
#######################################################
#                                                     #
#                        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 T0304TS383_2
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS383_2.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P      67      -       -           -
LGA    L      68      -       -           -
LGA    L      69      -       -           -
LGA    M      70      -       -           -
LGA    K      71      -       -           -
LGA    Q      72      -       -           -
LGA    L      73      -       -           -
LGA    E      74      -       -           -
LGA    L      75      D      16           #
LGA    M      76      -       -           -
LGA    L      77      R      17          4.803
LGA    T      78      P      18          1.459
LGA    S      79      W      19          4.108
LGA    G      80      W      20          4.182
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    P      84      P      28           #
LGA    R      85      C      29          4.634
LGA    H      86      F      30           #
LGA    Q      87      G      31          2.617
LGA    H      88      A      32          2.178
LGA    T      89      R      33          1.463
LGA    V      90      L      34          3.467
LGA    T      91      V      35          2.787
LGA    L      92      -       -           -
LGA    Y      93      -       -           -
LGA    A      94      Q      36           #
LGA    K      95      E      37          5.408
LGA    G      96      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    L      97      L      41          3.991
LGA    T      98      H      42          3.712
LGA    C      99      Y      43          4.390
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    K     100      A      48          4.203
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    A     101      F      54          1.577
LGA    D     102      S      55          3.534
LGA    T     103      D      56          2.032
LGA    L     104      A      57          2.324
LGA    S     105      D      58          2.817
LGA    S     106      A      59          4.867
LGA    C     107      Y      60          3.168
LGA    D     108      H      61          3.088
LGA    Y     109      L      62          4.161
LGA    V     110      D      63           #
LGA    -       -      Q      64           -
LGA    Y     111      A      65          2.979
LGA    L     112      F      66          4.076
LGA    -       -      P      67           -
LGA    -       -      L      68           -
LGA    A     113      L      69          2.728
LGA    -       -      M      70           -
LGA    -       -      K      71           -
LGA    -       -      Q      72           -
LGA    V     114      L      73          1.351
LGA    Y     115      E      74          3.869
LGA    -       -      L      75           -
LGA    -       -      M      76           -
LGA    P     116      L      77          1.327
LGA    -       -      T      78           -
LGA    T     117      S      79          2.857
LGA    P     118      G      80          4.277
LGA    E     119      E      81           -
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -
LGA    -       -      P     118           -
LGA    -       -      E     119           -
LGA    -       -      M     120           -
LGA    -       -      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50  107    5.0     32    3.45     3.12     16.040     0.901

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.637661 * X  +   0.762977 * Y  +  -0.106089 * Z  +  28.411781
  Y_new =   0.519552 * X  +   0.324301 * Y  +  -0.790503 * Z  + 120.618797
  Z_new =  -0.568730 * X  +  -0.559192 * Y  +  -0.603200 * Z  + 132.093918 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.394037    0.747556  [ DEG:  -137.1682     42.8318 ]
  Theta =   0.604961    2.536631  [ DEG:    34.6617    145.3383 ]
  Phi   =   2.457906   -0.683687  [ DEG:   140.8276    -39.1724 ]
 
# 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: T0304TS383_2                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS383_2.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50  107   5.0   32   3.45    3.12  16.040
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS383_2
PFRMAT TS
TARGET T0304
MODEL 2
PARENT 1eerB
ATOM      1  N   PRO    67      45.092   7.696  50.154  1.00  0.00
ATOM      2  CA  PRO    67      43.963   7.066  50.852  1.00  0.00
ATOM      3  C   PRO    67      43.045   8.085  51.528  1.00  0.00
ATOM      4  O   PRO    67      42.138   8.634  50.891  1.00  0.00
ATOM      5  N   LEU    68      43.277   8.322  52.821  1.00  0.00
ATOM      6  CA  LEU    68      42.499   9.297  53.581  1.00  0.00
ATOM      7  C   LEU    68      42.665  10.614  52.832  1.00  0.00
ATOM      8  O   LEU    68      41.874  11.551  52.976  1.00  0.00
ATOM      9  N   LEU    69      43.713  10.656  52.018  1.00  0.00
ATOM     10  CA  LEU    69      44.021  11.810  51.200  1.00  0.00
ATOM     11  C   LEU    69      42.931  11.952  50.131  1.00  0.00
ATOM     12  O   LEU    69      42.358  13.031  49.955  1.00  0.00
ATOM     13  N   MET    70      42.641  10.857  49.430  1.00  0.00
ATOM     14  CA  MET    70      41.628  10.858  48.378  1.00  0.00
ATOM     15  C   MET    70      40.282  11.373  48.866  1.00  0.00
ATOM     16  O   MET    70      39.613  12.141  48.173  1.00  0.00
ATOM     17  N   LYS    71      39.879  10.931  50.051  1.00  0.00
ATOM     18  CA  LYS    71      38.614  11.369  50.623  1.00  0.00
ATOM     19  C   LYS    71      38.675  12.879  50.845  1.00  0.00
ATOM     20  O   LYS    71      37.737  13.613  50.517  1.00  0.00
ATOM     21  N   GLN    72      39.790  13.335  51.405  1.00  0.00
ATOM     22  CA  GLN    72      39.982  14.757  51.665  1.00  0.00
ATOM     23  C   GLN    72      39.980  15.502  50.341  1.00  0.00
ATOM     24  O   GLN    72      39.383  16.571  50.213  1.00  0.00
ATOM     25  N   LEU    73      40.655  14.931  49.354  1.00  0.00
ATOM     26  CA  LEU    73      40.708  15.543  48.038  1.00  0.00
ATOM     27  C   LEU    73      39.283  15.570  47.497  1.00  0.00
ATOM     28  O   LEU    73      38.830  16.576  46.945  1.00  0.00
ATOM     29  N   GLU    74      38.582  14.453  47.684  1.00  0.00
ATOM     30  CA  GLU    74      37.203  14.300  47.221  1.00  0.00
ATOM     31  C   GLU    74      36.286  15.305  47.903  1.00  0.00
ATOM     32  O   GLU    74      35.428  15.918  47.262  1.00  0.00
ATOM     33  N   LEU    75      36.476  15.465  49.211  1.00  0.00
ATOM     34  CA  LEU    75      35.690  16.400  50.012  1.00  0.00
ATOM     35  C   LEU    75      35.798  17.837  49.477  1.00  0.00
ATOM     36  O   LEU    75      34.791  18.534  49.335  1.00  0.00
ATOM     37  N   MET    76      37.025  18.271  49.182  1.00  0.00
ATOM     38  CA  MET    76      37.276  19.621  48.676  1.00  0.00
ATOM     39  C   MET    76      36.776  19.829  47.255  1.00  0.00
ATOM     40  O   MET    76      36.278  20.905  46.911  1.00  0.00
ATOM     41  N   LEU    77      36.934  18.803  46.426  1.00  0.00
ATOM     42  CA  LEU    77      36.490  18.865  45.038  1.00  0.00
ATOM     43  C   LEU    77      34.975  18.872  45.020  1.00  0.00
ATOM     44  O   LEU    77      34.352  19.727  44.388  1.00  0.00
ATOM     45  N   THR    78      34.392  17.914  45.736  1.00  0.00
ATOM     46  CA  THR    78      32.946  17.777  45.830  1.00  0.00
ATOM     47  C   THR    78      32.264  19.101  46.146  1.00  0.00
ATOM     48  O   THR    78      31.103  19.303  45.806  1.00  0.00
ATOM     49  N   SER    79      32.990  20.003  46.798  1.00  0.00
ATOM     50  CA  SER    79      32.439  21.301  47.161  1.00  0.00
ATOM     51  C   SER    79      33.043  22.454  46.359  1.00  0.00
ATOM     52  O   SER    79      32.522  23.570  46.387  1.00  0.00
ATOM     53  N   GLY    80      34.132  22.196  45.640  1.00  0.00
ATOM     54  CA  GLY    80      34.751  23.261  44.867  1.00  0.00
ATOM     55  C   GLY    80      35.243  22.855  43.492  1.00  0.00
ATOM     56  O   GLY    80      36.435  22.983  43.204  1.00  0.00
ATOM     57  N   PRO    84      34.348  22.369  42.612  1.00  0.00
ATOM     58  CA  PRO    84      34.725  21.946  41.258  1.00  0.00
ATOM     59  C   PRO    84      35.054  23.099  40.315  1.00  0.00
ATOM     60  O   PRO    84      34.472  24.181  40.416  1.00  0.00
ATOM     61  N   ARG    85      36.000  22.846  39.413  1.00  0.00
ATOM     62  CA  ARG    85      36.436  23.816  38.415  1.00  0.00
ATOM     63  C   ARG    85      37.621  24.687  38.807  1.00  0.00
ATOM     64  O   ARG    85      38.302  25.224  37.929  1.00  0.00
ATOM     65  N   HIS    86      37.879  24.841  40.104  1.00  0.00
ATOM     66  CA  HIS    86      39.000  25.682  40.527  1.00  0.00
ATOM     67  C   HIS    86      40.167  24.936  41.153  1.00  0.00
ATOM     68  O   HIS    86      40.053  23.762  41.508  1.00  0.00
ATOM     69  N   GLN    87      41.294  25.634  41.279  1.00  0.00
ATOM     70  CA  GLN    87      42.505  25.061  41.861  1.00  0.00
ATOM     71  C   GLN    87      42.393  25.039  43.381  1.00  0.00
ATOM     72  O   GLN    87      42.318  26.085  44.020  1.00  0.00
ATOM     73  N   HIS    88      42.373  23.841  43.952  1.00  0.00
ATOM     74  CA  HIS    88      42.252  23.691  45.392  1.00  0.00
ATOM     75  C   HIS    88      43.553  23.234  46.024  1.00  0.00
ATOM     76  O   HIS    88      44.148  22.239  45.614  1.00  0.00
ATOM     77  N   THR    89      43.985  23.967  47.040  1.00  0.00
ATOM     78  CA  THR    89      45.206  23.632  47.747  1.00  0.00
ATOM     79  C   THR    89      44.858  23.396  49.199  1.00  0.00
ATOM     80  O   THR    89      44.002  24.079  49.753  1.00  0.00
ATOM     81  N   VAL    90      45.515  22.432  49.824  1.00  0.00
ATOM     82  CA  VAL    90      45.238  22.167  51.219  1.00  0.00
ATOM     83  C   VAL    90      46.430  21.534  51.907  1.00  0.00
ATOM     84  O   VAL    90      47.330  20.989  51.258  1.00  0.00
ATOM     85  N   THR    91      46.435  21.644  53.232  1.00  0.00
ATOM     86  CA  THR    91      47.483  21.093  54.068  1.00  0.00
ATOM     87  C   THR    91      46.789  20.331  55.187  1.00  0.00
ATOM     88  O   THR    91      45.697  20.702  55.614  1.00  0.00
ATOM     89  N   LEU    92      47.415  19.264  55.661  1.00  0.00
ATOM     90  CA  LEU    92      46.819  18.489  56.729  1.00  0.00
ATOM     91  C   LEU    92      47.629  18.588  58.012  1.00  0.00
ATOM     92  O   LEU    92      47.073  18.577  59.108  1.00  0.00
ATOM     93  N   TYR    93      48.945  18.700  57.873  1.00  0.00
ATOM     94  CA  TYR    93      49.829  18.788  59.030  1.00  0.00
ATOM     95  C   TYR    93      50.725  20.028  59.002  1.00  0.00
ATOM     96  O   TYR    93      51.742  20.077  59.697  1.00  0.00
ATOM     97  N   ALA    94      50.342  21.020  58.202  1.00  0.00
ATOM     98  CA  ALA    94      51.094  22.268  58.073  1.00  0.00
ATOM     99  C   ALA    94      52.513  22.030  57.580  1.00  0.00
ATOM    100  O   ALA    94      53.230  22.975  57.251  1.00  0.00
ATOM    101  N   LYS    95      52.914  20.764  57.529  1.00  0.00
ATOM    102  CA  LYS    95      54.249  20.388  57.065  1.00  0.00
ATOM    103  C   LYS    95      54.136  19.965  55.607  1.00  0.00
ATOM    104  O   LYS    95      55.139  19.735  54.930  1.00  0.00
ATOM    105  N   GLY    96      52.897  19.879  55.137  1.00  0.00
ATOM    106  CA  GLY    96      52.597  19.448  53.780  1.00  0.00
ATOM    107  C   GLY    96      51.661  20.406  53.061  1.00  0.00
ATOM    108  O   GLY    96      51.011  21.235  53.683  1.00  0.00
ATOM    109  N   LEU    97      51.588  20.265  51.742  1.00  0.00
ATOM    110  CA  LEU    97      50.715  21.085  50.918  1.00  0.00
ATOM    111  C   LEU    97      50.508  20.438  49.566  1.00  0.00
ATOM    112  O   LEU    97      51.465  20.035  48.902  1.00  0.00
ATOM    113  N   THR    98      49.249  20.355  49.158  1.00  0.00
ATOM    114  CA  THR    98      48.909  19.764  47.877  1.00  0.00
ATOM    115  C   THR    98      47.912  20.618  47.118  1.00  0.00
ATOM    116  O   THR    98      46.817  20.915  47.603  1.00  0.00
ATOM    117  N   CYS    99      48.306  21.015  45.919  1.00  0.00
ATOM    118  CA  CYS    99      47.445  21.799  45.060  1.00  0.00
ATOM    119  C   CYS    99      47.067  20.873  43.923  1.00  0.00
ATOM    120  O   CYS    99      47.910  20.148  43.393  1.00  0.00
ATOM    121  N   LYS   100      45.801  20.891  43.545  1.00  0.00
ATOM    122  CA  LYS   100      45.361  20.020  42.491  1.00  0.00
ATOM    123  C   LYS   100      44.137  20.556  41.803  1.00  0.00
ATOM    124  O   LYS   100      43.648  21.639  42.122  1.00  0.00
ATOM    125  N   ALA   101      38.564  17.710  30.643  1.00  0.00
ATOM    126  CA  ALA   101      39.210  17.791  29.342  1.00  0.00
ATOM    127  C   ALA   101      40.328  16.751  29.315  1.00  0.00
ATOM    128  O   ALA   101      41.349  16.915  29.989  1.00  0.00
ATOM    129  N   ASP   102      40.127  15.684  28.542  1.00  0.00
ATOM    130  CA  ASP   102      41.108  14.599  28.430  1.00  0.00
ATOM    131  C   ASP   102      41.654  14.443  27.008  1.00  0.00
ATOM    132  O   ASP   102      41.308  15.220  26.119  1.00  0.00
ATOM    133  N   THR   103      42.511  13.442  26.806  1.00  0.00
ATOM    134  CA  THR   103      43.119  13.156  25.499  1.00  0.00
ATOM    135  C   THR   103      43.848  14.356  24.875  1.00  0.00
ATOM    136  O   THR   103      43.228  15.363  24.528  1.00  0.00
ATOM    137  N   LEU   104      45.166  14.232  24.716  1.00  0.00
ATOM    138  CA  LEU   104      45.958  15.318  24.156  1.00  0.00
ATOM    139  C   LEU   104      46.615  16.100  25.283  1.00  0.00
ATOM    140  O   LEU   104      47.583  16.844  25.087  1.00  0.00
ATOM    141  N   SER   105      46.061  15.918  26.478  1.00  0.00
ATOM    142  CA  SER   105      46.554  16.560  27.687  1.00  0.00
ATOM    143  C   SER   105      47.593  15.639  28.327  1.00  0.00
ATOM    144  O   SER   105      47.276  14.864  29.230  1.00  0.00
ATOM    145  N   SER   106      48.829  15.725  27.847  1.00  0.00
ATOM    146  CA  SER   106      49.887  14.884  28.376  1.00  0.00
ATOM    147  C   SER   106      50.453  15.388  29.687  1.00  0.00
ATOM    148  O   SER   106      49.981  16.390  30.220  1.00  0.00
ATOM    149  N   CYS   107      51.477  14.716  30.234  1.00  0.00
ATOM    150  CA  CYS   107      52.073  15.146  31.502  1.00  0.00
ATOM    151  C   CYS   107      52.778  16.500  31.390  1.00  0.00
ATOM    152  O   CYS   107      53.024  17.170  32.395  1.00  0.00
ATOM    153  N   ASP   108      53.103  16.900  30.165  1.00  0.00
ATOM    154  CA  ASP   108      53.762  18.179  29.957  1.00  0.00
ATOM    155  C   ASP   108      52.772  19.210  29.452  1.00  0.00
ATOM    156  O   ASP   108      53.142  20.223  28.851  1.00  0.00
ATOM    157  N   TYR   109      51.496  18.944  29.702  1.00  0.00
ATOM    158  CA  TYR   109      50.425  19.827  29.272  1.00  0.00
ATOM    159  C   TYR   109      50.365  21.077  30.133  1.00  0.00
ATOM    160  O   TYR   109      49.836  22.111  29.709  1.00  0.00
ATOM    161  N   VAL   110      50.911  20.982  31.340  1.00  0.00
ATOM    162  CA  VAL   110      50.885  22.110  32.261  1.00  0.00
ATOM    163  C   VAL   110      52.188  22.317  33.007  1.00  0.00
ATOM    164  O   VAL   110      52.912  21.355  33.288  1.00  0.00
ATOM    165  N   TYR   111      52.472  23.585  33.314  1.00  0.00
ATOM    166  CA  TYR   111      53.664  23.976  34.066  1.00  0.00
ATOM    167  C   TYR   111      53.203  24.593  35.402  1.00  0.00
ATOM    168  O   TYR   111      52.427  25.554  35.416  1.00  0.00
ATOM    169  N   LEU   112      53.672  24.034  36.517  1.00  0.00
ATOM    170  CA  LEU   112      53.289  24.520  37.849  1.00  0.00
ATOM    171  C   LEU   112      54.362  25.317  38.609  1.00  0.00
ATOM    172  O   LEU   112      55.253  24.738  39.245  1.00  0.00
ATOM    173  N   ALA   113      54.252  26.642  38.562  1.00  0.00
ATOM    174  CA  ALA   113      55.197  27.520  39.246  1.00  0.00
ATOM    175  C   ALA   113      54.654  28.081  40.561  1.00  0.00
ATOM    176  O   ALA   113      53.449  28.311  40.707  1.00  0.00
ATOM    177  N   VAL   114      55.555  28.301  41.515  1.00  0.00
ATOM    178  CA  VAL   114      55.185  28.861  42.819  1.00  0.00
ATOM    179  C   VAL   114      56.290  29.735  43.393  1.00  0.00
ATOM    180  O   VAL   114      57.473  29.531  43.113  1.00  0.00
ATOM    181  N   TYR   115      55.907  30.710  44.205  1.00  0.00
ATOM    182  CA  TYR   115      56.904  31.575  44.807  1.00  0.00
ATOM    183  C   TYR   115      56.543  32.050  46.214  1.00  0.00
ATOM    184  O   TYR   115      55.554  32.762  46.413  1.00  0.00
ATOM    185  N   PRO   116      57.339  31.622  47.192  1.00  0.00
ATOM    186  CA  PRO   116      57.145  32.046  48.572  1.00  0.00
ATOM    187  C   PRO   116      57.637  33.474  48.501  1.00  0.00
ATOM    188  O   PRO   116      58.617  33.744  47.812  1.00  0.00
ATOM    189  N   THR   117      56.962  34.391  49.182  1.00  0.00
ATOM    190  CA  THR   117      57.384  35.775  49.135  1.00  0.00
ATOM    191  C   THR   117      58.882  35.907  49.432  1.00  0.00
ATOM    192  O   THR   117      59.429  35.191  50.284  1.00  0.00
ATOM    193  N   PRO   118      59.538  36.807  48.699  1.00  0.00
ATOM    194  CA  PRO   118      60.972  37.066  48.838  1.00  0.00
ATOM    195  C   PRO   118      61.826  35.820  48.621  1.00  0.00
ATOM    196  O   PRO   118      62.928  35.703  49.160  1.00  0.00
ATOM    197  N   GLU   119      61.292  34.893  47.826  1.00  0.00
ATOM    198  CA  GLU   119      61.977  33.652  47.474  1.00  0.00
ATOM    199  C   GLU   119      61.968  33.582  45.952  1.00  0.00
ATOM    200  O   GLU   119      61.115  34.182  45.297  1.00  0.00
TER
END
