
#######################################################
#                                                     #
#                        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 T0347AL509_1-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347AL509_1-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      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      H      51          4.270
LGA    I      52      I      52          1.591
LGA    V      53      V      53          0.622
LGA    P      54      P      54          0.659
LGA    V      55      V      55          0.694
LGA    V      56      V      56          1.068
LGA    A      57      A      57          1.597
LGA    G      58      G      58          1.567
LGA    P      59      P      59          1.268
LGA    K      60      K      60          1.874
LGA    D      61      D      61          2.449
LGA    R      62      R      62          2.024
LGA    A      63      A      63          1.044
LGA    Y      64      Y      64          0.695
LGA    L      65      L      65          0.680
LGA    I      66      I      66          0.876
LGA    D      67      D      67          1.151
LGA    H      68      H      68          1.663
LGA    H      69      H      69          0.788
LGA    H      70      H      70          1.078
LGA    L      71      L      71          1.489
LGA    V      72      V      72          1.214
LGA    L      73      L      73          0.603
LGA    A      74      A      74          0.711
LGA    L      75      L      75          0.734
LGA    S      76      S      76          0.555
LGA    K      77      K      77          0.174
LGA    E      78      E      78          0.120
LGA    G      79      G      79          0.277
LGA    V      80      V      80          0.484
LGA    E      81      E      81          0.587
LGA    H      82      H      82          0.581
LGA    V      83      V      83          0.719
LGA    L      84      L      84          1.217
LGA    T      85      T      85          0.884
LGA    S      86      S      86          0.793
LGA    E      87      E      87          0.850
LGA    V      88      V      88          1.692
LGA    A      89      A      89          1.222
LGA    K      90      K      90          4.940
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    F      91      V     102           #
LGA    S      92      M     103           -
LGA    H      93      D     104           -
LGA    -       -      H     105           -
LGA    L     108      R     106          5.617
LGA    -       -      N     107           -
LGA    -       -      L     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   89    5.0     41    1.73    97.56     43.874     2.238

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.228283 * X  +  -0.588652 * Y  +  -0.775484 * Z  +  41.354557
  Y_new =   0.633297 * X  +   0.515196 * Y  +  -0.577501 * Z  +  36.949123
  Z_new =   0.739474 * X  +  -0.622946 * Y  +   0.255181 * Z  +  12.870511 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.182011    1.959582  [ DEG:   -67.7242    112.2758 ]
  Theta =  -0.832288   -2.309304  [ DEG:   -47.6866   -132.3134 ]
  Phi   =   1.916766   -1.224826  [ DEG:   109.8226    -70.1774 ]
 
# 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: T0347AL509_1-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL509_1-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   89   5.0   41   1.73   97.56  43.874
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL509_1-D1
REMARK Aligment from pdb entry: 1vk1_A
ATOM     33  N   HIS    51      16.303  37.978 -13.239  1.00  0.00              
ATOM     34  CA  HIS    51      16.247  37.666 -11.821  1.00  0.00              
ATOM     35  C   HIS    51      14.898  37.037 -11.516  1.00  0.00              
ATOM     36  O   HIS    51      13.876  37.746 -11.514  1.00  0.00              
ATOM     37  N   ILE    52      14.852  35.722 -11.248  1.00  0.00              
ATOM     38  CA  ILE    52      13.551  35.053 -11.111  1.00  0.00              
ATOM     39  C   ILE    52      12.782  35.577  -9.911  1.00  0.00              
ATOM     40  O   ILE    52      13.377  35.989  -8.915  1.00  0.00              
ATOM     41  N   VAL    53      11.469  35.554 -10.008  1.00  0.00              
ATOM     42  CA  VAL    53      10.641  35.738  -8.838  1.00  0.00              
ATOM     43  C   VAL    53      10.956  34.648  -7.839  1.00  0.00              
ATOM     44  O   VAL    53      11.256  33.526  -8.232  1.00  0.00              
ATOM     45  N   PRO    54      10.859  34.961  -6.557  1.00  0.00              
ATOM     46  CA  PRO    54      10.809  33.933  -5.506  1.00  0.00              
ATOM     47  C   PRO    54       9.409  33.927  -4.955  1.00  0.00              
ATOM     48  O   PRO    54       8.898  34.979  -4.552  1.00  0.00              
ATOM     49  N   VAL    55       8.784  32.741  -4.978  1.00  0.00              
ATOM     50  CA  VAL    55       7.401  32.561  -4.601  1.00  0.00              
ATOM     51  C   VAL    55       7.254  31.437  -3.602  1.00  0.00              
ATOM     52  O   VAL    55       8.092  30.545  -3.529  1.00  0.00              
ATOM     53  N   VAL    56       6.145  31.442  -2.879  1.00  0.00              
ATOM     54  CA  VAL    56       5.757  30.325  -2.008  1.00  0.00              
ATOM     55  C   VAL    56       4.260  30.148  -2.102  1.00  0.00              
ATOM     56  O   VAL    56       3.514  31.118  -2.067  1.00  0.00              
ATOM     57  N   ALA    57       3.795  28.924  -2.216  1.00  0.00              
ATOM     58  CA  ALA    57       2.359  28.707  -2.316  1.00  0.00              
ATOM     59  C   ALA    57       1.662  29.086  -1.002  1.00  0.00              
ATOM     60  O   ALA    57       2.134  28.783   0.089  1.00  0.00              
ATOM     61  N   GLY    58       0.529  29.745  -1.123  1.00  0.00              
ATOM     62  CA  GLY    58      -0.319  30.061   0.024  1.00  0.00              
ATOM     63  C   GLY    58      -1.202  28.826   0.293  1.00  0.00              
ATOM     64  O   GLY    58      -1.947  28.396  -0.577  1.00  0.00              
ATOM     65  N   PRO    59      -1.110  28.238   1.497  1.00  0.00              
ATOM     66  CA  PRO    59      -1.878  27.012   1.791  1.00  0.00              
ATOM     67  C   PRO    59      -3.378  27.141   1.526  1.00  0.00              
ATOM     68  O   PRO    59      -3.975  28.188   1.793  1.00  0.00              
ATOM     69  N   LYS    60      -3.962  26.080   0.984  1.00  0.00              
ATOM     70  CA  LYS    60      -5.382  26.054   0.674  1.00  0.00              
ATOM     71  C   LYS    60      -5.783  26.798  -0.596  1.00  0.00              
ATOM     72  O   LYS    60      -6.975  26.905  -0.897  1.00  0.00              
ATOM     73  N   ASP    61      -4.389  27.971  -4.882  1.00  0.00              
ATOM     74  CA  ASP    61      -3.415  27.830  -5.954  1.00  0.00              
ATOM     75  C   ASP    61      -2.757  29.194  -6.283  1.00  0.00              
ATOM     76  O   ASP    61      -2.362  29.454  -7.409  1.00  0.00              
ATOM     77  N   ARG    62      -2.615  30.030  -5.269  1.00  0.00              
ATOM     78  CA  ARG    62      -1.990  31.338  -5.385  1.00  0.00              
ATOM     79  C   ARG    62      -0.648  31.305  -4.654  1.00  0.00              
ATOM     80  O   ARG    62      -0.397  30.416  -3.830  1.00  0.00              
ATOM     81  N   ALA    63       0.189  32.297  -4.941  1.00  0.00              
ATOM     82  CA  ALA    63       1.527  32.381  -4.399  1.00  0.00              
ATOM     83  C   ALA    63       1.769  33.690  -3.683  1.00  0.00              
ATOM     84  O   ALA    63       1.405  34.767  -4.174  1.00  0.00              
ATOM     85  N   TYR    64       2.407  33.589  -2.526  1.00  0.00              
ATOM     86  CA  TYR    64       3.055  34.704  -1.878  1.00  0.00              
ATOM     87  C   TYR    64       4.265  35.112  -2.679  1.00  0.00              
ATOM     88  O   TYR    64       5.112  34.286  -2.975  1.00  0.00              
ATOM     89  N   LEU    65       4.369  36.403  -3.004  1.00  0.00              
ATOM     90  CA  LEU    65       5.606  36.947  -3.522  1.00  0.00              
ATOM     91  C   LEU    65       6.564  37.040  -2.339  1.00  0.00              
ATOM     92  O   LEU    65       6.336  37.788  -1.417  1.00  0.00              
ATOM     93  N   ILE    66       7.643  36.277  -2.399  1.00  0.00              
ATOM     94  CA  ILE    66       8.702  36.332  -1.384  1.00  0.00              
ATOM     95  C   ILE    66       9.652  37.460  -1.783  1.00  0.00              
ATOM     96  O   ILE    66       9.953  38.322  -0.996  1.00  0.00              
ATOM     97  N   ASP    67      10.110  37.429  -3.029  1.00  0.00              
ATOM     98  CA  ASP    67      10.978  38.442  -3.576  1.00  0.00              
ATOM     99  C   ASP    67      10.576  38.731  -5.004  1.00  0.00              
ATOM    100  O   ASP    67      10.369  37.813  -5.786  1.00  0.00              
ATOM    101  N   HIS    68      10.491  40.013  -5.333  1.00  0.00              
ATOM    102  CA  HIS    68      10.197  40.451  -6.694  1.00  0.00              
ATOM    103  C   HIS    68       8.955  41.303  -6.870  1.00  0.00              
ATOM    104  O   HIS    68       8.384  41.332  -7.953  1.00  0.00              
ATOM    105  N   HIS    69       8.551  42.058  -5.857  1.00  0.00              
ATOM    106  CA  HIS    69       7.383  42.922  -5.978  1.00  0.00              
ATOM    107  C   HIS    69       7.491  43.916  -7.120  1.00  0.00              
ATOM    108  O   HIS    69       6.535  44.117  -7.858  1.00  0.00              
ATOM    109  N   HIS    70       8.645  44.555  -7.269  1.00  0.00              
ATOM    110  CA  HIS    70       8.806  45.560  -8.306  1.00  0.00              
ATOM    111  C   HIS    70       8.848  44.938  -9.685  1.00  0.00              
ATOM    112  O   HIS    70       8.317  45.527 -10.645  1.00  0.00              
ATOM    113  N   LEU    71       9.446  43.754  -9.796  1.00  0.00              
ATOM    114  CA  LEU    71       9.440  42.990 -11.047  1.00  0.00              
ATOM    115  C   LEU    71       8.039  42.558 -11.455  1.00  0.00              
ATOM    116  O   LEU    71       7.617  42.757 -12.597  1.00  0.00              
ATOM    117  N   VAL    72       7.279  42.014 -10.509  1.00  0.00              
ATOM    118  CA  VAL    72       5.888  41.629 -10.756  1.00  0.00              
ATOM    119  C   VAL    72       5.042  42.822 -11.161  1.00  0.00              
ATOM    120  O   VAL    72       4.330  42.782 -12.174  1.00  0.00              
ATOM    121  N   LEU    73       5.133  43.904 -10.404  1.00  0.00              
ATOM    122  CA  LEU    73       4.309  45.061 -10.667  1.00  0.00              
ATOM    123  C   LEU    73       4.709  45.727 -11.986  1.00  0.00              
ATOM    124  O   LEU    73       3.848  46.202 -12.730  1.00  0.00              
ATOM    125  N   ALA    74       6.007  45.765 -12.284  1.00  0.00              
ATOM    126  CA  ALA    74       6.463  46.333 -13.539  1.00  0.00              
ATOM    127  C   ALA    74       5.997  45.526 -14.735  1.00  0.00              
ATOM    128  O   ALA    74       5.540  46.085 -15.737  1.00  0.00              
ATOM    129  N   LEU    75       6.081  44.211 -14.629  1.00  0.00              
ATOM    130  CA  LEU    75       5.595  43.349 -15.685  1.00  0.00              
ATOM    131  C   LEU    75       4.089  43.498 -15.881  1.00  0.00              
ATOM    132  O   LEU    75       3.613  43.513 -17.016  1.00  0.00              
ATOM    133  N   SER    76       3.335  43.578 -14.796  1.00  0.00              
ATOM    134  CA  SER    76       1.899  43.797 -14.916  1.00  0.00              
ATOM    135  C   SER    76       1.618  45.121 -15.602  1.00  0.00              
ATOM    136  O   SER    76       0.766  45.190 -16.498  1.00  0.00              
ATOM    137  N   LYS    77       2.345  46.168 -15.226  1.00  0.00              
ATOM    138  CA  LYS    77       2.153  47.493 -15.840  1.00  0.00              
ATOM    139  C   LYS    77       2.451  47.453 -17.336  1.00  0.00              
ATOM    140  O   LYS    77       1.774  48.135 -18.133  1.00  0.00              
ATOM    141  N   GLU    78       3.439  46.656 -17.735  1.00  0.00              
ATOM    142  CA  GLU    78       3.807  46.513 -19.146  1.00  0.00              
ATOM    143  C   GLU    78       2.837  45.635 -19.941  1.00  0.00              
ATOM    144  O   GLU    78       2.924  45.566 -21.172  1.00  0.00              
ATOM    145  N   GLY    79       1.931  44.955 -19.259  1.00  0.00              
ATOM    146  CA  GLY    79       0.958  44.079 -19.899  1.00  0.00              
ATOM    147  C   GLY    79       1.415  42.641 -20.105  1.00  0.00              
ATOM    148  O   GLY    79       0.801  41.919 -20.872  1.00  0.00              
ATOM    149  N   VAL    80       2.454  42.199 -19.386  1.00  0.00              
ATOM    150  CA  VAL    80       2.919  40.838 -19.494  1.00  0.00              
ATOM    151  C   VAL    80       1.970  39.891 -18.778  1.00  0.00              
ATOM    152  O   VAL    80       1.082  40.334 -18.037  1.00  0.00              
ATOM    153  N   GLU    81       2.187  38.602 -18.978  1.00  0.00              
ATOM    154  CA  GLU    81       1.332  37.561 -18.439  1.00  0.00              
ATOM    155  C   GLU    81       1.983  36.648 -17.425  1.00  0.00              
ATOM    156  O   GLU    81       1.294  36.127 -16.570  1.00  0.00              
ATOM    157  N   HIS    82       3.291  36.413 -17.544  1.00  0.00              
ATOM    158  CA  HIS    82       3.956  35.410 -16.733  1.00  0.00              
ATOM    159  C   HIS    82       5.347  35.880 -16.362  1.00  0.00              
ATOM    160  O   HIS    82       5.870  36.815 -16.975  1.00  0.00              
ATOM    161  N   VAL    83       5.946  35.228 -15.369  1.00  0.00              
ATOM    162  CA  VAL    83       7.335  35.488 -15.052  1.00  0.00              
ATOM    163  C   VAL    83       8.004  34.205 -14.590  1.00  0.00              
ATOM    164  O   VAL    83       7.401  33.395 -13.885  1.00  0.00              
ATOM    165  N   LEU    84       9.282  34.021 -14.941  1.00  0.00              
ATOM    166  CA  LEU    84      10.052  32.901 -14.410  1.00  0.00              
ATOM    167  C   LEU    84      10.237  33.024 -12.902  1.00  0.00              
ATOM    168  O   LEU    84      10.567  34.102 -12.410  1.00  0.00              
ATOM    169  N   THR    85      10.018  31.918 -12.211  1.00  0.00              
ATOM    170  CA  THR    85       9.893  31.886 -10.780  1.00  0.00              
ATOM    171  C   THR    85      10.561  30.651 -10.173  1.00  0.00              
ATOM    172  O   THR    85      10.593  29.582 -10.766  1.00  0.00              
ATOM    173  N   SER    86      11.041  30.825  -8.954  1.00  0.00              
ATOM    174  CA  SER    86      11.519  29.729  -8.129  1.00  0.00              
ATOM    175  C   SER    86      10.502  29.579  -7.019  1.00  0.00              
ATOM    176  O   SER    86      10.194  30.550  -6.336  1.00  0.00              
ATOM    177  N   GLU    87       9.990  28.368  -6.835  1.00  0.00              
ATOM    178  CA  GLU    87       8.982  28.072  -5.833  1.00  0.00              
ATOM    179  C   GLU    87       9.668  27.481  -4.586  1.00  0.00              
ATOM    180  O   GLU    87      10.354  26.470  -4.681  1.00  0.00              
ATOM    181  N   VAL    88       9.490  28.137  -3.453  1.00  0.00              
ATOM    182  CA  VAL    88      10.106  27.813  -2.180  1.00  0.00              
ATOM    183  C   VAL    88       9.074  27.212  -1.233  1.00  0.00              
ATOM    184  O   VAL    88       7.869  27.480  -1.353  1.00  0.00              
ATOM    185  N   ALA    89       9.548  26.413  -0.274  1.00  0.00              
ATOM    186  CA  ALA    89       8.763  26.088   0.911  1.00  0.00              
ATOM    187  C   ALA    89       9.077  27.187   1.917  1.00  0.00              
ATOM    188  O   ALA    89      10.167  27.223   2.463  1.00  0.00              
ATOM    189  N   LYS    90       8.119  28.063   2.147  1.00  0.00              
ATOM    190  CA  LYS    90       8.376  29.280   2.921  1.00  0.00              
ATOM    191  C   LYS    90       8.841  28.965   4.352  1.00  0.00              
ATOM    192  O   LYS    90       9.678  29.670   4.896  1.00  0.00              
ATOM    193  N   PHE    91       8.334  27.873   4.936  1.00  0.00              
ATOM    194  CA  PHE    91       8.625  27.560   6.353  1.00  0.00              
ATOM    195  C   PHE    91       9.762  26.581   6.527  1.00  0.00              
ATOM    196  O   PHE    91      10.016  26.097   7.624  1.00  0.00              
ATOM    197  N   SER    92      10.495  26.350   5.452  1.00  0.00              
ATOM    198  CA  SER    92      11.775  25.709   5.546  1.00  0.00              
ATOM    199  C   SER    92      12.712  26.626   6.344  1.00  0.00              
ATOM    200  O   SER    92      12.716  27.854   6.127  1.00  0.00              
ATOM    201  N   HIS    93      13.497  26.048   7.257  1.00  0.00              
ATOM    202  CA  HIS    93      14.408  26.821   8.118  1.00  0.00              
ATOM    203  C   HIS    93      15.488  27.587   7.341  1.00  0.00              
ATOM    204  O   HIS    93      16.039  28.559   7.840  1.00  0.00              
ATOM    205  N   LEU   108      15.169  32.677   5.456  1.00  0.00              
ATOM    206  CA  LEU   108      15.215  33.642   6.561  1.00  0.00              
ATOM    207  C   LEU   108      14.710  34.995   6.102  1.00  0.00              
ATOM    208  O   LEU   108      14.872  35.370   4.940  1.00  0.00              
END
