
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0307AL044_4-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307AL044_4-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      18      -       -           -
LGA    T      19      -       -           -
LGA    A      20      -       -           -
LGA    I      21      I      10           #
LGA    I      22      M      11           -
LGA    K      23      T      12           #
LGA    M      24      F      13          4.943
LGA    A      25      S      14          3.446
LGA    K      26      G      15          0.603
LGA    S      27      Q      16          2.258
LGA    G      33      E      17          0.742
LGA    K      34      L      18          1.421
LGA    K      36      T      19          1.932
LGA    P      37      A      20          1.867
LGA    A      38      I      21          1.747
LGA    E      39      I      22          1.499
LGA    I      40      K      23          1.428
LGA    A      41      M      24          1.477
LGA    M      48      A      25          1.534
LGA    R      49      K      26          1.640
LGA    F      50      S      27          1.940
LGA    G      51      M      28          2.514
LGA    I      52      V      29          2.379
LGA    -       -      M      30           -
LGA    -       -      A      31           -
LGA    -       -      D      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      I      35           -
LGA    -       -      K      36           -
LGA    -       -      P      37           -
LGA    -       -      A      38           -
LGA    Q      54      E      39           #
LGA    D      55      I      40          4.431
LGA    -       -      A      41           -
LGA    Q      56      V      42          2.961
LGA    V      57      M      43           -
LGA    D      58      T      44           -
LGA    L      60      -       -           -
LGA    L      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      R      45          2.703
LGA    S      64      E      46          3.079
LGA    D      65      F      47          6.375
LGA    -       -      M      48           -
LGA    -       -      R      49           -
LGA    -       -      F      50           -
LGA    -       -      G      51           -
LGA    -       -      I      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    -       -      D      58           -
LGA    -       -      L      59           -
LGA    -       -      L      60           -
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      S      64           -
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      I      76           -
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    -       -      E      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      K      85           -
LGA    -       -      Y      86           -
LGA    -       -      V      87           -
LGA    -       -      A      88           -
LGA    -       -      S      89           -
LGA    -       -      Y      90           -
LGA    S      66      L      91          5.674
LGA    -       -      G      92           -
LGA    -       -      V      93           -
LGA    I      67      I      94          1.933
LGA    E      68      M      95          2.430
LGA    -       -      A      96           -
LGA    -       -      S      97           -
LGA    -       -      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    -       -      I     101           -
LGA    -       -      D     102           -
LGA    -       -      D     103           -
LGA    -       -      N     104           -
LGA    L      91      E     105          2.740
LGA    G      92      L     106          1.306
LGA    V      93      A     107          1.767
LGA    D     100      L     108           -
LGA    I     101      W     109           -
LGA    -       -      T     110           -
LGA    -       -      L     111           -
LGA    -       -      I     112           -
LGA    -       -      S     113           -
LGA    -       -      T     114           -
LGA    -       -      L     115           -
LGA    -       -      C     116           -
LGA    -       -      G     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      T     120           -
LGA    -       -      M     121           -
LGA    D     103      T     122           #
LGA    N     104      V     123           #
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44  123    5.0     28    2.81     3.57     16.183     0.961

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.475622 * X  +  -0.328341 * Y  +  -0.816074 * Z  +  51.649929
  Y_new =  -0.686125 * X  +   0.719029 * Y  +   0.110590 * Z  +  25.008364
  Z_new =   0.550470 * X  +   0.612527 * Y  +  -0.567269 * Z  + -30.505383 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.317852   -0.823741  [ DEG:   132.8031    -47.1969 ]
  Theta =  -0.582927   -2.558666  [ DEG:   -33.3992   -146.6008 ]
  Phi   =  -2.176944    0.964648  [ DEG:  -124.7297     55.2703 ]
 
# 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: T0307AL044_4-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307AL044_4-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  123   5.0   28   2.81    3.57  16.183
REMARK  ---------------------------------------------------------- 
MOLECULE T0307AL044_4-D1
REMARK Aligment from pdb entry: 1txj_A
ATOM      1  N   LEU    18      20.283  25.496  37.558  1.00  0.00              
ATOM      2  CA  LEU    18      19.998  26.870  37.935  1.00  0.00              
ATOM      3  C   LEU    18      18.484  27.037  37.973  1.00  0.00              
ATOM      4  O   LEU    18      17.936  27.602  38.918  1.00  0.00              
ATOM      5  N   THR    19      15.781  27.643  41.399  1.00  0.00              
ATOM      6  CA  THR    19      14.809  28.724  41.435  1.00  0.00              
ATOM      7  C   THR    19      13.350  28.323  41.464  1.00  0.00              
ATOM      8  O   THR    19      12.553  28.976  42.134  1.00  0.00              
ATOM      9  N   ALA    20      12.987  27.252  40.764  1.00  0.00              
ATOM     10  CA  ALA    20      11.591  26.854  40.724  1.00  0.00              
ATOM     11  C   ALA    20      11.215  25.514  41.339  1.00  0.00              
ATOM     12  O   ALA    20      10.075  25.329  41.754  1.00  0.00              
ATOM     13  N   ILE    21      12.145  24.573  41.395  1.00  0.00              
ATOM     14  CA  ILE    21      11.833  23.258  41.951  1.00  0.00              
ATOM     15  C   ILE    21      13.028  22.736  42.723  1.00  0.00              
ATOM     16  O   ILE    21      13.610  21.707  42.377  1.00  0.00              
ATOM     17  N   ILE    22      13.396  23.440  43.802  1.00  0.00              
ATOM     18  CA  ILE    22      14.536  23.072  44.641  1.00  0.00              
ATOM     19  C   ILE    22      14.595  21.633  45.132  1.00  0.00              
ATOM     20  O   ILE    22      15.673  21.129  45.410  1.00  0.00              
ATOM     21  N   LYS    23      13.452  20.969  45.234  1.00  0.00              
ATOM     22  CA  LYS    23      13.427  19.581  45.702  1.00  0.00              
ATOM     23  C   LYS    23      13.991  18.572  44.683  1.00  0.00              
ATOM     24  O   LYS    23      14.233  17.413  45.018  1.00  0.00              
ATOM     25  N   MET    24      14.191  19.020  43.445  1.00  0.00              
ATOM     26  CA  MET    24      14.723  18.160  42.381  1.00  0.00              
ATOM     27  C   MET    24      16.213  18.388  42.191  1.00  0.00              
ATOM     28  O   MET    24      16.893  17.600  41.527  1.00  0.00              
ATOM     29  N   ALA    25      18.957  18.049  44.093  1.00  0.00              
ATOM     30  CA  ALA    25      19.906  17.001  44.448  1.00  0.00              
ATOM     31  C   ALA    25      19.873  15.774  43.552  1.00  0.00              
ATOM     32  O   ALA    25      20.946  15.328  43.127  1.00  0.00              
ATOM     33  N   LYS    26      21.360  16.601  39.955  1.00  0.00              
ATOM     34  CA  LYS    26      22.810  16.713  39.977  1.00  0.00              
ATOM     35  C   LYS    26      23.489  15.357  40.100  1.00  0.00              
ATOM     36  O   LYS    26      24.434  15.060  39.381  1.00  0.00              
ATOM     37  N   SER    27      22.975  14.526  40.998  1.00  0.00              
ATOM     38  CA  SER    27      23.515  13.190  41.245  1.00  0.00              
ATOM     39  C   SER    27      23.304  12.229  40.080  1.00  0.00              
ATOM     40  O   SER    27      24.226  11.566  39.616  1.00  0.00              
ATOM     41  N   GLY    33      22.069  12.141  39.622  1.00  0.00              
ATOM     42  CA  GLY    33      21.752  11.172  38.585  1.00  0.00              
ATOM     43  C   GLY    33      22.031  11.547  37.146  1.00  0.00              
ATOM     44  O   GLY    33      22.101  10.669  36.287  1.00  0.00              
ATOM     45  N   LYS    34      22.196  12.834  36.877  1.00  0.00              
ATOM     46  CA  LYS    34      22.459  13.265  35.510  1.00  0.00              
ATOM     47  C   LYS    34      23.749  12.679  34.953  1.00  0.00              
ATOM     48  O   LYS    34      23.772  12.215  33.814  1.00  0.00              
ATOM     49  N   LYS    36      24.815  12.681  35.748  1.00  0.00              
ATOM     50  CA  LYS    36      26.104  12.172  35.265  1.00  0.00              
ATOM     51  C   LYS    36      26.046  10.799  34.614  1.00  0.00              
ATOM     52  O   LYS    36      26.481  10.640  33.471  1.00  0.00              
ATOM     53  N   PRO    37      25.543   9.777  35.328  1.00  0.00              
ATOM     54  CA  PRO    37      25.513   8.480  34.646  1.00  0.00              
ATOM     55  C   PRO    37      24.613   8.396  33.410  1.00  0.00              
ATOM     56  O   PRO    37      24.879   7.606  32.501  1.00  0.00              
ATOM     57  N   ALA    38      23.538   9.171  33.363  1.00  0.00              
ATOM     58  CA  ALA    38      22.694   9.113  32.173  1.00  0.00              
ATOM     59  C   ALA    38      23.470   9.732  30.990  1.00  0.00              
ATOM     60  O   ALA    38      23.505   9.172  29.887  1.00  0.00              
ATOM     61  N   GLU    39      24.072  10.889  31.225  1.00  0.00              
ATOM     62  CA  GLU    39      24.837  11.564  30.164  1.00  0.00              
ATOM     63  C   GLU    39      26.040  10.694  29.747  1.00  0.00              
ATOM     64  O   GLU    39      26.358  10.579  28.564  1.00  0.00              
ATOM     65  N   ILE    40      26.698  10.061  30.718  1.00  0.00              
ATOM     66  CA  ILE    40      27.832   9.198  30.406  1.00  0.00              
ATOM     67  C   ILE    40      27.350   8.049  29.508  1.00  0.00              
ATOM     68  O   ILE    40      28.073   7.601  28.598  1.00  0.00              
ATOM     69  N   ALA    41      26.134   7.573  29.758  1.00  0.00              
ATOM     70  CA  ALA    41      25.586   6.496  28.948  1.00  0.00              
ATOM     71  C   ALA    41      25.365   6.978  27.502  1.00  0.00              
ATOM     72  O   ALA    41      25.663   6.258  26.539  1.00  0.00              
ATOM     73  N   MET    48      24.823   8.191  27.358  1.00  0.00              
ATOM     74  CA  MET    48      24.580   8.764  26.033  1.00  0.00              
ATOM     75  C   MET    48      25.940   8.956  25.314  1.00  0.00              
ATOM     76  O   MET    48      26.114   8.492  24.178  1.00  0.00              
ATOM     77  N   ARG    49      26.908   9.585  25.987  1.00  0.00              
ATOM     78  CA  ARG    49      28.227   9.830  25.383  1.00  0.00              
ATOM     79  C   ARG    49      28.902   8.541  24.965  1.00  0.00              
ATOM     80  O   ARG    49      29.386   8.428  23.862  1.00  0.00              
ATOM     81  N   PHE    50      28.943   7.569  25.867  1.00  0.00              
ATOM     82  CA  PHE    50      29.541   6.288  25.548  1.00  0.00              
ATOM     83  C   PHE    50      28.960   5.687  24.283  1.00  0.00              
ATOM     84  O   PHE    50      29.660   5.031  23.513  1.00  0.00              
ATOM     85  N   GLY    51      27.673   5.915  24.048  1.00  0.00              
ATOM     86  CA  GLY    51      27.026   5.351  22.873  1.00  0.00              
ATOM     87  C   GLY    51      26.610   6.437  21.885  1.00  0.00              
ATOM     88  O   GLY    51      25.650   6.285  21.138  1.00  0.00              
ATOM     89  N   ILE    52      27.378   7.526  21.863  1.00  0.00              
ATOM     90  CA  ILE    52      27.045   8.701  21.040  1.00  0.00              
ATOM     91  C   ILE    52      26.593   8.442  19.612  1.00  0.00              
ATOM     92  O   ILE    52      25.568   8.983  19.174  1.00  0.00              
ATOM     93  N   GLN    54      27.326   7.605  18.890  1.00  0.00              
ATOM     94  CA  GLN    54      26.988   7.329  17.499  1.00  0.00              
ATOM     95  C   GLN    54      25.666   6.632  17.249  1.00  0.00              
ATOM     96  O   GLN    54      25.209   6.603  16.110  1.00  0.00              
ATOM     97  N   ASP    55      19.352  13.361  17.118  1.00  0.00              
ATOM     98  CA  ASP    55      18.945  14.390  18.058  1.00  0.00              
ATOM     99  C   ASP    55      17.926  15.297  17.430  1.00  0.00              
ATOM    100  O   ASP    55      17.987  15.573  16.218  1.00  0.00              
ATOM    101  N   GLN    56      17.015  15.795  18.256  1.00  0.00              
ATOM    102  CA  GLN    56      15.944  16.636  17.772  1.00  0.00              
ATOM    103  C   GLN    56      15.715  17.905  18.570  1.00  0.00              
ATOM    104  O   GLN    56      15.659  17.880  19.808  1.00  0.00              
ATOM    105  N   VAL    57      15.535  19.009  17.849  1.00  0.00              
ATOM    106  CA  VAL    57      15.245  20.271  18.496  1.00  0.00              
ATOM    107  C   VAL    57      13.742  20.435  18.383  1.00  0.00              
ATOM    108  O   VAL    57      13.096  19.843  17.515  1.00  0.00              
ATOM    109  N   ASP    58      10.247  23.017  18.158  1.00  0.00              
ATOM    110  CA  ASP    58       9.811  24.038  17.209  1.00  0.00              
ATOM    111  C   ASP    58      10.645  25.339  17.200  1.00  0.00              
ATOM    112  O   ASP    58      10.897  25.902  16.137  1.00  0.00              
ATOM    113  N   LEU    60      11.091  25.803  18.364  1.00  0.00              
ATOM    114  CA  LEU    60      11.884  27.036  18.433  1.00  0.00              
ATOM    115  C   LEU    60      13.310  26.881  17.906  1.00  0.00              
ATOM    116  O   LEU    60      14.030  27.868  17.747  1.00  0.00              
ATOM    117  N   LEU    61      20.125  25.944  22.702  1.00  0.00              
ATOM    118  CA  LEU    61      20.482  25.989  24.119  1.00  0.00              
ATOM    119  C   LEU    61      19.404  25.346  24.976  1.00  0.00              
ATOM    120  O   LEU    61      19.555  25.243  26.190  1.00  0.00              
ATOM    121  N   LYS    62      18.295  24.943  24.363  1.00  0.00              
ATOM    122  CA  LYS    62      17.223  24.321  25.137  1.00  0.00              
ATOM    123  C   LYS    62      17.399  22.800  25.115  1.00  0.00              
ATOM    124  O   LYS    62      18.456  22.302  24.743  1.00  0.00              
ATOM    125  N   ALA    63      16.372  22.057  25.510  1.00  0.00              
ATOM    126  CA  ALA    63      16.509  20.617  25.545  1.00  0.00              
ATOM    127  C   ALA    63      16.535  19.952  24.175  1.00  0.00              
ATOM    128  O   ALA    63      15.964  20.441  23.210  1.00  0.00              
ATOM    129  N   SER    64      17.219  18.822  24.103  1.00  0.00              
ATOM    130  CA  SER    64      17.258  18.025  22.891  1.00  0.00              
ATOM    131  C   SER    64      16.488  16.775  23.225  1.00  0.00              
ATOM    132  O   SER    64      16.518  16.331  24.360  1.00  0.00              
ATOM    133  N   ASP    65      15.788  16.216  22.249  1.00  0.00              
ATOM    134  CA  ASP    65      15.102  14.954  22.481  1.00  0.00              
ATOM    135  C   ASP    65      16.006  13.974  21.755  1.00  0.00              
ATOM    136  O   ASP    65      16.486  14.266  20.670  1.00  0.00              
ATOM    137  N   SER    66      16.278  12.835  22.378  1.00  0.00              
ATOM    138  CA  SER    66      17.186  11.833  21.816  1.00  0.00              
ATOM    139  C   SER    66      16.392  10.702  21.202  1.00  0.00              
ATOM    140  O   SER    66      15.332  10.325  21.682  1.00  0.00              
ATOM    141  N   ILE    67      16.943  10.130  20.150  1.00  0.00              
ATOM    142  CA  ILE    67      16.267   9.046  19.477  1.00  0.00              
ATOM    143  C   ILE    67      17.275   7.949  19.178  1.00  0.00              
ATOM    144  O   ILE    67      18.458   8.230  18.864  1.00  0.00              
ATOM    145  N   GLU    68      16.848   6.699  19.312  1.00  0.00              
ATOM    146  CA  GLU    68      17.741   5.588  18.998  1.00  0.00              
ATOM    147  C   GLU    68      16.888   4.384  18.597  1.00  0.00              
ATOM    148  O   GLU    68      15.687   4.376  18.847  1.00  0.00              
ATOM    149  N   LEU    91      17.502   3.389  17.954  1.00  0.00              
ATOM    150  CA  LEU    91      16.778   2.177  17.550  1.00  0.00              
ATOM    151  C   LEU    91      17.235   1.078  18.466  1.00  0.00              
ATOM    152  O   LEU    91      18.429   0.802  18.579  1.00  0.00              
ATOM    153  N   GLY    92      16.274   0.457  19.131  1.00  0.00              
ATOM    154  CA  GLY    92      16.562  -0.616  20.067  1.00  0.00              
ATOM    155  C   GLY    92      16.611  -1.964  19.342  1.00  0.00              
ATOM    156  O   GLY    92      15.705  -2.312  18.592  1.00  0.00              
ATOM    157  N   VAL    93      17.682  -2.707  19.584  1.00  0.00              
ATOM    158  CA  VAL    93      17.851  -4.002  18.958  1.00  0.00              
ATOM    159  C   VAL    93      17.520  -3.995  17.487  1.00  0.00              
ATOM    160  O   VAL    93      18.101  -3.243  16.700  1.00  0.00              
ATOM    161  N   ASP   100      16.556  -4.823  17.114  1.00  0.00              
ATOM    162  CA  ASP   100      16.163  -4.920  15.722  1.00  0.00              
ATOM    163  C   ASP   100      14.837  -4.230  15.447  1.00  0.00              
ATOM    164  O   ASP   100      14.230  -4.464  14.407  1.00  0.00              
ATOM    165  N   ILE   101      14.382  -3.382  16.366  1.00  0.00              
ATOM    166  CA  ILE   101      13.129  -2.670  16.147  1.00  0.00              
ATOM    167  C   ILE   101      13.256  -1.811  14.902  1.00  0.00              
ATOM    168  O   ILE   101      14.355  -1.398  14.538  1.00  0.00              
ATOM    169  N   ASP   103      12.128  -1.519  14.267  1.00  0.00              
ATOM    170  CA  ASP   103      12.144  -0.745  13.034  1.00  0.00              
ATOM    171  C   ASP   103      11.721   0.695  13.128  1.00  0.00              
ATOM    172  O   ASP   103      11.691   1.386  12.109  1.00  0.00              
ATOM    173  N   ASN   104      11.351   1.142  14.333  1.00  0.00              
ATOM    174  CA  ASN   104      11.015   2.548  14.530  1.00  0.00              
ATOM    175  C   ASN   104      11.780   2.907  15.780  1.00  0.00              
ATOM    176  O   ASN   104      12.012   2.053  16.648  1.00  0.00              
END
