
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0299AL586_1-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299AL586_1-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      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     103           -
LGA    -       -      F     104           -
LGA    -       -      Y     105           -
LGA    -       -      T     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      L     109           -
LGA    -       -      D     110           -
LGA    -       -      V     111           -
LGA    -       -      D     112           -
LGA    -       -      Q     113           -
LGA    -       -      V     114           -
LGA    -       -      I     115           -
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    D      81      V     118           #
LGA    E      83      E     119          3.393
LGA    A      84      S     120          1.920
LGA    E      85      L     121           #
LGA    L      86      -       -           -
LGA    E      87      -       -           -
LGA    A      91      E     122           #
LGA    W      92      L     123           -
LGA    R      95      K     124           -
LGA    D      96      D     125           -
LGA    -       -      E     126           -
LGA    -       -      V     127           -
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      F     130           -
LGA    L      97      G     131           #
LGA    -       -      K     132           -
LGA    A      98      L     133          4.883
LGA    R      99      G     134          1.672
LGA    K     100      I     135          1.479
LGA    D     101      F     136          1.047
LGA    F     102      W     137          0.138
LGA    L     103      G     138          0.752
LGA    F     104      K     139          0.953
LGA    Y     105      F     140          2.793
LGA    T     106      S     141           -
LGA    E     107      E     142           -
LGA    L     109      E     143           -
LGA    -       -      S     144           -
LGA    -       -      Y     145           -
LGA    -       -      S     146           -
LGA    -       -      K     147           -
LGA    D     112      T     148          2.965
LGA    V     114      A     149          2.168
LGA    I     115      Y     150          1.779
LGA    -       -      H     151           -
LGA    -       -      K     152           -
LGA    -       -      Y     153           -
LGA    T     117      L     154          2.139
LGA    V     118      L     155          2.285
LGA    -       -      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    E     126      F     159          2.098
LGA    -       -      Y     160           -
LGA    -       -      R     161           -
LGA    G     131      H     162          4.678
LGA    K     132      I     163          3.451
LGA    L     133      T     164           #
LGA    G     134      I     165          5.096
LGA    I     135      -       -           -
LGA    F     136      -       -           -
LGA    W     137      -       -           -
LGA    S     144      -       -           -
LGA    S     146      -       -           -
LGA    T     148      -       -           -
LGA    Y     150      -       -           -
LGA    H     151      -       -           -
LGA    Y     153      -       -           -
LGA    K     156      -       -           -
LGA    V     157      R     166          2.570
LGA    P     158      N     167          2.339
LGA    F     159      -       -           -
LGA    Y     160      -       -           -
LGA    H     162      -       -           -
LGA    I     163      -       -           -
LGA    N     167      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   89    5.0     21    2.74     4.76     17.379     0.741

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.406528 * X  +   0.814330 * Y  +   0.414249 * Z  + -34.057438
  Y_new =  -0.757406 * X  +   0.553947 * Y  +  -0.345658 * Z  +  61.837086
  Z_new =  -0.510952 * X  +  -0.173235 * Y  +   0.841973 * Z  + -22.146645 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.202917    2.938676  [ DEG:   -11.6263    168.3737 ]
  Theta =   0.536291    2.605301  [ DEG:    30.7272    149.2728 ]
  Phi   =  -1.078192    2.063401  [ DEG:   -61.7759    118.2241 ]
 
# 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: T0299AL586_1-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL586_1-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   89   5.0   21   2.74    4.76  17.379
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL586_1-D2
REMARK Aligment from pdb entry: 1k66_A
ATOM     81  N   LEU    79      16.777  65.520  -3.202  1.00  0.00              
ATOM     82  CA  LEU    79      17.985  64.701  -3.218  1.00  0.00              
ATOM     83  C   LEU    79      17.790  63.377  -2.484  1.00  0.00              
ATOM     84  O   LEU    79      16.880  63.231  -1.671  1.00  0.00              
ATOM     85  N   ASP    81      18.265  63.850   1.235  1.00  0.00              
ATOM     86  CA  ASP    81      17.090  64.341   1.948  1.00  0.00              
ATOM     87  C   ASP    81      16.108  63.195   2.193  1.00  0.00              
ATOM     88  O   ASP    81      15.527  63.067   3.274  1.00  0.00              
ATOM     89  N   GLU    83      16.636  59.971   2.542  1.00  0.00              
ATOM     90  CA  GLU    83      17.090  59.099   3.622  1.00  0.00              
ATOM     91  C   GLU    83      16.966  59.780   4.987  1.00  0.00              
ATOM     92  O   GLU    83      16.509  59.172   5.949  1.00  0.00              
ATOM     93  N   ALA    84      17.352  61.049   5.060  1.00  0.00              
ATOM     94  CA  ALA    84      17.275  61.802   6.310  1.00  0.00              
ATOM     95  C   ALA    84      15.820  61.873   6.780  1.00  0.00              
ATOM     96  O   ALA    84      15.522  61.697   7.961  1.00  0.00              
ATOM     97  N   GLU    85      14.922  62.128   5.833  1.00  0.00              
ATOM     98  CA  GLU    85      13.488  62.241   6.079  1.00  0.00              
ATOM     99  C   GLU    85      12.907  60.913   6.595  1.00  0.00              
ATOM    100  O   GLU    85      12.196  60.885   7.603  1.00  0.00              
ATOM    101  N   LEU    86      13.229  59.815   5.918  1.00  0.00              
ATOM    102  CA  LEU    86      12.717  58.506   6.304  1.00  0.00              
ATOM    103  C   LEU    86      13.282  57.983   7.627  1.00  0.00              
ATOM    104  O   LEU    86      12.553  57.396   8.425  1.00  0.00              
ATOM    105  N   GLU    87      14.570  58.211   7.864  1.00  0.00              
ATOM    106  CA  GLU    87      15.210  57.759   9.098  1.00  0.00              
ATOM    107  C   GLU    87      15.056  58.759  10.234  1.00  0.00              
ATOM    108  O   GLU    87      15.445  58.478  11.371  1.00  0.00              
ATOM    109  N   ALA    91      19.495  66.890   7.714  1.00  0.00              
ATOM    110  CA  ALA    91      19.106  67.639   6.515  1.00  0.00              
ATOM    111  C   ALA    91      17.656  68.132   6.533  1.00  0.00              
ATOM    112  O   ALA    91      17.320  69.100   5.847  1.00  0.00              
ATOM    113  N   TRP    92      16.803  67.461   7.301  1.00  0.00              
ATOM    114  CA  TRP    92      15.387  67.821   7.388  1.00  0.00              
ATOM    115  C   TRP    92      14.920  67.735   8.842  1.00  0.00              
ATOM    116  O   TRP    92      15.291  66.809   9.561  1.00  0.00              
ATOM    117  N   ARG    95       6.590  63.378   8.653  1.00  0.00              
ATOM    118  CA  ARG    95       5.871  62.172   9.069  1.00  0.00              
ATOM    119  C   ARG    95       6.246  60.979   8.200  1.00  0.00              
ATOM    120  O   ARG    95       6.725  61.146   7.080  1.00  0.00              
ATOM    121  N   ASP    96       6.051  59.777   8.725  1.00  0.00              
ATOM    122  CA  ASP    96       6.358  58.573   7.969  1.00  0.00              
ATOM    123  C   ASP    96       5.335  58.470   6.840  1.00  0.00              
ATOM    124  O   ASP    96       4.125  58.540   7.074  1.00  0.00              
ATOM    125  N   LEU    97       5.805  58.322   5.594  1.00  0.00              
ATOM    126  CA  LEU    97       4.843  58.224   4.497  1.00  0.00              
ATOM    127  C   LEU    97       4.195  56.853   4.409  1.00  0.00              
ATOM    128  O   LEU    97       4.775  55.854   4.845  1.00  0.00              
ATOM    129  N   ALA    98       2.991  56.826   3.844  1.00  0.00              
ATOM    130  CA  ALA    98       2.242  55.588   3.651  1.00  0.00              
ATOM    131  C   ALA    98       2.681  54.960   2.332  1.00  0.00              
ATOM    132  O   ALA    98       2.614  53.743   2.158  1.00  0.00              
ATOM    133  N   ARG    99       3.113  55.806   1.400  1.00  0.00              
ATOM    134  CA  ARG    99       3.580  55.364   0.090  1.00  0.00              
ATOM    135  C   ARG    99       4.704  56.289  -0.362  1.00  0.00              
ATOM    136  O   ARG    99       4.695  57.482  -0.055  1.00  0.00              
ATOM    137  N   LYS   100       5.665  55.730  -1.090  1.00  0.00              
ATOM    138  CA  LYS   100       6.806  56.487  -1.594  1.00  0.00              
ATOM    139  C   LYS   100       6.889  56.408  -3.116  1.00  0.00              
ATOM    140  O   LYS   100       6.836  55.315  -3.687  1.00  0.00              
ATOM    141  N   ASP   101       6.999  57.567  -3.766  1.00  0.00              
ATOM    142  CA  ASP   101       7.149  57.637  -5.222  1.00  0.00              
ATOM    143  C   ASP   101       8.609  58.070  -5.352  1.00  0.00              
ATOM    144  O   ASP   101       8.980  59.168  -4.943  1.00  0.00              
ATOM    145  N   PHE   102       9.433  57.197  -5.917  1.00  0.00              
ATOM    146  CA  PHE   102      10.865  57.446  -6.002  1.00  0.00              
ATOM    147  C   PHE   102      11.501  57.396  -7.378  1.00  0.00              
ATOM    148  O   PHE   102      11.326  56.427  -8.105  1.00  0.00              
ATOM    149  N   LEU   103      12.249  58.439  -7.731  1.00  0.00              
ATOM    150  CA  LEU   103      12.955  58.444  -9.001  1.00  0.00              
ATOM    151  C   LEU   103      14.325  57.822  -8.729  1.00  0.00              
ATOM    152  O   LEU   103      14.938  58.085  -7.688  1.00  0.00              
ATOM    153  N   PHE   104      14.799  56.986  -9.648  1.00  0.00              
ATOM    154  CA  PHE   104      16.107  56.359  -9.485  1.00  0.00              
ATOM    155  C   PHE   104      17.215  57.383  -9.707  1.00  0.00              
ATOM    156  O   PHE   104      18.292  57.289  -9.112  1.00  0.00              
ATOM    157  N   TYR   105      16.944  58.365 -10.561  1.00  0.00              
ATOM    158  CA  TYR   105      17.921  59.404 -10.871  1.00  0.00              
ATOM    159  C   TYR   105      17.721  60.626  -9.979  1.00  0.00              
ATOM    160  O   TYR   105      16.738  61.357 -10.119  1.00  0.00              
ATOM    161  N   THR   106      18.662  60.846  -9.065  1.00  0.00              
ATOM    162  CA  THR   106      18.579  61.966  -8.133  1.00  0.00              
ATOM    163  C   THR   106      19.944  62.565  -7.851  1.00  0.00              
ATOM    164  O   THR   106      20.962  61.881  -7.946  1.00  0.00              
ATOM    165  N   GLU   107      19.982  63.861  -7.502  1.00  0.00              
ATOM    166  CA  GLU   107      21.261  64.507  -7.197  1.00  0.00              
ATOM    167  C   GLU   107      21.712  64.000  -5.826  1.00  0.00              
ATOM    168  O   GLU   107      20.881  63.602  -4.999  1.00  0.00              
ATOM    169  N   LEU   109      22.998  61.392  -3.267  1.00  0.00              
ATOM    170  CA  LEU   109      22.839  59.944  -3.250  1.00  0.00              
ATOM    171  C   LEU   109      21.671  59.676  -4.196  1.00  0.00              
ATOM    172  O   LEU   109      20.613  60.287  -4.063  1.00  0.00              
ATOM    173  N   ASP   112      18.705  54.742  -6.603  1.00  0.00              
ATOM    174  CA  ASP   112      19.060  53.329  -6.573  1.00  0.00              
ATOM    175  C   ASP   112      19.620  52.999  -5.197  1.00  0.00              
ATOM    176  O   ASP   112      19.257  51.991  -4.590  1.00  0.00              
ATOM    177  N   VAL   114      19.125  54.817  -2.478  1.00  0.00              
ATOM    178  CA  VAL   114      18.071  55.056  -1.494  1.00  0.00              
ATOM    179  C   VAL   114      17.228  53.794  -1.341  1.00  0.00              
ATOM    180  O   VAL   114      16.943  53.352  -0.231  1.00  0.00              
ATOM    181  N   ILE   115      16.826  53.218  -2.468  1.00  0.00              
ATOM    182  CA  ILE   115      16.010  52.011  -2.440  1.00  0.00              
ATOM    183  C   ILE   115      16.701  50.874  -1.695  1.00  0.00              
ATOM    184  O   ILE   115      16.091  50.213  -0.862  1.00  0.00              
ATOM    185  N   THR   117      16.646  51.513   2.077  1.00  0.00              
ATOM    186  CA  THR   117      15.284  51.369   2.582  1.00  0.00              
ATOM    187  C   THR   117      14.875  49.918   2.812  1.00  0.00              
ATOM    188  O   THR   117      14.317  49.581   3.855  1.00  0.00              
ATOM    189  N   VAL   118      15.158  49.070   1.832  1.00  0.00              
ATOM    190  CA  VAL   118      14.779  47.668   1.912  1.00  0.00              
ATOM    191  C   VAL   118      15.589  46.837   2.898  1.00  0.00              
ATOM    192  O   VAL   118      15.322  45.648   3.081  1.00  0.00              
ATOM    193  N   GLU   126      11.222  50.484   7.458  1.00  0.00              
ATOM    194  CA  GLU   126      11.053  51.143   6.170  1.00  0.00              
ATOM    195  C   GLU   126      10.808  50.200   4.993  1.00  0.00              
ATOM    196  O   GLU   126      10.158  50.583   4.025  1.00  0.00              
ATOM    197  N   GLY   131       7.189  49.936   3.658  1.00  0.00              
ATOM    198  CA  GLY   131       6.512  51.016   2.951  1.00  0.00              
ATOM    199  C   GLY   131       6.509  50.794   1.441  1.00  0.00              
ATOM    200  O   GLY   131       7.566  50.676   0.819  1.00  0.00              
ATOM    201  N   LYS   132       5.314  50.737   0.832  1.00  0.00              
ATOM    202  CA  LYS   132       5.234  50.530  -0.616  1.00  0.00              
ATOM    203  C   LYS   132       6.031  51.593  -1.364  1.00  0.00              
ATOM    204  O   LYS   132       5.843  52.792  -1.136  1.00  0.00              
ATOM    205  N   LEU   133       6.926  51.146  -2.238  1.00  0.00              
ATOM    206  CA  LEU   133       7.745  52.045  -3.043  1.00  0.00              
ATOM    207  C   LEU   133       7.405  51.878  -4.516  1.00  0.00              
ATOM    208  O   LEU   133       7.478  50.773  -5.064  1.00  0.00              
ATOM    209  N   GLY   134       7.015  52.977  -5.149  1.00  0.00              
ATOM    210  CA  GLY   134       6.705  52.955  -6.569  1.00  0.00              
ATOM    211  C   GLY   134       7.813  53.736  -7.260  1.00  0.00              
ATOM    212  O   GLY   134       8.047  54.904  -6.951  1.00  0.00              
ATOM    213  N   ILE   135       8.523  53.078  -8.167  1.00  0.00              
ATOM    214  CA  ILE   135       9.589  53.736  -8.902  1.00  0.00              
ATOM    215  C   ILE   135       8.966  54.492 -10.086  1.00  0.00              
ATOM    216  O   ILE   135       8.166  53.928 -10.824  1.00  0.00              
ATOM    217  N   PHE   136       9.287  55.775 -10.240  1.00  0.00              
ATOM    218  CA  PHE   136       8.783  56.541 -11.389  1.00  0.00              
ATOM    219  C   PHE   136       9.993  57.333 -11.856  1.00  0.00              
ATOM    220  O   PHE   136      10.438  58.279 -11.194  1.00  0.00              
ATOM    221  N   TRP   137      10.519  56.923 -13.006  1.00  0.00              
ATOM    222  CA  TRP   137      11.740  57.490 -13.549  1.00  0.00              
ATOM    223  C   TRP   137      11.731  57.492 -15.077  1.00  0.00              
ATOM    224  O   TRP   137      10.855  56.890 -15.698  1.00  0.00              
ATOM    225  N   SER   144      14.269  56.316 -16.671  1.00  0.00              
ATOM    226  CA  SER   144      15.054  55.133 -17.003  1.00  0.00              
ATOM    227  C   SER   144      14.220  53.919 -17.388  1.00  0.00              
ATOM    228  O   SER   144      13.339  53.491 -16.640  1.00  0.00              
ATOM    229  N   SER   146      16.039  51.298 -18.650  1.00  0.00              
ATOM    230  CA  SER   146      17.133  50.336 -18.712  1.00  0.00              
ATOM    231  C   SER   146      16.740  49.002 -18.083  1.00  0.00              
ATOM    232  O   SER   146      16.300  48.953 -16.932  1.00  0.00              
ATOM    233  N   THR   148      18.096  48.381 -14.543  1.00  0.00              
ATOM    234  CA  THR   148      17.433  49.060 -13.434  1.00  0.00              
ATOM    235  C   THR   148      16.139  48.345 -13.075  1.00  0.00              
ATOM    236  O   THR   148      15.837  48.138 -11.901  1.00  0.00              
ATOM    237  N   TYR   150      15.629  46.630  -9.439  1.00  0.00              
ATOM    238  CA  TYR   150      14.554  47.172  -8.618  1.00  0.00              
ATOM    239  C   TYR   150      13.582  46.082  -8.187  1.00  0.00              
ATOM    240  O   TYR   150      13.265  45.962  -7.004  1.00  0.00              
ATOM    241  N   HIS   151      13.104  45.283  -9.136  1.00  0.00              
ATOM    242  CA  HIS   151      12.174  44.222  -8.778  1.00  0.00              
ATOM    243  C   HIS   151      12.826  43.170  -7.883  1.00  0.00              
ATOM    244  O   HIS   151      12.140  42.505  -7.112  1.00  0.00              
ATOM    245  N   TYR   153      14.562  43.804  -5.434  1.00  0.00              
ATOM    246  CA  TYR   153      14.427  44.360  -4.087  1.00  0.00              
ATOM    247  C   TYR   153      12.954  44.493  -3.701  1.00  0.00              
ATOM    248  O   TYR   153      12.612  45.079  -2.675  1.00  0.00              
ATOM    249  N   LYS   156      10.372  46.223  -5.136  1.00  0.00              
ATOM    250  CA  LYS   156       9.734  47.533  -5.172  1.00  0.00              
ATOM    251  C   LYS   156       8.279  47.108  -5.427  1.00  0.00              
ATOM    252  O   LYS   156       8.039  45.963  -5.825  1.00  0.00              
ATOM    253  N   VAL   157       7.312  47.991  -5.206  1.00  0.00              
ATOM    254  CA  VAL   157       5.916  47.629  -5.455  1.00  0.00              
ATOM    255  C   VAL   157       5.622  47.567  -6.950  1.00  0.00              
ATOM    256  O   VAL   157       4.862  46.713  -7.418  1.00  0.00              
ATOM    257  N   PRO   158       6.231  48.482  -7.693  1.00  0.00              
ATOM    258  CA  PRO   158       6.036  48.560  -9.134  1.00  0.00              
ATOM    259  C   PRO   158       6.965  49.599  -9.754  1.00  0.00              
ATOM    260  O   PRO   158       7.466  50.497  -9.066  1.00  0.00              
ATOM    261  N   PHE   159       7.184  49.462 -11.058  1.00  0.00              
ATOM    262  CA  PHE   159       8.072  50.343 -11.810  1.00  0.00              
ATOM    263  C   PHE   159       7.292  51.089 -12.891  1.00  0.00              
ATOM    264  O   PHE   159       6.577  50.481 -13.683  1.00  0.00              
ATOM    265  N   TYR   160       7.433  52.411 -12.919  1.00  0.00              
ATOM    266  CA  TYR   160       6.745  53.217 -13.921  1.00  0.00              
ATOM    267  C   TYR   160       7.717  54.119 -14.668  1.00  0.00              
ATOM    268  O   TYR   160       8.481  54.867 -14.051  1.00  0.00              
ATOM    269  N   HIS   162       8.297  57.305 -16.786  1.00  0.00              
ATOM    270  CA  HIS   162       7.594  58.563 -17.001  1.00  0.00              
ATOM    271  C   HIS   162       7.259  58.771 -18.478  1.00  0.00              
ATOM    272  O   HIS   162       8.154  58.854 -19.315  1.00  0.00              
ATOM    273  N   ILE   163       5.964  58.865 -18.819  1.00  0.00              
ATOM    274  CA  ILE   163       5.647  59.071 -20.235  1.00  0.00              
ATOM    275  C   ILE   163       5.775  60.555 -20.574  1.00  0.00              
ATOM    276  O   ILE   163       5.470  61.404 -19.744  1.00  0.00              
ATOM    277  N   ASN   167       0.518  60.633 -19.524  1.00  0.00              
ATOM    278  CA  ASN   167       0.895  60.980 -18.158  1.00  0.00              
ATOM    279  C   ASN   167      -0.357  61.150 -17.302  1.00  0.00              
ATOM    280  O   ASN   167      -0.392  60.744 -16.142  1.00  0.00              
END
