
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0299AL381_5-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299AL381_5-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    L      79      D     101           #
LGA    E      80      F     102          4.643
LGA    D      81      L     103          2.800
LGA    F      82      F     104           #
LGA    E      83      -       -           -
LGA    A      84      Y     105          1.032
LGA    E      85      T     106          1.878
LGA    L      86      -       -           -
LGA    E      87      -       -           -
LGA    N      88      E     107          0.882
LGA    L      89      G     108          0.676
LGA    A      98      L     109          4.579
LGA    R      99      D     110          2.013
LGA    K     100      V     111          2.948
LGA    D     101      D     112          2.964
LGA    -       -      Q     113           -
LGA    -       -      V     114           -
LGA    F     102      I     115          0.628
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    L     103      V     118          2.193
LGA    F     104      E     119          1.286
LGA    -       -      S     120           -
LGA    Y     105      L     121          2.348
LGA    T     106      E     122          1.071
LGA    E     107      L     123          1.966
LGA    G     108      K     124          2.130
LGA    L     109      D     125          2.239
LGA    D     110      -       -           -
LGA    V     111      E     126          5.161
LGA    -       -      V     127           -
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      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    -       -      K     139           -
LGA    -       -      F     140           -
LGA    D     112      S     141          3.663
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    -       -      S     144           -
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)   26   89    5.0     20    2.69     5.00     15.687     0.717

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.166751 * X  +  -0.773900 * Y  +  -0.610960 * Z  +  78.186172
  Y_new =  -0.026838 * X  +   0.615843 * Y  +  -0.787411 * Z  +  25.503637
  Z_new =   0.985634 * X  +   0.147699 * Y  +   0.081923 * Z  + -74.523903 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.064383   -2.077210  [ DEG:    60.9846   -119.0154 ]
  Theta =  -1.401085   -1.740507  [ DEG:   -80.2763    -99.7237 ]
  Phi   =  -0.159579    2.982014  [ DEG:    -9.1432    170.8568 ]
 
# 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_5-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_5-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26   89   5.0   20   2.69    5.00  15.687
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_5-D2
REMARK Aligment from pdb entry: 1z5nA
ATOM    185  N   LEU    79      10.537  53.665  -0.539  1.00  0.00              
ATOM    186  CA  LEU    79       9.853  54.704   0.206  1.00  0.00              
ATOM    187  C   LEU    79       8.320  54.665   0.197  1.00  0.00              
ATOM    188  O   LEU    79       7.691  54.608   1.270  1.00  0.00              
ATOM    189  N   GLU    80       7.708  54.656  -0.983  1.00  0.00              
ATOM    190  CA  GLU    80       6.250  54.687  -1.042  1.00  0.00              
ATOM    191  C   GLU    80       5.558  53.444  -0.505  1.00  0.00              
ATOM    192  O   GLU    80       4.431  53.524   0.003  1.00  0.00              
ATOM    193  N   ASP    81       6.229  52.298  -0.615  1.00  0.00              
ATOM    194  CA  ASP    81       5.686  51.061  -0.108  1.00  0.00              
ATOM    195  C   ASP    81       5.711  51.128   1.435  1.00  0.00              
ATOM    196  O   ASP    81       4.788  50.671   2.108  1.00  0.00              
ATOM    197  N   PHE    82       6.779  51.686   1.992  1.00  0.00              
ATOM    198  CA  PHE    82       6.875  51.798   3.446  1.00  0.00              
ATOM    199  C   PHE    82       5.805  52.793   3.929  1.00  0.00              
ATOM    200  O   PHE    82       5.158  52.586   4.961  1.00  0.00              
ATOM    201  N   GLU    83       5.613  53.861   3.158  1.00  0.00              
ATOM    202  CA  GLU    83       4.632  54.889   3.485  1.00  0.00              
ATOM    203  C   GLU    83       3.215  54.314   3.408  1.00  0.00              
ATOM    204  O   GLU    83       2.353  54.616   4.230  1.00  0.00              
ATOM    205  N   ALA    84       2.995  53.471   2.409  1.00  0.00              
ATOM    206  CA  ALA    84       1.702  52.836   2.194  1.00  0.00              
ATOM    207  C   ALA    84       1.374  51.920   3.390  1.00  0.00              
ATOM    208  O   ALA    84       0.255  51.956   3.918  1.00  0.00              
ATOM    209  N   GLU    85       2.349  51.114   3.813  1.00  0.00              
ATOM    210  CA  GLU    85       2.137  50.229   4.960  1.00  0.00              
ATOM    211  C   GLU    85       1.916  51.020   6.254  1.00  0.00              
ATOM    212  O   GLU    85       1.005  50.696   7.035  1.00  0.00              
ATOM    213  N   LEU    86       2.720  52.063   6.481  1.00  0.00              
ATOM    214  CA  LEU    86       2.584  52.873   7.706  1.00  0.00              
ATOM    215  C   LEU    86       1.235  53.567   7.725  1.00  0.00              
ATOM    216  O   LEU    86       0.629  53.750   8.801  1.00  0.00              
ATOM    217  N   GLU    87       0.772  53.945   6.532  1.00  0.00              
ATOM    218  CA  GLU    87      -0.512  54.608   6.378  1.00  0.00              
ATOM    219  C   GLU    87      -1.594  53.675   6.880  1.00  0.00              
ATOM    220  O   GLU    87      -2.542  54.103   7.519  1.00  0.00              
ATOM    221  N   ASN    88      -1.445  52.390   6.572  1.00  0.00              
ATOM    222  CA  ASN    88      -2.410  51.388   6.975  1.00  0.00              
ATOM    223  C   ASN    88      -2.330  51.085   8.458  1.00  0.00              
ATOM    224  O   ASN    88      -3.326  50.713   9.073  1.00  0.00              
ATOM    225  N   LEU    89      -1.141  51.220   9.035  1.00  0.00              
ATOM    226  CA  LEU    89      -0.996  50.969  10.462  1.00  0.00              
ATOM    227  C   LEU    89      -1.094  52.273  11.241  1.00  0.00              
ATOM    228  O   LEU    89      -0.986  52.302  12.464  1.00  0.00              
ATOM    229  N   ALA    98      -1.304  53.362  10.503  1.00  0.00              
ATOM    230  CA  ALA    98      -1.436  54.672  11.117  1.00  0.00              
ATOM    231  C   ALA    98      -0.165  55.017  11.921  1.00  0.00              
ATOM    232  O   ALA    98      -0.234  55.537  13.035  1.00  0.00              
ATOM    233  N   ARG    99       1.004  54.720  11.337  1.00  0.00              
ATOM    234  CA  ARG    99       2.298  55.019  11.976  1.00  0.00              
ATOM    235  C   ARG    99       3.035  56.140  11.225  1.00  0.00              
ATOM    236  O   ARG    99       3.082  56.152  10.002  1.00  0.00              
ATOM    237  N   LYS   100       3.585  57.122  11.956  1.00  0.00              
ATOM    238  CA  LYS   100       4.305  58.225  11.293  1.00  0.00              
ATOM    239  C   LYS   100       5.599  57.780  10.629  1.00  0.00              
ATOM    240  O   LYS   100       6.346  56.986  11.200  1.00  0.00              
ATOM    241  N   ASP   101       5.870  58.288   9.427  1.00  0.00              
ATOM    242  CA  ASP   101       7.115  57.939   8.744  1.00  0.00              
ATOM    243  C   ASP   101       7.757  59.183   8.189  1.00  0.00              
ATOM    244  O   ASP   101       7.186  60.263   8.245  1.00  0.00              
ATOM    245  N   PHE   102       8.974  59.014   7.692  1.00  0.00              
ATOM    246  CA  PHE   102       9.731  60.064   7.038  1.00  0.00              
ATOM    247  C   PHE   102      10.860  59.333   6.325  1.00  0.00              
ATOM    248  O   PHE   102      11.365  58.329   6.824  1.00  0.00              
ATOM    249  N   LEU   103      11.227  59.844   5.151  1.00  0.00              
ATOM    250  CA  LEU   103      12.267  59.273   4.341  1.00  0.00              
ATOM    251  C   LEU   103      13.448  60.229   4.410  1.00  0.00              
ATOM    252  O   LEU   103      13.273  61.431   4.259  1.00  0.00              
ATOM    253  N   PHE   104      14.642  59.710   4.660  1.00  0.00              
ATOM    254  CA  PHE   104      15.821  60.551   4.722  1.00  0.00              
ATOM    255  C   PHE   104      16.867  59.763   3.977  1.00  0.00              
ATOM    256  O   PHE   104      17.388  58.779   4.494  1.00  0.00              
ATOM    257  N   TYR   105      17.138  60.170   2.739  1.00  0.00              
ATOM    258  CA  TYR   105      18.103  59.467   1.912  1.00  0.00              
ATOM    259  C   TYR   105      19.207  60.374   1.356  1.00  0.00              
ATOM    260  O   TYR   105      19.058  61.597   1.274  1.00  0.00              
ATOM    261  N   THR   106      20.329  59.755   1.003  1.00  0.00              
ATOM    262  CA  THR   106      21.456  60.477   0.428  1.00  0.00              
ATOM    263  C   THR   106      21.495  60.182  -1.071  1.00  0.00              
ATOM    264  O   THR   106      21.241  59.063  -1.481  1.00  0.00              
ATOM    265  N   GLU   107      21.850  61.181  -1.870  1.00  0.00              
ATOM    266  CA  GLU   107      21.912  61.044  -3.330  1.00  0.00              
ATOM    267  C   GLU   107      23.155  60.283  -3.807  1.00  0.00              
ATOM    268  O   GLU   107      24.277  60.570  -3.404  1.00  0.00              
ATOM    269  N   GLY   108      22.947  59.307  -4.679  1.00  0.00              
ATOM    270  CA  GLY   108      24.042  58.500  -5.197  1.00  0.00              
ATOM    271  C   GLY   108      24.297  58.703  -6.712  1.00  0.00              
ATOM    272  O   GLY   108      25.375  58.377  -7.221  1.00  0.00              
ATOM    273  N   LEU   109      23.308  59.249  -7.411  1.00  0.00              
ATOM    274  CA  LEU   109      23.395  59.463  -8.857  1.00  0.00              
ATOM    275  C   LEU   109      22.278  60.424  -9.250  1.00  0.00              
ATOM    276  O   LEU   109      21.556  60.934  -8.384  1.00  0.00              
ATOM    277  N   ASP   110      22.129  60.692 -10.540  1.00  0.00              
ATOM    278  CA  ASP   110      21.071  61.603 -10.967  1.00  0.00              
ATOM    279  C   ASP   110      20.106  60.951 -11.942  1.00  0.00              
ATOM    280  O   ASP   110      19.452  61.612 -12.749  1.00  0.00              
ATOM    281  N   VAL   111      20.050  59.632 -11.876  1.00  0.00              
ATOM    282  CA  VAL   111      19.142  58.844 -12.682  1.00  0.00              
ATOM    283  C   VAL   111      19.251  58.945 -14.196  1.00  0.00              
ATOM    284  O   VAL   111      18.278  58.677 -14.897  1.00  0.00              
ATOM    285  N   ASP   112      20.415  59.310 -14.716  1.00  0.00              
ATOM    286  CA  ASP   112      20.583  59.395 -16.174  1.00  0.00              
ATOM    287  C   ASP   112      21.294  58.141 -16.724  1.00  0.00              
ATOM    288  O   ASP   112      21.386  57.108 -16.040  1.00  0.00              
END
