
#######################################################
#                                                     #
#                        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 (  193),  selected   48 , name T0347AL333_1-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347AL333_1-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      17      P       7           -
LGA    R      18      R       8           -
LGA    P      19      L       9           -
LGA    T      20      S      10           -
LGA    Q      21      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    I      22      P      19          4.374
LGA    V      24      T      20          2.174
LGA    G      25      Q      21           -
LGA    F      26      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      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    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    R      27      P      59           #
LGA    W      36      K      60          3.085
LGA    R      37      D      61          2.186
LGA    A      63      R      62           #
LGA    Y      64      A      63          3.695
LGA    L      65      Y      64          2.054
LGA    I      66      L      65          1.763
LGA    D      67      I      66          1.616
LGA    H      68      D      67          3.849
LGA    H      69      H      68          2.571
LGA    V      80      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    E      81      T      85           #
LGA    H      82      S      86           -
LGA    V      83      E      87          5.404
LGA    L      84      V      88          5.657
LGA    T      85      A      89          3.430
LGA    S      86      K      90          3.417
LGA    E      87      F      91          4.040
LGA    V      88      S      92          4.594
LGA    A      89      H      93          5.051
LGA    K      90      -       -           -
LGA    F      91      -       -           -
LGA    S      92      -       -           -
LGA    H      93      -       -           -
LGA    L      94      L      94           #
LGA    G      95      G      95          0.441
LGA    K      96      K      96          1.682
LGA    D      97      D      97          1.974
LGA    E      98      E      98          1.289
LGA    F      99      F      99          1.570
LGA    W     100      W     100          1.791
LGA    S     101      S     101          1.460
LGA    V     102      V     102          1.537
LGA    M     103      M     103          1.564
LGA    D     104      D     104          1.708
LGA    H     105      H     105          2.087
LGA    R     106      R     106          2.256
LGA    N     107      N     107          2.905
LGA    L     108      L     108          4.336

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   89    5.0     31    3.07    48.39     23.250     0.979

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.347972 * X  +  -0.458543 * Y  +  -0.817713 * Z  +  77.887474
  Y_new =  -0.859990 * X  +  -0.191155 * Y  +   0.473155 * Z  +  54.664959
  Z_new =  -0.373272 * X  +   0.867870 * Y  +  -0.327826 * Z  +  -0.076409 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.931963   -1.209629  [ DEG:   110.6933    -69.3067 ]
  Theta =   0.382534    2.759059  [ DEG:    21.9176    158.0824 ]
  Phi   =  -1.955282    1.186311  [ DEG:  -112.0294     67.9706 ]
 
# 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_1-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_1-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   89   5.0   31   3.07   48.39  23.250
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_1-D1
REMARK Aligment from pdb entry: 1cxq_A
ATOM     13  N   LEU    17      15.081  53.764  -2.627  1.00  0.00              
ATOM     14  CA  LEU    17      14.296  53.678  -3.858  1.00  0.00              
ATOM     15  C   LEU    17      14.014  52.256  -4.282  1.00  0.00              
ATOM     16  O   LEU    17      13.504  52.004  -5.371  1.00  0.00              
ATOM     17  N   ARG    18      14.339  51.282  -3.421  1.00  0.00              
ATOM     18  CA  ARG    18      14.200  49.893  -3.783  1.00  0.00              
ATOM     19  C   ARG    18      12.733  49.473  -3.883  1.00  0.00              
ATOM     20  O   ARG    18      11.801  50.251  -3.636  1.00  0.00              
ATOM     21  N   PRO    19      12.497  48.236  -4.296  1.00  0.00              
ATOM     22  CA  PRO    19      11.149  47.740  -4.554  1.00  0.00              
ATOM     23  C   PRO    19      10.269  47.770  -3.294  1.00  0.00              
ATOM     24  O   PRO    19      10.718  47.541  -2.179  1.00  0.00              
ATOM     25  N   THR    20       9.006  48.020  -3.513  1.00  0.00              
ATOM     26  CA  THR    20       8.030  48.050  -2.436  1.00  0.00              
ATOM     27  C   THR    20       7.845  46.653  -1.838  1.00  0.00              
ATOM     28  O   THR    20       7.959  45.637  -2.542  1.00  0.00              
ATOM     29  N   GLN    21       7.502  46.649  -0.570  1.00  0.00              
ATOM     30  CA  GLN    21       7.448  45.398   0.240  1.00  0.00              
ATOM     31  C   GLN    21       6.100  44.752   0.085  1.00  0.00              
ATOM     32  O   GLN    21       5.236  44.867   0.954  1.00  0.00              
ATOM     33  N   ILE    22       5.869  44.147  -1.100  1.00  0.00              
ATOM     34  CA  ILE    22       4.582  43.586  -1.493  1.00  0.00              
ATOM     35  C   ILE    22       4.756  42.118  -1.815  1.00  0.00              
ATOM     36  O   ILE    22       5.654  41.745  -2.569  1.00  0.00              
ATOM     37  N   VAL    24       3.920  41.259  -1.209  1.00  0.00              
ATOM     38  CA  VAL    24       3.916  39.845  -1.494  1.00  0.00              
ATOM     39  C   VAL    24       2.750  39.467  -2.370  1.00  0.00              
ATOM     40  O   VAL    24       1.727  40.175  -2.401  1.00  0.00              
ATOM     41  N   GLY    25       2.861  38.311  -3.034  1.00  0.00              
ATOM     42  CA  GLY    25       1.738  37.610  -3.621  1.00  0.00              
ATOM     43  C   GLY    25       1.651  36.236  -2.944  1.00  0.00              
ATOM     44  O   GLY    25       2.663  35.586  -2.797  1.00  0.00              
ATOM     45  N   PHE    26       0.435  35.817  -2.581  1.00  0.00              
ATOM     46  CA  PHE    26       0.230  34.525  -1.912  1.00  0.00              
ATOM     47  C   PHE    26      -0.879  33.760  -2.599  1.00  0.00              
ATOM     48  O   PHE    26      -1.873  34.329  -2.991  1.00  0.00              
ATOM     49  N   ARG    27      -0.691  32.435  -2.699  1.00  0.00              
ATOM     50  CA  ARG    27      -1.684  31.549  -3.282  1.00  0.00              
ATOM     51  C   ARG    27      -1.574  30.188  -2.612  1.00  0.00              
ATOM     52  O   ARG    27      -0.610  29.889  -1.942  1.00  0.00              
ATOM     53  N   TRP    36      -2.583  29.354  -2.801  1.00  0.00              
ATOM     54  CA  TRP    36      -2.541  27.946  -2.491  1.00  0.00              
ATOM     55  C   TRP    36      -2.502  27.121  -3.784  1.00  0.00              
ATOM     56  O   TRP    36      -3.207  27.459  -4.731  1.00  0.00              
ATOM     57  N   ARG    37      -1.723  26.051  -3.771  1.00  0.00              
ATOM     58  CA  ARG    37      -1.655  25.131  -4.924  1.00  0.00              
ATOM     59  C   ARG    37      -1.634  23.716  -4.401  1.00  0.00              
ATOM     60  O   ARG    37      -0.934  23.392  -3.422  1.00  0.00              
ATOM    105  N   ALA    63       0.779  26.345   0.609  1.00  0.00              
ATOM    106  CA  ALA    63       0.629  27.790   0.684  1.00  0.00              
ATOM    107  C   ALA    63       1.960  28.368   0.239  1.00  0.00              
ATOM    108  O   ALA    63       3.000  28.025   0.789  1.00  0.00              
ATOM    109  N   TYR    64       1.915  29.252  -0.762  1.00  0.00              
ATOM    110  CA  TYR    64       3.076  29.794  -1.416  1.00  0.00              
ATOM    111  C   TYR    64       3.005  31.327  -1.395  1.00  0.00              
ATOM    112  O   TYR    64       2.030  31.912  -1.843  1.00  0.00              
ATOM    113  N   LEU    65       4.035  31.945  -0.850  1.00  0.00              
ATOM    114  CA  LEU    65       4.239  33.384  -0.923  1.00  0.00              
ATOM    115  C   LEU    65       5.493  33.654  -1.723  1.00  0.00              
ATOM    116  O   LEU    65       6.521  33.043  -1.514  1.00  0.00              
ATOM    117  N   ILE    66       5.374  34.634  -2.632  1.00  0.00              
ATOM    118  CA  ILE    66       6.531  35.218  -3.295  1.00  0.00              
ATOM    119  C   ILE    66       6.644  36.676  -2.864  1.00  0.00              
ATOM    120  O   ILE    66       5.671  37.452  -2.896  1.00  0.00              
ATOM    121  N   ASP    67       7.846  37.040  -2.435  1.00  0.00              
ATOM    122  CA  ASP    67       8.144  38.445  -2.174  1.00  0.00              
ATOM    123  C   ASP    67       8.423  39.091  -3.486  1.00  0.00              
ATOM    124  O   ASP    67       9.414  38.752  -4.143  1.00  0.00              
ATOM    125  N   HIS    68       7.607  40.021  -3.924  1.00  0.00              
ATOM    126  CA  HIS    68       7.805  40.609  -5.253  1.00  0.00              
ATOM    127  C   HIS    68       9.069  41.480  -5.269  1.00  0.00              
ATOM    128  O   HIS    68       9.532  41.772  -6.359  1.00  0.00              
ATOM    129  N   HIS    69       9.589  41.895  -4.119  1.00  0.00              
ATOM    130  CA  HIS    69      10.802  42.713  -4.114  1.00  0.00              
ATOM    131  C   HIS    69      12.031  41.881  -4.427  1.00  0.00              
ATOM    132  O   HIS    69      12.971  42.349  -5.079  1.00  0.00              
ATOM    133  N   VAL    80      12.113  40.668  -3.957  1.00  0.00              
ATOM    134  CA  VAL    80      13.303  39.880  -4.056  1.00  0.00              
ATOM    135  C   VAL    80      13.135  38.622  -4.867  1.00  0.00              
ATOM    136  O   VAL    80      14.147  37.945  -5.206  1.00  0.00              
ATOM    137  N   GLU    81      11.930  38.195  -5.106  1.00  0.00              
ATOM    138  CA  GLU    81      11.533  36.923  -5.729  1.00  0.00              
ATOM    139  C   GLU    81      11.729  35.717  -4.815  1.00  0.00              
ATOM    140  O   GLU    81      11.467  34.594  -5.241  1.00  0.00              
ATOM    141  N   HIS    82      12.028  35.922  -3.573  1.00  0.00              
ATOM    142  CA  HIS    82      12.135  34.842  -2.569  1.00  0.00              
ATOM    143  C   HIS    82      10.755  34.217  -2.399  1.00  0.00              
ATOM    144  O   HIS    82       9.761  34.917  -2.431  1.00  0.00              
ATOM    145  N   VAL    83      10.754  32.943  -2.139  1.00  0.00              
ATOM    146  CA  VAL    83       9.533  32.177  -1.885  1.00  0.00              
ATOM    147  C   VAL    83       9.574  31.593  -0.481  1.00  0.00              
ATOM    148  O   VAL    83      10.591  31.129   0.020  1.00  0.00              
ATOM    149  N   LEU    84       8.392  31.568   0.142  1.00  0.00              
ATOM    150  CA  LEU    84       8.152  30.779   1.341  1.00  0.00              
ATOM    151  C   LEU    84       7.035  29.819   1.012  1.00  0.00              
ATOM    152  O   LEU    84       5.979  30.244   0.517  1.00  0.00              
ATOM    153  N   THR    85       7.189  28.546   1.351  1.00  0.00              
ATOM    154  CA  THR    85       6.141  27.536   1.163  1.00  0.00              
ATOM    155  C   THR    85       5.981  26.749   2.438  1.00  0.00              
ATOM    156  O   THR    85       6.944  26.382   3.102  1.00  0.00              
ATOM    157  N   SER    86       4.700  26.506   2.773  1.00  0.00              
ATOM    158  CA  SER    86       4.317  25.623   3.877  1.00  0.00              
ATOM    159  C   SER    86       3.258  24.651   3.390  1.00  0.00              
ATOM    160  O   SER    86       2.528  24.917   2.432  1.00  0.00              
ATOM    161  N   GLU    87       3.151  23.494   4.027  1.00  0.00              
ATOM    162  CA AGLU    87       2.118  22.538   3.601  1.00  0.00              
ATOM    163  CA BGLU    87       2.211  22.393   3.788  1.00  0.00              
ATOM    164  C   GLU    87       1.053  22.423   4.708  1.00  0.00              
ATOM    165  O   GLU    87       1.268  22.624   5.904  1.00  0.00              
ATOM    166  N   VAL    88      -0.137  22.119   4.228  1.00  0.00              
ATOM    167  CA  VAL    88      -1.353  22.154   5.003  1.00  0.00              
ATOM    168  C   VAL    88      -2.276  21.004   4.578  1.00  0.00              
ATOM    169  O   VAL    88      -2.360  20.657   3.388  1.00  0.00              
ATOM    170  N   ALA    89      -3.014  20.482   5.545  1.00  0.00              
ATOM    171  CA  ALA    89      -3.993  19.437   5.228  1.00  0.00              
ATOM    172  C   ALA    89      -5.228  19.945   4.556  1.00  0.00              
ATOM    173  O   ALA    89      -5.858  19.213   3.802  1.00  0.00              
ATOM    174  N   LYS    90      -5.644  21.165   4.845  1.00  0.00              
ATOM    175  CA  LYS    90      -6.887  21.733   4.318  1.00  0.00              
ATOM    176  C   LYS    90      -6.675  23.183   3.936  1.00  0.00              
ATOM    177  O   LYS    90      -5.955  23.910   4.604  1.00  0.00              
ATOM    178  N   PHE    91      -7.371  23.649   2.928  1.00  0.00              
ATOM    179  CA  PHE    91      -7.320  25.042   2.514  1.00  0.00              
ATOM    180  C   PHE    91      -8.321  25.775   3.353  1.00  0.00              
ATOM    181  O   PHE    91      -9.561  25.571   3.230  1.00  0.00              
ATOM    182  N   SER    92      -7.892  26.550   4.305  1.00  0.00              
ATOM    183  CA  SER    92      -8.726  27.265   5.258  1.00  0.00              
ATOM    184  C   SER    92      -8.106  28.657   5.533  1.00  0.00              
ATOM    185  O   SER    92      -6.941  28.900   5.278  1.00  0.00              
ATOM    186  N   HIS    93      -8.932  29.515   6.103  1.00  0.00              
ATOM    187  CA  HIS    93      -8.447  30.795   6.596  1.00  0.00              
ATOM    188  C   HIS    93      -7.302  30.640   7.583  1.00  0.00              
ATOM    189  O   HIS    93      -6.282  31.354   7.487  1.00  0.00              
ATOM    190  N   LEU    94      -7.461  29.741   8.565  1.00  0.00              
ATOM    191  CA  LEU    94      -6.407  29.606   9.556  1.00  0.00              
ATOM    192  C   LEU    94      -5.148  29.050   8.903  1.00  0.00              
ATOM    193  O   LEU    94      -4.049  29.441   9.319  1.00  0.00              
ATOM    194  N   GLY    95      -5.236  28.182   7.879  1.00  0.00              
ATOM    195  CA  GLY    95      -4.021  27.713   7.213  1.00  0.00              
ATOM    196  C   GLY    95      -3.271  28.890   6.578  1.00  0.00              
ATOM    197  O   GLY    95      -2.061  28.984   6.645  1.00  0.00              
ATOM    198  N   LYS    96      -4.018  29.808   5.910  1.00  0.00              
ATOM    199  CA  LYS    96      -3.389  30.982   5.338  1.00  0.00              
ATOM    200  C   LYS    96      -2.651  31.811   6.390  1.00  0.00              
ATOM    201  O   LYS    96      -1.550  32.324   6.169  1.00  0.00              
ATOM    202  N   ASP    97      -3.302  31.979   7.540  1.00  0.00              
ATOM    203  CA  ASP    97      -2.732  32.745   8.653  1.00  0.00              
ATOM    204  C   ASP    97      -1.503  32.081   9.199  1.00  0.00              
ATOM    205  O   ASP    97      -0.469  32.725   9.460  1.00  0.00              
ATOM    206  N   GLU    98      -1.557  30.747   9.395  1.00  0.00              
ATOM    207  CA  GLU    98      -0.360  30.036   9.832  1.00  0.00              
ATOM    208  C   GLU    98       0.772  30.200   8.862  1.00  0.00              
ATOM    209  O   GLU    98       1.943  30.373   9.254  1.00  0.00              
ATOM    210  N   PHE    99       0.470  30.099   7.563  1.00  0.00              
ATOM    211  CA  PHE    99       1.454  30.293   6.519  1.00  0.00              
ATOM    212  C   PHE    99       2.084  31.676   6.613  1.00  0.00              
ATOM    213  O   PHE    99       3.313  31.817   6.601  1.00  0.00              
ATOM    214  N   TRP   100       1.261  32.711   6.672  1.00  0.00              
ATOM    215  CA  TRP   100       1.818  34.074   6.721  1.00  0.00              
ATOM    216  C   TRP   100       2.609  34.293   7.978  1.00  0.00              
ATOM    217  O   TRP   100       3.597  35.045   7.945  1.00  0.00              
ATOM    218  N   SER   101       2.214  33.706   9.108  1.00  0.00              
ATOM    219  CA  SER   101       3.014  33.868  10.316  1.00  0.00              
ATOM    220  C   SER   101       4.446  33.401  10.043  1.00  0.00              
ATOM    221  O   SER   101       5.434  34.045  10.422  1.00  0.00              
ATOM    222  N   VAL   102       4.561  32.237   9.411  1.00  0.00              
ATOM    223  CA  VAL   102       5.882  31.714   9.054  1.00  0.00              
ATOM    224  C   VAL   102       6.584  32.599   8.039  1.00  0.00              
ATOM    225  O   VAL   102       7.779  32.879   8.145  1.00  0.00              
ATOM    226  N   MET   103       5.843  33.061   7.022  1.00  0.00              
ATOM    227  CA  MET   103       6.460  33.936   6.015  1.00  0.00              
ATOM    228  C   MET   103       6.979  35.215   6.624  1.00  0.00              
ATOM    229  O   MET   103       8.051  35.700   6.222  1.00  0.00              
ATOM    230  N   ASP   104       6.282  35.790   7.602  1.00  0.00              
ATOM    231  CA  ASP   104       6.755  37.002   8.288  1.00  0.00              
ATOM    232  C   ASP   104       8.046  36.713   9.047  1.00  0.00              
ATOM    233  O   ASP   104       8.969  37.531   9.046  1.00  0.00              
ATOM    234  N   HIS   105       8.121  35.558   9.704  1.00  0.00              
ATOM    235  CA  HIS   105       9.364  35.165  10.404  1.00  0.00              
ATOM    236  C   HIS   105      10.523  35.107   9.449  1.00  0.00              
ATOM    237  O   HIS   105      11.661  35.472   9.822  1.00  0.00              
ATOM    238  N   ARG   106      10.308  34.635   8.226  1.00  0.00              
ATOM    239  CA  ARG   106      11.363  34.484   7.247  1.00  0.00              
ATOM    240  C   ARG   106      11.711  35.788   6.543  1.00  0.00              
ATOM    241  O   ARG   106      12.880  36.154   6.417  1.00  0.00              
ATOM    242  N   ASN   107      10.710  36.490   6.034  1.00  0.00              
ATOM    243  CA  ASN   107      10.865  37.623   5.148  1.00  0.00              
ATOM    244  C   ASN   107      10.725  38.990   5.794  1.00  0.00              
ATOM    245  O   ASN   107      11.057  40.008   5.144  1.00  0.00              
ATOM    246  N   LEU   108      10.179  39.066   6.984  1.00  0.00              
ATOM    247  CA  LEU   108       9.823  40.325   7.597  1.00  0.00              
ATOM    248  C   LEU   108       8.362  40.642   7.337  1.00  0.00              
ATOM    249  O   LEU   108       7.645  39.942   6.628  1.00  0.00              
END
