
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0304TS383_2-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS383_2-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    P      67      P      67          1.384
LGA    L      68      L      68          1.468
LGA    L      69      L      69          1.517
LGA    M      70      M      70          1.344
LGA    K      71      K      71          0.832
LGA    Q      72      Q      72          0.386
LGA    L      73      L      73          0.597
LGA    E      74      E      74          0.259
LGA    L      75      L      75          0.784
LGA    M      76      M      76          1.069
LGA    L      77      L      77          1.428
LGA    T      78      T      78          1.329
LGA    S      79      S      79          1.683
LGA    G      80      G      80          2.095
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    P      84      N      83          2.318
LGA    R      85      P      84          3.307
LGA    -       -      R      85           -
LGA    H      86      H      86          2.836
LGA    Q      87      Q      87          3.596
LGA    -       -      H      88           -
LGA    H      88      T      89          3.703
LGA    T      89      V      90          1.408
LGA    V      90      T      91          1.496
LGA    T      91      L      92          1.760
LGA    L      92      Y      93          1.416
LGA    Y      93      A      94          3.213
LGA    A      94      K      95           -
LGA    -       -      G      96           -
LGA    K      95      L      97          3.158
LGA    G      96      T      98          0.812
LGA    L      97      C      99          2.238
LGA    T      98      K     100          1.578
LGA    C      99      A     101          1.762
LGA    K     100      D     102          2.038
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    A     101      C     107          4.568
LGA    D     102      D     108           #
LGA    T     103      Y     109           -
LGA    L     104      V     110           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      -       -           -
LGA    D     108      -       -           -
LGA    Y     109      -       -           -
LGA    V     110      -       -           -
LGA    Y     111      -       -           -
LGA    L     112      Y     111           #
LGA    A     113      L     112           -
LGA    V     114      A     113           -
LGA    Y     115      V     114           -
LGA    P     116      Y     115           -
LGA    T     117      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48  101    5.0     31    2.12    51.61     26.983     1.397

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.040379 * X  +  -0.999111 * Y  +   0.012089 * Z  +  75.461662
  Y_new =   0.673893 * X  +   0.018298 * Y  +  -0.738602 * Z  + 135.725647
  Z_new =   0.737725 * X  +   0.037971 * Y  +   0.674033 * Z  + -35.379665 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.056274   -3.085318  [ DEG:     3.2243   -176.7757 ]
  Theta =  -0.829694   -2.311899  [ DEG:   -47.5380   -132.4620 ]
  Phi   =   1.510949   -1.630644  [ DEG:    86.5710    -93.4290 ]
 
# 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-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS383_2-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48  101   5.0   31   2.12   51.61  26.983
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS383_2-D1
PFRMAT TS
TARGET T0304
MODEL 2
PARENT 1eerB
ATOM      1  N   PRO    67      54.294  19.695  40.994  1.00  0.00
ATOM      2  CA  PRO    67      55.751  19.521  41.068  1.00  0.00
ATOM      3  C   PRO    67      56.514  20.824  40.826  1.00  0.00
ATOM      4  O   PRO    67      56.722  21.612  41.756  1.00  0.00
ATOM      5  N   LEU    68      56.940  21.036  39.579  1.00  0.00
ATOM      6  CA  LEU    68      57.651  22.253  39.200  1.00  0.00
ATOM      7  C   LEU    68      56.712  23.397  39.569  1.00  0.00
ATOM      8  O   LEU    68      57.121  24.552  39.724  1.00  0.00
ATOM      9  N   LEU    69      55.442  23.040  39.715  1.00  0.00
ATOM     10  CA  LEU    69      54.406  23.979  40.093  1.00  0.00
ATOM     11  C   LEU    69      54.657  24.424  41.538  1.00  0.00
ATOM     12  O   LEU    69      54.679  25.622  41.832  1.00  0.00
ATOM     13  N   MET    70      54.858  23.456  42.431  1.00  0.00
ATOM     14  CA  MET    70      55.102  23.745  43.841  1.00  0.00
ATOM     15  C   MET    70      56.260  24.707  44.048  1.00  0.00
ATOM     16  O   MET    70      56.182  25.619  44.873  1.00  0.00
ATOM     17  N   LYS    71      57.343  24.490  43.311  1.00  0.00
ATOM     18  CA  LYS    71      58.507  25.358  43.415  1.00  0.00
ATOM     19  C   LYS    71      58.104  26.769  42.989  1.00  0.00
ATOM     20  O   LYS    71      58.442  27.758  43.647  1.00  0.00
ATOM     21  N   GLN    72      57.377  26.850  41.879  1.00  0.00
ATOM     22  CA  GLN    72      56.919  28.136  41.366  1.00  0.00
ATOM     23  C   GLN    72      55.988  28.767  42.386  1.00  0.00
ATOM     24  O   GLN    72      56.057  29.967  42.655  1.00  0.00
ATOM     25  N   LEU    73      55.112  27.951  42.954  1.00  0.00
ATOM     26  CA  LEU    73      54.183  28.440  43.959  1.00  0.00
ATOM     27  C   LEU    73      55.014  28.918  45.144  1.00  0.00
ATOM     28  O   LEU    73      54.765  29.988  45.707  1.00  0.00
ATOM     29  N   GLU    74      56.015  28.115  45.500  1.00  0.00
ATOM     30  CA  GLU    74      56.906  28.412  46.620  1.00  0.00
ATOM     31  C   GLU    74      57.677  29.702  46.374  1.00  0.00
ATOM     32  O   GLU    74      57.824  30.534  47.273  1.00  0.00
ATOM     33  N   LEU    75      58.168  29.856  45.147  1.00  0.00
ATOM     34  CA  LEU    75      58.920  31.041  44.742  1.00  0.00
ATOM     35  C   LEU    75      58.102  32.328  44.943  1.00  0.00
ATOM     36  O   LEU    75      58.604  33.315  45.484  1.00  0.00
ATOM     37  N   MET    76      56.842  32.306  44.504  1.00  0.00
ATOM     38  CA  MET    76      55.955  33.464  44.619  1.00  0.00
ATOM     39  C   MET    76      55.533  33.755  46.051  1.00  0.00
ATOM     40  O   MET    76      55.408  34.916  46.451  1.00  0.00
ATOM     41  N   LEU    77      55.291  32.693  46.814  1.00  0.00
ATOM     42  CA  LEU    77      54.888  32.830  48.209  1.00  0.00
ATOM     43  C   LEU    77      56.073  33.347  49.001  1.00  0.00
ATOM     44  O   LEU    77      55.964  34.328  49.738  1.00  0.00
ATOM     45  N   THR    78      57.211  32.680  48.824  1.00  0.00
ATOM     46  CA  THR    78      58.445  33.044  49.505  1.00  0.00
ATOM     47  C   THR    78      58.737  34.535  49.405  1.00  0.00
ATOM     48  O   THR    78      59.410  35.099  50.262  1.00  0.00
ATOM     49  N   SER    79      58.226  35.172  48.357  1.00  0.00
ATOM     50  CA  SER    79      58.446  36.597  48.153  1.00  0.00
ATOM     51  C   SER    79      57.186  37.435  48.365  1.00  0.00
ATOM     52  O   SER    79      57.263  38.661  48.455  1.00  0.00
ATOM     53  N   GLY    80      56.027  36.788  48.452  1.00  0.00
ATOM     54  CA  GLY    80      54.797  37.540  48.642  1.00  0.00
ATOM     55  C   GLY    80      53.809  36.920  49.611  1.00  0.00
ATOM     56  O   GLY    80      52.676  36.623  49.226  1.00  0.00
ATOM     57  N   PRO    84      54.203  36.719  50.883  1.00  0.00
ATOM     58  CA  PRO    84      53.321  36.124  51.895  1.00  0.00
ATOM     59  C   PRO    84      52.203  37.048  52.366  1.00  0.00
ATOM     60  O   PRO    84      52.377  38.266  52.431  1.00  0.00
ATOM     61  N   ARG    85      51.059  36.444  52.681  1.00  0.00
ATOM     62  CA  ARG    85      49.884  37.157  53.169  1.00  0.00
ATOM     63  C   ARG    85      48.883  37.596  52.110  1.00  0.00
ATOM     64  O   ARG    85      47.715  37.825  52.431  1.00  0.00
ATOM     65  N   HIS    86      49.318  37.721  50.857  1.00  0.00
ATOM     66  CA  HIS    86      48.393  38.156  49.809  1.00  0.00
ATOM     67  C   HIS    86      48.036  37.093  48.782  1.00  0.00
ATOM     68  O   HIS    86      48.680  36.047  48.701  1.00  0.00
ATOM     69  N   GLN    87      46.995  37.375  48.001  1.00  0.00
ATOM     70  CA  GLN    87      46.525  36.459  46.965  1.00  0.00
ATOM     71  C   GLN    87      47.424  36.556  45.738  1.00  0.00
ATOM     72  O   GLN    87      47.494  37.596  45.091  1.00  0.00
ATOM     73  N   HIS    88      48.116  35.465  45.428  1.00  0.00
ATOM     74  CA  HIS    88      49.019  35.440  44.291  1.00  0.00
ATOM     75  C   HIS    88      48.469  34.605  43.151  1.00  0.00
ATOM     76  O   HIS    88      48.093  33.447  43.330  1.00  0.00
ATOM     77  N   THR    89      48.436  35.201  41.968  1.00  0.00
ATOM     78  CA  THR    89      47.950  34.510  40.788  1.00  0.00
ATOM     79  C   THR    89      49.066  34.482  39.768  1.00  0.00
ATOM     80  O   THR    89      49.822  35.441  39.644  1.00  0.00
ATOM     81  N   VAL    90      49.179  33.386  39.034  1.00  0.00
ATOM     82  CA  VAL    90      50.218  33.304  38.031  1.00  0.00
ATOM     83  C   VAL    90      49.839  32.342  36.923  1.00  0.00
ATOM     84  O   VAL    90      48.955  31.492  37.086  1.00  0.00
ATOM     85  N   THR    91      50.500  32.513  35.783  1.00  0.00
ATOM     86  CA  THR    91      50.287  31.685  34.612  1.00  0.00
ATOM     87  C   THR    91      51.664  31.261  34.124  1.00  0.00
ATOM     88  O   THR    91      52.636  32.000  34.272  1.00  0.00
ATOM     89  N   LEU    92      51.755  30.071  33.549  1.00  0.00
ATOM     90  CA  LEU    92      53.031  29.600  33.055  1.00  0.00
ATOM     91  C   LEU    92      53.039  29.486  31.539  1.00  0.00
ATOM     92  O   LEU    92      54.061  29.720  30.898  1.00  0.00
ATOM     93  N   TYR    93      51.892  29.140  30.966  1.00  0.00
ATOM     94  CA  TYR    93      51.778  28.984  29.521  1.00  0.00
ATOM     95  C   TYR    93      50.668  29.847  28.914  1.00  0.00
ATOM     96  O   TYR    93      50.218  29.586  27.797  1.00  0.00
ATOM     97  N   ALA    94      50.238  30.867  29.653  1.00  0.00
ATOM     98  CA  ALA    94      49.186  31.779  29.205  1.00  0.00
ATOM     99  C   ALA    94      47.880  31.051  28.928  1.00  0.00
ATOM    100  O   ALA    94      46.845  31.680  28.709  1.00  0.00
ATOM    101  N   LYS    95      47.932  29.723  28.939  1.00  0.00
ATOM    102  CA  LYS    95      46.750  28.896  28.699  1.00  0.00
ATOM    103  C   LYS    95      46.201  28.460  30.050  1.00  0.00
ATOM    104  O   LYS    95      45.124  27.870  30.141  1.00  0.00
ATOM    105  N   GLY    96      46.958  28.773  31.096  1.00  0.00
ATOM    106  CA  GLY    96      46.612  28.398  32.459  1.00  0.00
ATOM    107  C   GLY    96      46.672  29.577  33.417  1.00  0.00
ATOM    108  O   GLY    96      47.255  30.608  33.109  1.00  0.00
ATOM    109  N   LEU    97      46.077  29.400  34.592  1.00  0.00
ATOM    110  CA  LEU    97      46.074  30.423  35.625  1.00  0.00
ATOM    111  C   LEU    97      45.725  29.814  36.965  1.00  0.00
ATOM    112  O   LEU    97      44.745  29.078  37.093  1.00  0.00
ATOM    113  N   THR    98      46.529  30.140  37.968  1.00  0.00
ATOM    114  CA  THR    98      46.305  29.632  39.309  1.00  0.00
ATOM    115  C   THR    98      46.424  30.732  40.347  1.00  0.00
ATOM    116  O   THR    98      47.452  31.406  40.456  1.00  0.00
ATOM    117  N   CYS    99      45.355  30.910  41.106  1.00  0.00
ATOM    118  CA  CYS    99      45.336  31.892  42.168  1.00  0.00
ATOM    119  C   CYS    99      45.324  31.090  43.452  1.00  0.00
ATOM    120  O   CYS    99      44.604  30.097  43.569  1.00  0.00
ATOM    121  N   LYS   100      46.117  31.515  44.420  1.00  0.00
ATOM    122  CA  LYS   100      46.180  30.790  45.658  1.00  0.00
ATOM    123  C   LYS   100      46.615  31.671  46.795  1.00  0.00
ATOM    124  O   LYS   100      46.831  32.870  46.628  1.00  0.00
ATOM    125  N   ALA   101      46.006  30.295  59.501  1.00  0.00
ATOM    126  CA  ALA   101      44.784  30.086  60.261  1.00  0.00
ATOM    127  C   ALA   101      44.212  28.730  59.853  1.00  0.00
ATOM    128  O   ALA   101      43.710  28.575  58.736  1.00  0.00
ATOM    129  N   ASP   102      44.296  27.755  60.758  1.00  0.00
ATOM    130  CA  ASP   102      43.802  26.398  60.498  1.00  0.00
ATOM    131  C   ASP   102      42.667  25.993  61.445  1.00  0.00
ATOM    132  O   ASP   102      42.228  26.794  62.269  1.00  0.00
ATOM    133  N   THR   103      42.197  24.752  61.314  1.00  0.00
ATOM    134  CA  THR   103      41.116  24.211  62.148  1.00  0.00
ATOM    135  C   THR   103      39.836  25.060  62.139  1.00  0.00
ATOM    136  O   THR   103      39.827  26.198  62.613  1.00  0.00
ATOM    137  N   LEU   104      38.750  24.490  61.614  1.00  0.00
ATOM    138  CA  LEU   104      37.490  25.215  61.534  1.00  0.00
ATOM    139  C   LEU   104      37.322  25.787  60.135  1.00  0.00
ATOM    140  O   LEU   104      36.221  26.149  59.702  1.00  0.00
ATOM    141  N   SER   105      38.448  25.865  59.431  1.00  0.00
ATOM    142  CA  SER   105      38.497  26.365  58.065  1.00  0.00
ATOM    143  C   SER   105      38.303  25.182  57.117  1.00  0.00
ATOM    144  O   SER   105      39.273  24.607  56.621  1.00  0.00
ATOM    145  N   SER   106      37.046  24.821  56.877  1.00  0.00
ATOM    146  CA  SER   106      36.753  23.701  56.002  1.00  0.00
ATOM    147  C   SER   106      36.842  24.052  54.532  1.00  0.00
ATOM    148  O   SER   106      37.184  25.181  54.185  1.00  0.00
ATOM    149  N   CYS   107      36.533  23.104  53.635  1.00  0.00
ATOM    150  CA  CYS   107      36.599  23.372  52.195  1.00  0.00
ATOM    151  C   CYS   107      35.559  24.401  51.744  1.00  0.00
ATOM    152  O   CYS   107      35.687  25.000  50.673  1.00  0.00
ATOM    153  N   ASP   108      34.531  24.604  52.560  1.00  0.00
ATOM    154  CA  ASP   108      33.501  25.573  52.222  1.00  0.00
ATOM    155  C   ASP   108      33.693  26.850  53.017  1.00  0.00
ATOM    156  O   ASP   108      32.766  27.645  53.197  1.00  0.00
ATOM    157  N   TYR   109      34.916  27.043  53.496  1.00  0.00
ATOM    158  CA  TYR   109      35.257  28.212  54.288  1.00  0.00
ATOM    159  C   TYR   109      35.369  29.452  53.419  1.00  0.00
ATOM    160  O   TYR   109      35.239  30.581  53.907  1.00  0.00
ATOM    161  N   VAL   110      35.606  29.242  52.129  1.00  0.00
ATOM    162  CA  VAL   110      35.760  30.358  51.206  1.00  0.00
ATOM    163  C   VAL   110      35.061  30.152  49.878  1.00  0.00
ATOM    164  O   VAL   110      34.939  29.018  49.400  1.00  0.00
ATOM    165  N   TYR   111      34.603  31.264  49.298  1.00  0.00
ATOM    166  CA  TYR   111      33.937  31.268  47.995  1.00  0.00
ATOM    167  C   TYR   111      34.814  32.074  47.015  1.00  0.00
ATOM    168  O   TYR   111      35.134  33.239  47.270  1.00  0.00
ATOM    169  N   LEU   112      35.208  31.447  45.906  1.00  0.00
ATOM    170  CA  LEU   112      36.062  32.103  44.907  1.00  0.00
ATOM    171  C   LEU   112      35.368  32.529  43.604  1.00  0.00
ATOM    172  O   LEU   112      35.182  31.718  42.687  1.00  0.00
ATOM    173  N   ALA   113      35.016  33.810  43.518  1.00  0.00
ATOM    174  CA  ALA   113      34.356  34.352  42.333  1.00  0.00
ATOM    175  C   ALA   113      35.304  35.131  41.421  1.00  0.00
ATOM    176  O   ALA   113      36.261  35.761  41.884  1.00  0.00
ATOM    177  N   VAL   114      35.029  35.083  40.120  1.00  0.00
ATOM    178  CA  VAL   114      35.835  35.802  39.128  1.00  0.00
ATOM    179  C   VAL   114      34.993  36.280  37.955  1.00  0.00
ATOM    180  O   VAL   114      33.975  35.676  37.613  1.00  0.00
ATOM    181  N   TYR   115      35.420  37.368  37.329  1.00  0.00
ATOM    182  CA  TYR   115      34.680  37.877  36.189  1.00  0.00
ATOM    183  C   TYR   115      35.560  38.518  35.116  1.00  0.00
ATOM    184  O   TYR   115      36.224  39.532  35.358  1.00  0.00
ATOM    185  N   PRO   116      35.582  37.898  33.938  1.00  0.00
ATOM    186  CA  PRO   116      36.333  38.434  32.810  1.00  0.00
ATOM    187  C   PRO   116      35.460  39.607  32.422  1.00  0.00
ATOM    188  O   PRO   116      34.238  39.494  32.466  1.00  0.00
ATOM    189  N   THR   117      36.066  40.732  32.066  1.00  0.00
ATOM    190  CA  THR   117      35.276  41.888  31.699  1.00  0.00
ATOM    191  C   THR   117      34.209  41.521  30.660  1.00  0.00
ATOM    192  O   THR   117      34.452  40.708  29.756  1.00  0.00
TER
END
