N   LEU   103       7.753  58.653   7.931  1.00  0.00              
ATOM    250  CA  LEU   103       8.738  58.217   6.958  1.00  0.00              
ATOM    251  C   LEU   103       9.993  59.051   7.206  1.00  0.00              
ATOM    252  O   LEU   103       9.918  60.277   7.280  1.00  0.00              
ATOM    253  N   PHE   104      11.132  58.382   7.382  1.00  0.00              
ATOM    254  CA  PHE   104      12.407  59.069   7.577  1.00  0.00              
ATOM    255  C   PHE   104      13.419  58.364   6.679  1.00  0.00              
ATOM    256  O   PHE   104      14.042  57.378   7.076  1.00  0.00              
ATOM    257  N   TYR   105      13.559  58.858   5.459  1.00  0.00              
ATOM    258  CA  TYR   105      14.486  58.272   4.494  1.00  0.00              
ATOM    259  C   TYR   105      15.584  59.280   4.145  1.00  0.00              
ATOM    260  O   TYR   105      15.521  60.449   4.541  1.00  0.00              
ATOM    261  N   THR   106      16.589  58.816   3.406  1.00  0.00              
ATOM    262  CA  THR   106      17.690  59.673   2.978  1.00  0.00              
ATOM    263  C   THR   106      17.748  59.643   1.455  1.00  0.00              
ATOM    264  O   THR   106      17.339  58.663   0.836  1.00  0.00              
ATOM    265  N   GLU   107      18.274  60.714   0.868  1.00  0.00              
ATOM    266  CA  GLU   107      18.377  60.881  -0.580  1.00  0.00              
ATOM    267  C   GLU   107      19.569  60.146  -1.231  1.00  0.00              
ATOM    268  O   GLU   107      20.719  60.305  -0.814  1.00  0.00              
ATOM    269  N   GLY   108      19.288  59.354  -2.266  1.00  0.00              
ATOM    270  CA  GLY   108      20.330  58.616  -2.981  1.00  0.00              
ATOM    271  C   GLY   108      20.362  58.998  -4.459  1.00  0.00              
ATOM    272  O   GLY   108      21.202  58.514  -5.209  1.00  0.00              
ATOM    273  N   LEU   109      19.442  59.872  -4.866  1.00  0.00              
ATOM    274  CA  LEU   109      19.351  60.330  -6.250  1.00  0.00              
ATOM    275  C   LEU   109      18.273  61.405  -6.316  1.00  0.00              
ATOM    276  O   LEU   109      17.567  61.618  -5.331  1.00  0.00              
ATOM    277  N   ASP   110      18.154  62.079  -7.464  1.00  0.00              
ATOM    278  CA  ASP   110      17.142  63.117  -7.633  1.00  0.00              
ATOM    279  C   ASP   110      16.120  62.755  -8.697  1.00  0.00              
ATOM    280  O   ASP   110      15.582  63.608  -9.403  1.00  0.00              
ATOM    281  N   VAL   111      15.872  61.459  -8.810  1.00  0.00              
ATOM    282  CA  VAL   111      14.862  60.941  -9.717  1.00  0.00              
ATOM    283  C   VAL   111      14.915  61.418 -11.156  1.00  0.00              
ATOM    284  O   VAL   111      13.894  61.386 -11.838  1.00  0.00              
ATOM    285  N   ASP   112      16.079  61.869 -11.622  1.00  0.00              
ATOM    286  CA  ASP   112      16.200  62.321 -13.016  1.00  0.00              
ATOM    287  C   ASP   112      16.841  61.202 -13.850  1.00  0.00              
ATOM    288  O   ASP   112      16.963  60.066 -13.375  1.00  0.00              
ATOM    289  N   GLN   113      17.268  61.510 -15.073  1.00  0.00              
ATOM    290  CA  GLN   113      17.848  60.480 -15.926  1.00  0.00              
ATOM    291  C   GLN   113      19.139  59.855 -15.393  1.00  0.00              
ATOM    292  O   GLN   113      19.561  58.819 -15.877  1.00  0.00              
ATOM    293  N   VAL   114      19.743  60.476 -14.389  1.00  0.00              
ATOM    294  CA  VAL   114      20.965  59.964 -13.773  1.00  0.00              
ATOM    295  C   VAL   114      20.621  59.186 -12.502  1.00  0.00              
ATOM    296  O   VAL   114      21.511  58.711 -11.799  1.00  0.00              
ATOM    297  N   ILE   115      19.330  59.048 -12.211  1.00  0.00              
ATOM    298  CA  ILE   115      18.908  58.378 -10.982  1.00  0.00              
ATOM    299  C   ILE   115      19.469  56.974 -10.734  1.00  0.00              
ATOM    300  O   ILE   115      19.815  56.655  -9.598  1.00  0.00              
ATOM    301  N   ALA   116      19.558  56.133 -11.762  1.00  0.00              
ATOM    302  CA  ALA   116      20.096  54.784 -11.565  1.00  0.00              
ATOM    303  C   ALA   116      21.609  54.846 -11.247  1.00  0.00              
ATOM    304  O   ALA   116      22.086  54.191 -10.320  1.00  0.00              
ATOM    305  N   THR   117      22.356  55.630 -12.018  1.00  0.00              
ATOM    306  CA  THR   117      23.785  55.803 -11.756  1.00  0.00              
ATOM    307  C   THR   117      23.976  56.286 -10.309  1.00  0.00              
ATOM    308  O   THR   117      24.796  55.748  -9.557  1.00  0.00              
END
