
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0347AL333_3-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347AL333_3-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    A      13      P       7           -
LGA    I      14      R       8           -
LGA    D      15      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    K      16      K      16           #
LGA    L      17      L      17          0.749
LGA    R      18      R      18          4.222
LGA    P      19      P      19           -
LGA    D      61      T      20           -
LGA    R      62      Q      21           -
LGA    A      63      I      22           -
LGA    Y      64      A      23           -
LGA    A      74      V      24           -
LGA    L      75      G      25           -
LGA    S      76      F      26           -
LGA    K      77      R      27           -
LGA    E      78      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    G      79      H      51          2.512
LGA    V      80      I      52          3.863
LGA    E      81      -       -           -
LGA    H      82      -       -           -
LGA    V      83      -       -           -
LGA    L      84      V      53          2.896
LGA    T      85      P      54          1.600
LGA    S      86      V      55          1.289
LGA    E      87      V      56          0.653
LGA    V      88      A      57          1.871
LGA    A      89      G      58          2.743
LGA    K      90      P      59          3.379
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    F      91      G      95           #
LGA    S      92      K      96          1.949
LGA    H      93      D      97          3.386
LGA    L      94      E      98          1.641
LGA    G      95      -       -           -
LGA    K      96      F      99          0.948
LGA    D      97      W     100          1.437
LGA    E      98      S     101          1.957
LGA    F      99      V     102          2.207
LGA    W     100      M     103          1.689
LGA    S     101      D     104          0.380
LGA    V     102      H     105          3.253
LGA    -       -      R     106           -
LGA    M     103      N     107          3.558
LGA    D     104      L     108          2.679

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   89    5.0     23    2.45     8.70     18.243     0.902

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.442373 * X  +   0.315189 * Y  +   0.839621 * Z  + -96.792900
  Y_new =   0.887093 * X  +   0.291374 * Y  +   0.358005 * Z  + -47.606396
  Z_new =  -0.131804 * X  +   0.903193 * Y  +  -0.408497 * Z  + -43.505882 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.995546   -1.146047  [ DEG:   114.3364    -65.6636 ]
  Theta =   0.132189    3.009404  [ DEG:     7.5739    172.4261 ]
  Phi   =   2.033385   -1.108208  [ DEG:   116.5044    -63.4956 ]
 
# 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: T0347AL333_3-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_3-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   89   5.0   23   2.45    8.70  18.243
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_3-D1
REMARK Aligment from pdb entry: 1a8y
ATOM      1  N   ALA    13      10.690  43.520  -3.007  1.00  0.00              
ATOM      2  CA  ALA    13      11.434  42.356  -2.532  1.00  0.00              
ATOM      3  C   ALA    13      10.445  41.246  -2.218  1.00  0.00              
ATOM      4  O   ALA    13      10.677  40.118  -2.637  1.00  0.00              
ATOM      5  N   ILE    14       9.335  41.549  -1.532  1.00  0.00              
ATOM      6  CA  ILE    14       8.276  40.575  -1.277  1.00  0.00              
ATOM      7  C   ILE    14       7.070  41.054  -2.070  1.00  0.00              
ATOM      8  O   ILE    14       6.486  42.088  -1.787  1.00  0.00              
ATOM      9  N   ASP    15       6.716  40.319  -3.121  1.00  0.00              
ATOM     10  CA  ASP    15       5.565  40.566  -3.978  1.00  0.00              
ATOM     11  C   ASP    15       4.498  39.523  -3.699  1.00  0.00              
ATOM     12  O   ASP    15       4.791  38.515  -3.068  1.00  0.00              
ATOM     13  N   LYS    16       3.256  39.711  -4.141  1.00  0.00              
ATOM     14  CA  LYS    16       2.233  38.746  -3.871  1.00  0.00              
ATOM     15  C   LYS    16       1.651  38.328  -5.197  1.00  0.00              
ATOM     16  O   LYS    16       1.362  39.192  -6.033  1.00  0.00              
ATOM     17  N   LEU    17       1.538  37.006  -5.463  1.00  0.00              
ATOM     18  CA  LEU    17       0.872  36.559  -6.688  1.00  0.00              
ATOM     19  C   LEU    17      -0.608  36.848  -6.501  1.00  0.00              
ATOM     20  O   LEU    17      -1.285  36.233  -5.686  1.00  0.00              
ATOM     21  N   ARG    18      -1.048  37.891  -7.200  1.00  0.00              
ATOM     22  CA  ARG    18      -2.415  38.385  -7.183  1.00  0.00              
ATOM     23  C   ARG    18      -3.127  37.957  -8.454  1.00  0.00              
ATOM     24  O   ARG    18      -2.526  38.004  -9.529  1.00  0.00              
ATOM     25  N   PRO    19      -4.392  37.544  -8.453  1.00  0.00              
ATOM     26  CA  PRO    19      -5.091  37.089  -9.659  1.00  0.00              
ATOM     27  C   PRO    19      -5.231  38.115 -10.770  1.00  0.00              
ATOM     28  O   PRO    19      -5.221  37.755 -11.936  1.00  0.00              
ATOM     29  N   ASP    61      -5.341  39.404 -10.443  1.00  0.00              
ATOM     30  CA  ASP    61      -5.503  40.481 -11.402  1.00  0.00              
ATOM     31  C   ASP    61      -4.248  40.910 -12.098  1.00  0.00              
ATOM     32  O   ASP    61      -4.296  41.652 -13.077  1.00  0.00              
ATOM     33  N   ARG    62      -3.114  40.433 -11.558  1.00  0.00              
ATOM     34  CA  ARG    62      -1.734  40.680 -11.995  1.00  0.00              
ATOM     35  C   ARG    62      -0.975  39.408 -12.333  1.00  0.00              
ATOM     36  O   ARG    62       0.010  39.528 -13.045  1.00  0.00              
ATOM     37  N   ALA    63      -1.388  38.196 -11.925  1.00  0.00              
ATOM     38  CA  ALA    63      -0.565  36.992 -11.945  1.00  0.00              
ATOM     39  C   ALA    63       0.508  36.663 -12.979  1.00  0.00              
ATOM     40  O   ALA    63       1.533  36.038 -12.633  1.00  0.00              
ATOM     41  N   TYR    64       0.307  37.151 -14.214  1.00  0.00              
ATOM     42  CA  TYR    64       1.240  36.955 -15.301  1.00  0.00              
ATOM     43  C   TYR    64       2.312  38.038 -15.401  1.00  0.00              
ATOM     44  O   TYR    64       3.385  37.805 -15.948  1.00  0.00              
ATOM     45  N   ALA    74       2.049  39.251 -14.906  1.00  0.00              
ATOM     46  CA  ALA    74       2.976  40.373 -14.831  1.00  0.00              
ATOM     47  C   ALA    74       3.986  39.988 -13.786  1.00  0.00              
ATOM     48  O   ALA    74       5.163  39.993 -14.112  1.00  0.00              
ATOM     49  N   LEU    75       3.595  39.620 -12.560  1.00  0.00              
ATOM     50  CA  LEU    75       4.537  39.210 -11.516  1.00  0.00              
ATOM     51  C   LEU    75       5.246  37.890 -11.895  1.00  0.00              
ATOM     52  O   LEU    75       6.411  37.734 -11.559  1.00  0.00              
ATOM     53  N   SER    76       4.682  36.929 -12.646  1.00  0.00              
ATOM     54  CA  SER    76       5.393  35.709 -12.964  1.00  0.00              
ATOM     55  C   SER    76       6.440  35.877 -14.036  1.00  0.00              
ATOM     56  O   SER    76       7.417  35.134 -14.061  1.00  0.00              
ATOM     57  N   LYS    77       6.259  36.824 -14.948  1.00  0.00              
ATOM     58  CA  LYS    77       7.194  36.988 -16.030  1.00  0.00              
ATOM     59  C   LYS    77       8.338  37.927 -15.674  1.00  0.00              
ATOM     60  O   LYS    77       9.242  38.138 -16.477  1.00  0.00              
ATOM     61  N   GLU    78       8.367  38.457 -14.442  1.00  0.00              
ATOM     62  CA  GLU    78       9.474  39.247 -13.897  1.00  0.00              
ATOM     63  C   GLU    78      10.327  38.352 -12.973  1.00  0.00              
ATOM     64  O   GLU    78      10.494  38.513 -11.748  1.00  0.00              
ATOM     65  N   GLY    79      10.856  37.318 -13.632  1.00  0.00              
ATOM     66  CA  GLY    79      11.733  36.365 -12.989  1.00  0.00              
ATOM     67  C   GLY    79      13.083  36.994 -12.739  1.00  0.00              
ATOM     68  O   GLY    79      13.540  37.755 -13.583  1.00  0.00              
ATOM     69  N   VAL    80      13.708  36.782 -11.576  1.00  0.00              
ATOM     70  CA  VAL    80      15.049  37.259 -11.349  1.00  0.00              
ATOM     71  C   VAL    80      16.052  36.336 -12.038  1.00  0.00              
ATOM     72  O   VAL    80      16.621  35.392 -11.491  1.00  0.00              
ATOM     73  N   GLU    81      16.210  36.646 -13.331  1.00  0.00              
ATOM     74  CA  GLU    81      17.117  36.000 -14.280  1.00  0.00              
ATOM     75  C   GLU    81      17.010  34.473 -14.297  1.00  0.00              
ATOM     76  O   GLU    81      17.892  33.727 -13.872  1.00  0.00              
ATOM     77  N   HIS    82      15.841  34.043 -14.789  1.00  0.00              
ATOM     78  CA  HIS    82      15.496  32.645 -14.965  1.00  0.00              
ATOM     79  C   HIS    82      14.886  31.980 -13.741  1.00  0.00              
ATOM     80  O   HIS    82      14.252  30.931 -13.852  1.00  0.00              
ATOM     81  N   VAL    83      15.031  32.600 -12.569  1.00  0.00              
ATOM     82  CA  VAL    83      14.622  31.996 -11.314  1.00  0.00              
ATOM     83  C   VAL    83      13.543  32.744 -10.531  1.00  0.00              
ATOM     84  O   VAL    83      13.302  33.941 -10.695  1.00  0.00              
ATOM     85  N   LEU    84      12.824  32.019  -9.689  1.00  0.00              
ATOM     86  CA  LEU    84      11.872  32.663  -8.803  1.00  0.00              
ATOM     87  C   LEU    84      12.000  32.003  -7.460  1.00  0.00              
ATOM     88  O   LEU    84      12.218  30.799  -7.380  1.00  0.00              
ATOM     89  N   THR    85      11.928  32.790  -6.392  1.00  0.00              
ATOM     90  CA  THR    85      11.850  32.222  -5.068  1.00  0.00              
ATOM     91  C   THR    85      10.354  32.351  -4.773  1.00  0.00              
ATOM     92  O   THR    85       9.758  33.413  -4.856  1.00  0.00              
ATOM     93  N   SER    86       9.683  31.246  -4.497  1.00  0.00              
ATOM     94  CA  SER    86       8.250  31.211  -4.278  1.00  0.00              
ATOM     95  C   SER    86       7.978  30.626  -2.927  1.00  0.00              
ATOM     96  O   SER    86       8.417  29.530  -2.587  1.00  0.00              
ATOM     97  N   GLU    87       7.166  31.366  -2.197  1.00  0.00              
ATOM     98  CA  GLU    87       6.748  30.937  -0.889  1.00  0.00              
ATOM     99  C   GLU    87       5.233  30.748  -0.854  1.00  0.00              
ATOM    100  O   GLU    87       4.493  31.610  -1.293  1.00  0.00              
ATOM    101  N   VAL    88       4.738  29.583  -0.441  1.00  0.00              
ATOM    102  CA  VAL    88       3.324  29.372  -0.196  1.00  0.00              
ATOM    103  C   VAL    88       3.077  29.565   1.287  1.00  0.00              
ATOM    104  O   VAL    88       3.807  29.063   2.133  1.00  0.00              
ATOM    105  N   ALA    89       2.038  30.276   1.655  1.00  0.00              
ATOM    106  CA  ALA    89       1.679  30.477   3.047  1.00  0.00              
ATOM    107  C   ALA    89       0.209  30.798   3.084  1.00  0.00              
ATOM    108  O   ALA    89      -0.218  31.742   2.432  1.00  0.00              
ATOM    109  N   LYS    90      -0.645  30.050   3.783  1.00  0.00              
ATOM    110  CA  LYS    90      -2.019  30.538   3.878  1.00  0.00              
ATOM    111  C   LYS    90      -2.088  31.600   4.957  1.00  0.00              
ATOM    112  O   LYS    90      -1.931  31.279   6.132  1.00  0.00              
ATOM    113  N   PHE    91      -2.281  32.870   4.573  1.00  0.00              
ATOM    114  CA  PHE    91      -2.406  33.974   5.520  1.00  0.00              
ATOM    115  C   PHE    91      -3.458  33.684   6.584  1.00  0.00              
ATOM    116  O   PHE    91      -3.315  34.104   7.728  1.00  0.00              
ATOM    117  N   SER    92      -4.520  32.936   6.266  1.00  0.00              
ATOM    118  CA  SER    92      -5.522  32.580   7.266  1.00  0.00              
ATOM    119  C   SER    92      -5.075  31.546   8.287  1.00  0.00              
ATOM    120  O   SER    92      -5.435  31.711   9.449  1.00  0.00              
ATOM    121  N   HIS    93      -4.282  30.524   7.892  1.00  0.00              
ATOM    122  CA  HIS    93      -3.772  29.450   8.749  1.00  0.00              
ATOM    123  C   HIS    93      -2.914  30.106   9.822  1.00  0.00              
ATOM    124  O   HIS    93      -2.217  31.064   9.494  1.00  0.00              
ATOM    125  N   LEU    94      -2.961  29.707  11.104  1.00  0.00              
ATOM    126  CA  LEU    94      -2.060  30.179  12.133  1.00  0.00              
ATOM    127  C   LEU    94      -0.617  29.979  11.706  1.00  0.00              
ATOM    128  O   LEU    94       0.127  30.948  11.732  1.00  0.00              
ATOM    129  N   GLY    95      -0.226  28.796  11.206  1.00  0.00              
ATOM    130  CA  GLY    95       1.140  28.508  10.780  1.00  0.00              
ATOM    131  C   GLY    95       1.569  29.187   9.513  1.00  0.00              
ATOM    132  O   GLY    95       2.753  29.452   9.322  1.00  0.00              
ATOM    133  N   LYS    96       0.612  29.454   8.632  1.00  0.00              
ATOM    134  CA  LYS    96       0.883  30.126   7.371  1.00  0.00              
ATOM    135  C   LYS    96       1.246  31.577   7.633  1.00  0.00              
ATOM    136  O   LYS    96       2.236  32.110   7.130  1.00  0.00              
ATOM    137  N   ASP    97       0.443  32.198   8.489  1.00  0.00              
ATOM    138  CA  ASP    97       0.661  33.565   8.877  1.00  0.00              
ATOM    139  C   ASP    97       1.980  33.806   9.626  1.00  0.00              
ATOM    140  O   ASP    97       2.618  34.847   9.430  1.00  0.00              
ATOM    141  N   GLU    98       2.394  32.861  10.488  1.00  0.00              
ATOM    142  CA  GLU    98       3.649  32.939  11.228  1.00  0.00              
ATOM    143  C   GLU    98       4.804  32.892  10.249  1.00  0.00              
ATOM    144  O   GLU    98       5.789  33.594  10.446  1.00  0.00              
ATOM    145  N   PHE    99       4.698  32.087   9.186  1.00  0.00              
ATOM    146  CA  PHE    99       5.738  31.974   8.180  1.00  0.00              
ATOM    147  C   PHE    99       5.750  33.225   7.349  1.00  0.00              
ATOM    148  O   PHE    99       6.814  33.669   6.919  1.00  0.00              
ATOM    149  N   TRP   100       4.562  33.801   7.149  1.00  0.00              
ATOM    150  CA  TRP   100       4.452  35.056   6.437  1.00  0.00              
ATOM    151  C   TRP   100       5.212  36.142   7.187  1.00  0.00              
ATOM    152  O   TRP   100       5.905  36.942   6.570  1.00  0.00              
ATOM    153  N   SER   101       5.137  36.161   8.519  1.00  0.00              
ATOM    154  CA  SER   101       5.903  37.085   9.359  1.00  0.00              
ATOM    155  C   SER   101       7.419  36.985   9.252  1.00  0.00              
ATOM    156  O   SER   101       8.115  37.993   9.311  1.00  0.00              
ATOM    157  N   VAL   102       7.930  35.767   9.130  1.00  0.00              
ATOM    158  CA  VAL   102       9.348  35.473   9.027  1.00  0.00              
ATOM    159  C   VAL   102       9.817  35.965   7.682  1.00  0.00              
ATOM    160  O   VAL   102      10.823  36.644   7.550  1.00  0.00              
ATOM    161  N   MET   103       9.028  35.636   6.669  1.00  0.00              
ATOM    162  CA  MET   103       9.272  35.996   5.288  1.00  0.00              
ATOM    163  C   MET   103       9.244  37.506   5.090  1.00  0.00              
ATOM    164  O   MET   103      10.009  38.071   4.326  1.00  0.00              
ATOM    165  N   ASP   104       8.372  38.193   5.823  1.00  0.00              
ATOM    166  CA  ASP   104       8.318  39.647   5.796  1.00  0.00              
ATOM    167  C   ASP   104       9.565  40.259   6.415  1.00  0.00              
ATOM    168  O   ASP   104      10.018  41.315   6.011  1.00  0.00              
END
