
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0354TS550_2
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS550_2.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      E       2           -
LGA    I       3      I       3          2.366
LGA    Q       4      Q       4          1.742
LGA    E       5      E       5          2.438
LGA    I       6      I       6          2.151
LGA    S       7      S       7          1.925
LGA    K       8      K       8          2.602
LGA    L       9      L       9          1.222
LGA    A      10      A      10          2.402
LGA    I      11      I      11          3.708
LGA    E      12      E      12          2.724
LGA    A      13      A      13          0.948
LGA    L      14      L      14          3.870
LGA    E      15      E      15          4.201
LGA    D      16      D      16          1.620
LGA    I      17      I      17          2.333
LGA    K      18      K      18          0.721
LGA    G      19      -       -           -
LGA    K      20      G      19          5.607
LGA    D      21      K      20          2.956
LGA    I      22      D      21          3.959
LGA    I      23      I      22          3.528
LGA    E      24      I      23          2.708
LGA    L      25      E      24          2.428
LGA    D      26      L      25          1.596
LGA    -       -      D      26           -
LGA    -       -      T      27           -
LGA    -       -      S      28           -
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    R      36      M      37          1.532
LGA    M      37      I      38          1.632
LGA    I      38      V      39          0.943
LGA    V      39      A      40          2.485
LGA    A      40      T      41          1.151
LGA    T      41      G      42          1.470
LGA    G      42      D      43          1.322
LGA    D      43      S      44          1.243
LGA    S      44      N      45          3.795
LGA    N      45      -       -           -
LGA    R      46      R      46          2.933
LGA    Q      47      Q      47          1.910
LGA    V      48      V      48          1.269
LGA    K      49      K      49          1.264
LGA    A      50      A      50          1.206
LGA    L      51      L      51          0.722
LGA    A      52      A      52          0.419
LGA    N      53      N      53          0.353
LGA    S      54      S      54          0.868
LGA    V      55      V      55          0.743
LGA    Q      56      Q      56          0.645
LGA    V      57      V      57          1.706
LGA    K      58      K      58          1.769
LGA    L      59      L      59          0.770
LGA    K      60      K      60          1.548
LGA    E      61      E      61          3.238
LGA    -       -      A      62           -
LGA    -       -      G      63           -
LGA    -       -      V      64           -
LGA    -       -      D      65           -
LGA    -       -      I      66           -
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    -       -      S      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      W      77           -
LGA    -       -      V      78           -
LGA    -       -      L      79           -
LGA    -       -      V      80           -
LGA    -       -      D      81           -
LGA    -       -      A      82           -
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    -       -      H      88           -
LGA    -       -      V      89           -
LGA    -       -      M      90           -
LGA    -       -      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    -       -      V      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      Y      97           -
LGA    -       -      Y      98           -
LGA    -       -      D      99           -
LGA    -       -      I     100           -
LGA    -       -      E     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    -       -      G     106           -
LGA    -       -      Q     107           -
LGA    -       -      K     108           -
LGA    -       -      P     109           -
LGA    -       -      S     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      V     113           -
LGA    -       -      G     114           -
LGA    -       -      A     115           -
LGA    -       -      A     116           -
LGA    -       -      K     117           -
LGA    -       -      P     118           -
LGA    -       -      W     119           -
LGA    -       -      S     120           -
LGA    -       -      A     121           -
LGA    -       -      V     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50  122    5.0     48    2.31    68.75     28.893     1.990

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.627042 * X  +   0.722700 * Y  +  -0.290728 * Z  +  11.868317
  Y_new =  -0.771293 * X  +   0.523674 * Y  +  -0.361763 * Z  +  25.051319
  Z_new =  -0.109199 * X  +   0.451077 * Y  +   0.885779 * Z  +   7.443047 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.471014   -2.670578  [ DEG:    26.9871   -153.0129 ]
  Theta =   0.109418    3.032175  [ DEG:     6.2692    173.7308 ]
  Phi   =  -0.888194    2.253399  [ DEG:   -50.8898    129.1102 ]
 
# 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: T0354TS550_2                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS550_2.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50  122   5.0   48   2.31   68.75  28.893
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS550_2
PFRMAT TS
TARGET T0354
MODEL 2
PARENT 1in0_A
ATOM      1  N   ILE     3      49.389  21.396  16.450  1.00  0.00
ATOM      2  CA  ILE     3      48.644  20.911  17.607  1.00  0.00
ATOM      3  C   ILE     3      49.533  20.454  18.779  1.00  0.00
ATOM      4  O   ILE     3      49.229  20.599  19.955  1.00  0.00
ATOM      5  N   GLN     4      50.667  19.849  18.489  1.00  0.00
ATOM      6  CA  GLN     4      51.624  19.307  19.400  1.00  0.00
ATOM      7  C   GLN     4      52.025  20.480  20.300  1.00  0.00
ATOM      8  O   GLN     4      52.009  20.478  21.539  1.00  0.00
ATOM      9  N   GLU     5      52.360  21.561  19.605  1.00  0.00
ATOM     10  CA  GLU     5      52.729  22.724  20.413  1.00  0.00
ATOM     11  C   GLU     5      51.536  23.270  21.210  1.00  0.00
ATOM     12  O   GLU     5      51.757  23.914  22.242  1.00  0.00
ATOM     13  N   ILE     6      50.310  23.095  20.717  1.00  0.00
ATOM     14  CA  ILE     6      49.154  23.618  21.400  1.00  0.00
ATOM     15  C   ILE     6      48.772  22.831  22.692  1.00  0.00
ATOM     16  O   ILE     6      48.317  23.330  23.750  1.00  0.00
ATOM     17  N   SER     7      48.920  21.514  22.636  1.00  0.00
ATOM     18  CA  SER     7      48.578  20.604  23.702  1.00  0.00
ATOM     19  C   SER     7      49.584  20.907  24.820  1.00  0.00
ATOM     20  O   SER     7      49.253  20.981  25.999  1.00  0.00
ATOM     21  N   LYS     8      50.797  21.198  24.352  1.00  0.00
ATOM     22  CA  LYS     8      51.847  21.556  25.282  1.00  0.00
ATOM     23  C   LYS     8      51.497  22.829  26.017  1.00  0.00
ATOM     24  O   LYS     8      51.567  22.841  27.246  1.00  0.00
ATOM     25  N   LEU     9      51.040  23.829  25.284  1.00  0.00
ATOM     26  CA  LEU     9      50.640  25.100  25.868  1.00  0.00
ATOM     27  C   LEU     9      49.477  24.899  26.850  1.00  0.00
ATOM     28  O   LEU     9      49.445  25.522  27.901  1.00  0.00
ATOM     29  N   ALA    10      48.476  24.108  26.578  1.00  0.00
ATOM     30  CA  ALA    10      47.310  23.856  27.408  1.00  0.00
ATOM     31  C   ALA    10      47.681  23.145  28.704  1.00  0.00
ATOM     32  O   ALA    10      47.160  23.492  29.779  1.00  0.00
ATOM     33  N   ILE    11      48.648  22.212  28.609  1.00  0.00
ATOM     34  CA  ILE    11      49.185  21.549  29.793  1.00  0.00
ATOM     35  C   ILE    11      49.826  22.612  30.680  1.00  0.00
ATOM     36  O   ILE    11      49.384  22.713  31.817  1.00  0.00
ATOM     37  N   GLU    12      50.739  23.426  30.090  1.00  0.00
ATOM     38  CA  GLU    12      51.327  24.468  30.919  1.00  0.00
ATOM     39  C   GLU    12      50.261  25.313  31.621  1.00  0.00
ATOM     40  O   GLU    12      50.349  25.656  32.799  1.00  0.00
ATOM     41  N   ALA    13      49.266  25.735  30.875  1.00  0.00
ATOM     42  CA  ALA    13      48.193  26.584  31.324  1.00  0.00
ATOM     43  C   ALA    13      47.393  25.861  32.419  1.00  0.00
ATOM     44  O   ALA    13      47.047  26.573  33.362  1.00  0.00
ATOM     45  N   LEU    14      47.175  24.569  32.318  1.00  0.00
ATOM     46  CA  LEU    14      46.515  23.866  33.446  1.00  0.00
ATOM     47  C   LEU    14      47.424  23.800  34.669  1.00  0.00
ATOM     48  O   LEU    14      46.944  23.871  35.802  1.00  0.00
ATOM     49  N   GLU    15      48.758  23.733  34.480  1.00  0.00
ATOM     50  CA  GLU    15      49.615  23.729  35.666  1.00  0.00
ATOM     51  C   GLU    15      49.555  25.091  36.340  1.00  0.00
ATOM     52  O   GLU    15      49.628  25.142  37.573  1.00  0.00
ATOM     53  N   ASP    16      49.503  26.176  35.564  1.00  0.00
ATOM     54  CA  ASP    16      49.449  27.502  36.214  1.00  0.00
ATOM     55  C   ASP    16      48.135  27.643  36.988  1.00  0.00
ATOM     56  O   ASP    16      48.006  28.143  38.098  1.00  0.00
ATOM     57  N   ILE    17      47.083  27.207  36.340  1.00  0.00
ATOM     58  CA  ILE    17      45.736  27.314  36.778  1.00  0.00
ATOM     59  C   ILE    17      45.542  26.567  38.115  1.00  0.00
ATOM     60  O   ILE    17      44.829  27.106  38.930  1.00  0.00
ATOM     61  N   LYS    18      43.560  27.017  37.840  1.00  0.00
ATOM     62  CA  LYS    18      42.579  26.702  38.903  1.00  0.00
ATOM     63  C   LYS    18      42.087  25.233  38.939  1.00  0.00
ATOM     64  O   LYS    18      42.214  24.480  37.980  1.00  0.00
ATOM     65  N   GLY    19      41.553  24.828  40.080  1.00  0.00
ATOM     66  CA  GLY    19      40.952  23.528  40.217  1.00  0.00
ATOM     67  C   GLY    19      39.535  23.621  39.718  1.00  0.00
ATOM     68  O   GLY    19      39.104  22.754  38.976  1.00  0.00
ATOM     69  N   LYS    20      38.798  24.641  40.178  1.00  0.00
ATOM     70  CA  LYS    20      37.473  25.020  39.630  1.00  0.00
ATOM     71  C   LYS    20      37.722  26.052  38.546  1.00  0.00
ATOM     72  O   LYS    20      38.107  27.176  38.841  1.00  0.00
ATOM     73  N   ASP    21      37.100  25.672  37.241  1.00  0.00
ATOM     74  CA  ASP    21      37.826  26.348  36.109  1.00  0.00
ATOM     75  C   ASP    21      38.480  25.261  35.291  1.00  0.00
ATOM     76  O   ASP    21      39.279  24.425  35.735  1.00  0.00
ATOM     77  N   ILE    22      38.088  25.159  34.033  1.00  0.00
ATOM     78  CA  ILE    22      38.563  24.104  33.148  1.00  0.00
ATOM     79  C   ILE    22      39.161  24.730  31.880  1.00  0.00
ATOM     80  O   ILE    22      38.528  25.659  31.348  1.00  0.00
ATOM     81  N   ILE    23      40.318  24.239  31.410  1.00  0.00
ATOM     82  CA  ILE    23      40.956  24.633  30.189  1.00  0.00
ATOM     83  C   ILE    23      41.193  23.338  29.412  1.00  0.00
ATOM     84  O   ILE    23      42.148  22.610  29.660  1.00  0.00
ATOM     85  N   GLU    24      40.320  22.955  28.495  1.00  0.00
ATOM     86  CA  GLU    24      40.512  21.722  27.749  1.00  0.00
ATOM     87  C   GLU    24      40.707  21.958  26.241  1.00  0.00
ATOM     88  O   GLU    24      40.124  22.827  25.566  1.00  0.00
ATOM     89  N   LEU    25      41.549  21.064  25.726  1.00  0.00
ATOM     90  CA  LEU    25      41.849  21.076  24.311  1.00  0.00
ATOM     91  C   LEU    25      41.018  20.028  23.609  1.00  0.00
ATOM     92  O   LEU    25      41.146  18.906  24.047  1.00  0.00
ATOM     93  N   ASP    26      40.278  20.297  22.553  1.00  0.00
ATOM     94  CA  ASP    26      39.615  19.207  21.830  1.00  0.00
ATOM     95  C   ASP    26      40.466  19.067  20.554  1.00  0.00
ATOM     96  O   ASP    26      40.255  19.788  19.589  1.00  0.00
ATOM     97  N   ARG    36      39.629  23.013  18.988  1.00  0.00
ATOM     98  CA  ARG    36      39.049  23.969  19.928  1.00  0.00
ATOM     99  C   ARG    36      39.623  23.822  21.335  1.00  0.00
ATOM    100  O   ARG    36      40.177  22.819  21.767  1.00  0.00
ATOM    101  N   MET    37      39.613  24.934  22.024  1.00  0.00
ATOM    102  CA  MET    37      40.091  24.989  23.400  1.00  0.00
ATOM    103  C   MET    37      38.857  25.512  24.171  1.00  0.00
ATOM    104  O   MET    37      38.371  26.626  23.852  1.00  0.00
ATOM    105  N   ILE    38      38.353  24.588  25.027  1.00  0.00
ATOM    106  CA  ILE    38      37.183  25.083  25.746  1.00  0.00
ATOM    107  C   ILE    38      37.572  25.541  27.146  1.00  0.00
ATOM    108  O   ILE    38      38.243  24.840  27.884  1.00  0.00
ATOM    109  N   VAL    39      37.261  26.774  27.515  1.00  0.00
ATOM    110  CA  VAL    39      37.536  27.363  28.810  1.00  0.00
ATOM    111  C   VAL    39      36.211  27.527  29.599  1.00  0.00
ATOM    112  O   VAL    39      35.232  28.109  29.116  1.00  0.00
ATOM    113  N   ALA    40      36.178  27.039  30.846  1.00  0.00
ATOM    114  CA  ALA    40      34.923  27.160  31.614  1.00  0.00
ATOM    115  C   ALA    40      35.189  27.579  33.043  1.00  0.00
ATOM    116  O   ALA    40      36.082  27.017  33.716  1.00  0.00
ATOM    117  N   THR    41      34.447  28.553  33.544  1.00  0.00
ATOM    118  CA  THR    41      34.597  28.865  34.997  1.00  0.00
ATOM    119  C   THR    41      33.334  29.476  35.587  1.00  0.00
ATOM    120  O   THR    41      32.230  29.496  35.013  1.00  0.00
ATOM    121  N   GLY    42      33.877  29.119  37.158  1.00  0.00
ATOM    122  CA  GLY    42      32.926  29.252  38.257  1.00  0.00
ATOM    123  C   GLY    42      32.541  30.721  38.384  1.00  0.00
ATOM    124  O   GLY    42      31.480  31.061  38.909  1.00  0.00
ATOM    125  N   ASP    43      33.410  31.595  37.891  1.00  0.00
ATOM    126  CA  ASP    43      33.154  33.028  37.944  1.00  0.00
ATOM    127  C   ASP    43      32.363  33.499  36.742  1.00  0.00
ATOM    128  O   ASP    43      32.211  32.782  35.757  1.00  0.00
ATOM    129  N   SER    44      31.867  34.726  36.839  1.00  0.00
ATOM    130  CA  SER    44      31.112  35.337  35.760  1.00  0.00
ATOM    131  C   SER    44      32.140  36.084  34.913  1.00  0.00
ATOM    132  O   SER    44      32.863  36.942  35.423  1.00  0.00
ATOM    133  N   ASN    45      32.358  35.765  33.831  1.00  0.00
ATOM    134  CA  ASN    45      33.046  36.326  32.655  1.00  0.00
ATOM    135  C   ASN    45      34.391  36.834  33.168  1.00  0.00
ATOM    136  O   ASN    45      35.382  36.816  32.441  1.00  0.00
ATOM    137  N   ARG    46      34.448  37.394  34.391  1.00  0.00
ATOM    138  CA  ARG    46      35.751  37.955  34.759  1.00  0.00
ATOM    139  C   ARG    46      36.795  36.852  34.709  1.00  0.00
ATOM    140  O   ARG    46      37.899  36.901  34.177  1.00  0.00
ATOM    141  N   GLN    47      36.421  35.786  35.414  1.00  0.00
ATOM    142  CA  GLN    47      37.308  34.631  35.627  1.00  0.00
ATOM    143  C   GLN    47      37.650  34.097  34.236  1.00  0.00
ATOM    144  O   GLN    47      38.822  33.748  34.043  1.00  0.00
ATOM    145  N   VAL    48      36.760  34.053  33.271  1.00  0.00
ATOM    146  CA  VAL    48      37.092  33.706  31.885  1.00  0.00
ATOM    147  C   VAL    48      38.231  34.585  31.346  1.00  0.00
ATOM    148  O   VAL    48      39.291  34.066  30.969  1.00  0.00
ATOM    149  N   LYS    49      38.074  35.903  31.454  1.00  0.00
ATOM    150  CA  LYS    49      39.148  36.790  31.038  1.00  0.00
ATOM    151  C   LYS    49      40.471  36.338  31.689  1.00  0.00
ATOM    152  O   LYS    49      41.549  36.351  31.025  1.00  0.00
ATOM    153  N   ALA    50      40.330  35.966  32.995  1.00  0.00
ATOM    154  CA  ALA    50      41.547  35.549  33.708  1.00  0.00
ATOM    155  C   ALA    50      42.152  34.279  33.126  1.00  0.00
ATOM    156  O   ALA    50      43.390  34.093  33.039  1.00  0.00
ATOM    157  N   LEU    51      41.220  33.397  32.698  1.00  0.00
ATOM    158  CA  LEU    51      41.781  32.160  32.114  1.00  0.00
ATOM    159  C   LEU    51      42.457  32.531  30.776  1.00  0.00
ATOM    160  O   LEU    51      43.481  31.950  30.407  1.00  0.00
ATOM    161  N   ALA    52      41.874  33.493  30.073  1.00  0.00
ATOM    162  CA  ALA    52      42.433  33.865  28.744  1.00  0.00
ATOM    163  C   ALA    52      43.851  34.373  28.836  1.00  0.00
ATOM    164  O   ALA    52      44.773  33.972  28.079  1.00  0.00
ATOM    165  N   ASN    53      44.064  35.209  29.893  1.00  0.00
ATOM    166  CA  ASN    53      45.435  35.683  30.115  1.00  0.00
ATOM    167  C   ASN    53      46.421  34.521  30.347  1.00  0.00
ATOM    168  O   ASN    53      47.582  34.646  29.971  1.00  0.00
ATOM    169  N   SER    54      45.995  33.433  30.986  1.00  0.00
ATOM    170  CA  SER    54      46.852  32.303  31.279  1.00  0.00
ATOM    171  C   SER    54      47.315  31.651  29.964  1.00  0.00
ATOM    172  O   SER    54      48.484  31.358  29.689  1.00  0.00
ATOM    173  N   VAL    55      46.308  31.380  29.164  1.00  0.00
ATOM    174  CA  VAL    55      46.372  30.781  27.841  1.00  0.00
ATOM    175  C   VAL    55      47.415  31.526  26.998  1.00  0.00
ATOM    176  O   VAL    55      48.474  30.995  26.728  1.00  0.00
ATOM    177  N   GLN    56      47.123  32.800  26.825  1.00  0.00
ATOM    178  CA  GLN    56      48.044  33.692  26.111  1.00  0.00
ATOM    179  C   GLN    56      49.439  33.657  26.732  1.00  0.00
ATOM    180  O   GLN    56      50.504  33.699  26.080  1.00  0.00
ATOM    181  N   VAL    57      49.416  33.594  28.077  1.00  0.00
ATOM    182  CA  VAL    57      50.662  33.537  28.829  1.00  0.00
ATOM    183  C   VAL    57      51.392  32.211  28.524  1.00  0.00
ATOM    184  O   VAL    57      52.621  32.230  28.467  1.00  0.00
ATOM    185  N   LYS    58      50.670  31.152  28.248  1.00  0.00
ATOM    186  CA  LYS    58      51.277  29.889  27.888  1.00  0.00
ATOM    187  C   LYS    58      51.727  29.829  26.437  1.00  0.00
ATOM    188  O   LYS    58      52.753  29.154  26.143  1.00  0.00
ATOM    189  N   LEU    59      51.033  30.477  25.498  1.00  0.00
ATOM    190  CA  LEU    59      51.535  30.524  24.089  1.00  0.00
ATOM    191  C   LEU    59      52.894  31.255  24.047  1.00  0.00
ATOM    192  O   LEU    59      53.895  30.798  23.507  1.00  0.00
ATOM    193  N   LYS    60      52.958  32.393  24.744  1.00  0.00
ATOM    194  CA  LYS    60      54.208  33.131  24.855  1.00  0.00
ATOM    195  C   LYS    60      55.331  32.223  25.364  1.00  0.00
ATOM    196  O   LYS    60      56.422  32.305  24.770  1.00  0.00
ATOM    197  N   GLU    61      55.071  31.411  26.402  1.00  0.00
ATOM    198  CA  GLU    61      56.142  30.540  26.919  1.00  0.00
ATOM    199  C   GLU    61      56.545  29.503  25.861  1.00  0.00
ATOM    200  O   GLU    61      57.701  29.101  25.666  1.00  0.00
TER
END
