
#######################################################
#                                                     #
#                        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   47 (  188),  selected   47 , name T0354AL243_1
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354AL243_1.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I       6      M       1           -
LGA    S       7      E       2           -
LGA    K       8      I       3           -
LGA    L       9      Q       4           -
LGA    A      10      E       5           -
LGA    I      11      I       6           -
LGA    E      12      S       7           -
LGA    A      13      K       8           -
LGA    L      14      L       9           -
LGA    -       -      A      10           -
LGA    -       -      I      11           -
LGA    -       -      E      12           -
LGA    -       -      A      13           -
LGA    -       -      L      14           -
LGA    -       -      E      15           -
LGA    -       -      D      16           -
LGA    -       -      I      17           -
LGA    -       -      K      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      I      22           -
LGA    -       -      I      23           -
LGA    -       -      E      24           -
LGA    -       -      L      25           -
LGA    -       -      D      26           -
LGA    E      15      T      27           #
LGA    D      16      -       -           -
LGA    I      17      S      28           #
LGA    K      18      K      29          1.370
LGA    G      19      L      30          2.973
LGA    K      20      T      31          2.536
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    D      21      M      37          3.364
LGA    I      22      I      38          2.726
LGA    I      23      V      39          3.361
LGA    E      24      A      40          3.165
LGA    L      25      T      41          2.833
LGA    D      26      G      42          3.193
LGA    T      27      -       -           -
LGA    S      28      -       -           -
LGA    K      29      -       -           -
LGA    Q      47      D      43          4.840
LGA    V      48      S      44          2.350
LGA    K      49      N      45          2.123
LGA    A      50      R      46          0.831
LGA    L      51      Q      47          1.199
LGA    A      52      V      48          1.595
LGA    N      53      K      49          0.918
LGA    S      54      A      50          0.536
LGA    V      55      L      51          1.360
LGA    Q      56      A      52          0.987
LGA    V      57      N      53          0.469
LGA    K      58      S      54          0.575
LGA    L      59      V      55          0.834
LGA    K      60      Q      56          1.170
LGA    E      61      V      57          1.334
LGA    A      62      K      58          1.664
LGA    G      63      L      59          1.784
LGA    S      69      K      60           -
LGA    -       -      E      61           -
LGA    -       -      A      62           -
LGA    -       -      G      63           -
LGA    -       -      V      64           -
LGA    -       -      D      65           -
LGA    -       -      I      66           -
LGA    E      70      V      67           #
LGA    V      78      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    L      79      V      78          3.574
LGA    V      80      L      79          4.977
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    D      81      M      90          2.528
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)   47  122    5.0     29    2.43     6.90     18.926     1.145

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.630409 * X  +  -0.305631 * Y  +  -0.713565 * Z  +  96.059311
  Y_new =   0.084843 * X  +  -0.940851 * Y  +   0.328026 * Z  +  69.206047
  Z_new =  -0.771613 * X  +   0.146249 * Y  +   0.619051 * Z  +   6.734314 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.231993   -2.909599  [ DEG:    13.2922   -166.7078 ]
  Theta =   0.881373    2.260219  [ DEG:    50.4990    129.5010 ]
  Phi   =   3.007812   -0.133780  [ DEG:   172.3349     -7.6651 ]
 
# 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: T0354AL243_1                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354AL243_1.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   47  122   5.0   29   2.43    6.90  18.926
REMARK  ---------------------------------------------------------- 
MOLECULE T0354AL243_1
REMARK Aligment from pdb entry: 1evkA
ATOM      1  N   ILE     6      48.360  23.982  -4.318  1.00  0.00              
ATOM      2  CA  ILE     6      47.544  25.098  -3.874  1.00  0.00              
ATOM      3  C   ILE     6      47.218  24.971  -2.391  1.00  0.00              
ATOM      4  O   ILE     6      46.626  23.977  -1.956  1.00  0.00              
ATOM      5  N   SER     7      47.569  25.982  -1.609  1.00  0.00              
ATOM      6  CA  SER     7      47.304  25.894  -0.186  1.00  0.00              
ATOM      7  C   SER     7      45.823  25.985   0.138  1.00  0.00              
ATOM      8  O   SER     7      45.365  25.382   1.109  1.00  0.00              
ATOM      9  N   LYS     8      45.064  26.726  -0.674  1.00  0.00              
ATOM     10  CA  LYS     8      43.627  26.807  -0.463  1.00  0.00              
ATOM     11  C   LYS     8      43.085  25.385  -0.600  1.00  0.00              
ATOM     12  O   LYS     8      42.327  24.915   0.242  1.00  0.00              
ATOM     13  N   LEU     9      43.493  24.701  -1.668  1.00  0.00              
ATOM     14  CA  LEU     9      43.052  23.332  -1.924  1.00  0.00              
ATOM     15  C   LEU     9      43.516  22.383  -0.817  1.00  0.00              
ATOM     16  O   LEU     9      42.753  21.529  -0.354  1.00  0.00              
ATOM     17  N   ALA    10      44.760  22.535  -0.382  1.00  0.00              
ATOM     18  CA  ALA    10      45.261  21.664   0.663  1.00  0.00              
ATOM     19  C   ALA    10      44.431  21.773   1.948  1.00  0.00              
ATOM     20  O   ALA    10      44.174  20.773   2.621  1.00  0.00              
ATOM     21  N   ILE    11      44.019  22.987   2.292  1.00  0.00              
ATOM     22  CA  ILE    11      43.212  23.183   3.479  1.00  0.00              
ATOM     23  C   ILE    11      41.876  22.466   3.267  1.00  0.00              
ATOM     24  O   ILE    11      41.308  21.902   4.200  1.00  0.00              
ATOM     25  N   GLU    12      41.374  22.484   2.035  1.00  0.00              
ATOM     26  CA  GLU    12      40.118  21.808   1.757  1.00  0.00              
ATOM     27  C   GLU    12      40.277  20.304   1.953  1.00  0.00              
ATOM     28  O   GLU    12      39.406  19.646   2.516  1.00  0.00              
ATOM     29  N   ALA    13      41.405  19.762   1.498  1.00  0.00              
ATOM     30  CA  ALA    13      41.677  18.334   1.637  1.00  0.00              
ATOM     31  C   ALA    13      41.798  17.927   3.112  1.00  0.00              
ATOM     32  O   ALA    13      41.271  16.891   3.517  1.00  0.00              
ATOM     33  N   LEU    14      42.475  18.750   3.913  1.00  0.00              
ATOM     34  CA  LEU    14      42.640  18.484   5.345  1.00  0.00              
ATOM     35  C   LEU    14      41.299  18.612   6.071  1.00  0.00              
ATOM     36  O   LEU    14      41.001  17.860   7.013  1.00  0.00              
ATOM     37  N   GLU    15      40.487  19.579   5.650  1.00  0.00              
ATOM     38  CA  GLU    15      39.186  19.764   6.278  1.00  0.00              
ATOM     39  C   GLU    15      38.356  18.491   6.149  1.00  0.00              
ATOM     40  O   GLU    15      37.694  18.082   7.099  1.00  0.00              
ATOM     41  N   ASP    16      38.410  17.858   4.983  1.00  0.00              
ATOM     42  CA  ASP    16      37.642  16.638   4.767  1.00  0.00              
ATOM     43  C   ASP    16      38.335  15.444   5.430  1.00  0.00              
ATOM     44  O   ASP    16      37.676  14.591   6.017  1.00  0.00              
ATOM     45  N   ILE    17      39.663  15.409   5.366  1.00  0.00              
ATOM     46  CA  ILE    17      40.430  14.334   5.991  1.00  0.00              
ATOM     47  C   ILE    17      40.170  14.291   7.503  1.00  0.00              
ATOM     48  O   ILE    17      39.965  13.217   8.067  1.00  0.00              
ATOM     49  N   LYS    18      40.142  15.449   8.158  1.00  0.00              
ATOM     50  CA  LYS    18      39.919  15.489   9.610  1.00  0.00              
ATOM     51  C   LYS    18      38.450  15.638   9.978  1.00  0.00              
ATOM     52  O   LYS    18      38.092  15.595  11.157  1.00  0.00              
ATOM     53  N   GLY    19      37.605  15.818   8.964  1.00  0.00              
ATOM     54  CA  GLY    19      36.180  16.007   9.175  1.00  0.00              
ATOM     55  C   GLY    19      35.981  17.226  10.075  1.00  0.00              
ATOM     56  O   GLY    19      35.071  17.267  10.902  1.00  0.00              
ATOM     57  N   LYS    20      36.842  18.226   9.908  1.00  0.00              
ATOM     58  CA  LYS    20      36.726  19.422  10.716  1.00  0.00              
ATOM     59  C   LYS    20      37.443  19.340  12.053  1.00  0.00              
ATOM     60  O   LYS    20      37.564  20.342  12.735  1.00  0.00              
ATOM     61  N   ASP    21      42.153  26.733  19.910  1.00  0.00              
ATOM     62  CA  ASP    21      42.656  25.528  20.551  1.00  0.00              
ATOM     63  C   ASP    21      42.011  25.234  21.902  1.00  0.00              
ATOM     64  O   ASP    21      41.827  24.073  22.285  1.00  0.00              
ATOM     65  N   ILE    22      41.641  26.290  22.611  1.00  0.00              
ATOM     66  CA  ILE    22      41.091  26.123  23.939  1.00  0.00              
ATOM     67  C   ILE    22      40.003  27.115  24.297  1.00  0.00              
ATOM     68  O   ILE    22      40.143  28.307  24.046  1.00  0.00              
ATOM     69  N   ILE    23      38.909  26.629  24.882  1.00  0.00              
ATOM     70  CA  ILE    23      37.883  27.530  25.364  1.00  0.00              
ATOM     71  C   ILE    23      37.755  27.268  26.867  1.00  0.00              
ATOM     72  O   ILE    23      37.641  26.114  27.306  1.00  0.00              
ATOM     73  N   GLU    24      37.803  28.334  27.656  1.00  0.00              
ATOM     74  CA  GLU    24      37.683  28.214  29.109  1.00  0.00              
ATOM     75  C   GLU    24      36.326  28.782  29.478  1.00  0.00              
ATOM     76  O   GLU    24      35.926  29.836  28.977  1.00  0.00              
ATOM     77  N   LEU    25      35.613  28.081  30.354  1.00  0.00              
ATOM     78  CA  LEU    25      34.282  28.513  30.725  1.00  0.00              
ATOM     79  C   LEU    25      33.956  28.424  32.212  1.00  0.00              
ATOM     80  O   LEU    25      34.472  27.573  32.938  1.00  0.00              
ATOM     81  N   ASP    26      33.100  29.326  32.661  1.00  0.00              
ATOM     82  CA  ASP    26      32.698  29.365  34.061  1.00  0.00              
ATOM     83  C   ASP    26      31.333  28.702  34.222  1.00  0.00              
ATOM     84  O   ASP    26      30.611  28.517  33.242  1.00  0.00              
ATOM     85  N   THR    27      30.988  28.331  35.453  1.00  0.00              
ATOM     86  CA  THR    27      29.690  27.725  35.726  1.00  0.00              
ATOM     87  C   THR    27      28.739  28.882  36.001  1.00  0.00              
ATOM     88  O   THR    27      27.653  28.962  35.434  1.00  0.00              
ATOM     89  N   SER    28      29.168  29.784  36.874  1.00  0.00              
ATOM     90  CA  SER    28      28.381  30.952  37.224  1.00  0.00              
ATOM     91  C   SER    28      29.302  32.152  37.126  1.00  0.00              
ATOM     92  O   SER    28      30.526  32.000  37.091  1.00  0.00              
ATOM     93  N   LYS    29      28.731  33.349  37.087  1.00  0.00              
ATOM     94  CA  LYS    29      29.551  34.548  36.980  1.00  0.00              
ATOM     95  C   LYS    29      30.428  34.744  38.206  1.00  0.00              
ATOM     96  O   LYS    29      31.017  35.807  38.404  1.00  0.00              
ATOM     97  N   GLN    47      30.533  33.695  39.010  1.00  0.00              
ATOM     98  CA  GLN    47      31.338  33.734  40.215  1.00  0.00              
ATOM     99  C   GLN    47      32.772  33.276  39.938  1.00  0.00              
ATOM    100  O   GLN    47      33.683  33.561  40.723  1.00  0.00              
ATOM    101  N   VAL    48      32.972  32.555  38.833  1.00  0.00              
ATOM    102  CA  VAL    48      34.312  32.106  38.468  1.00  0.00              
ATOM    103  C   VAL    48      34.825  32.964  37.307  1.00  0.00              
ATOM    104  O   VAL    48      35.912  32.732  36.788  1.00  0.00              
ATOM    105  N   LYS    49      34.031  33.944  36.902  1.00  0.00              
ATOM    106  CA  LYS    49      34.388  34.827  35.798  1.00  0.00              
ATOM    107  C   LYS    49      35.802  35.377  35.910  1.00  0.00              
ATOM    108  O   LYS    49      36.610  35.237  34.989  1.00  0.00              
ATOM    109  N   ALA    50      36.091  36.000  37.047  1.00  0.00              
ATOM    110  CA  ALA    50      37.393  36.594  37.305  1.00  0.00              
ATOM    111  C   ALA    50      38.502  35.563  37.101  1.00  0.00              
ATOM    112  O   ALA    50      39.509  35.831  36.435  1.00  0.00              
ATOM    113  N   LEU    51      38.304  34.376  37.666  1.00  0.00              
ATOM    114  CA  LEU    51      39.276  33.296  37.554  1.00  0.00              
ATOM    115  C   LEU    51      39.451  32.863  36.096  1.00  0.00              
ATOM    116  O   LEU    51      40.561  32.554  35.658  1.00  0.00              
ATOM    117  N   ALA    52      38.347  32.820  35.353  1.00  0.00              
ATOM    118  CA  ALA    52      38.392  32.427  33.943  1.00  0.00              
ATOM    119  C   ALA    52      39.232  33.414  33.126  1.00  0.00              
ATOM    120  O   ALA    52      40.103  33.004  32.360  1.00  0.00              
ATOM    121  N   ASN    53      38.981  34.708  33.301  1.00  0.00              
ATOM    122  CA  ASN    53      39.738  35.738  32.586  1.00  0.00              
ATOM    123  C   ASN    53      41.226  35.623  32.905  1.00  0.00              
ATOM    124  O   ASN    53      42.086  35.724  32.019  1.00  0.00              
ATOM    125  N   SER    54      41.514  35.392  34.181  1.00  0.00              
ATOM    126  CA  SER    54      42.874  35.251  34.667  1.00  0.00              
ATOM    127  C   SER    54      43.595  34.134  33.911  1.00  0.00              
ATOM    128  O   SER    54      44.691  34.332  33.392  1.00  0.00              
ATOM    129  N   VAL    55      42.968  32.961  33.848  1.00  0.00              
ATOM    130  CA  VAL    55      43.547  31.812  33.155  1.00  0.00              
ATOM    131  C   VAL    55      43.628  32.024  31.655  1.00  0.00              
ATOM    132  O   VAL    55      44.543  31.506  31.006  1.00  0.00              
ATOM    133  N   GLN    56      42.660  32.756  31.104  1.00  0.00              
ATOM    134  CA  GLN    56      42.644  33.032  29.663  1.00  0.00              
ATOM    135  C   GLN    56      43.881  33.871  29.290  1.00  0.00              
ATOM    136  O   GLN    56      44.518  33.627  28.265  1.00  0.00              
ATOM    137  N   VAL    57      44.237  34.846  30.126  1.00  0.00              
ATOM    138  CA  VAL    57      45.426  35.657  29.844  1.00  0.00              
ATOM    139  C   VAL    57      46.693  34.806  29.920  1.00  0.00              
ATOM    140  O   VAL    57      47.607  34.971  29.110  1.00  0.00              
ATOM    141  N   LYS    58      46.736  33.886  30.884  1.00  0.00              
ATOM    142  CA  LYS    58      47.897  33.020  31.056  1.00  0.00              
ATOM    143  C   LYS    58      48.121  32.139  29.840  1.00  0.00              
ATOM    144  O   LYS    58      49.238  32.068  29.328  1.00  0.00              
ATOM    145  N   LEU    59      47.075  31.452  29.377  1.00  0.00              
ATOM    146  CA  LEU    59      47.228  30.599  28.205  1.00  0.00              
ATOM    147  C   LEU    59      47.572  31.488  27.013  1.00  0.00              
ATOM    148  O   LEU    59      48.446  31.159  26.215  1.00  0.00              
ATOM    149  N   LYS    60      46.902  32.627  26.904  1.00  0.00              
ATOM    150  CA  LYS    60      47.179  33.533  25.790  1.00  0.00              
ATOM    151  C   LYS    60      48.661  33.977  25.778  1.00  0.00              
ATOM    152  O   LYS    60      49.326  33.917  24.741  1.00  0.00              
ATOM    153  N   GLU    61      49.183  34.400  26.928  1.00  0.00              
ATOM    154  CA  GLU    61      50.589  34.819  26.992  1.00  0.00              
ATOM    155  C   GLU    61      51.489  33.638  26.692  1.00  0.00              
ATOM    156  O   GLU    61      52.623  33.804  26.245  1.00  0.00              
ATOM    157  N   ALA    62      50.955  32.443  26.921  1.00  0.00              
ATOM    158  CA  ALA    62      51.680  31.211  26.675  1.00  0.00              
ATOM    159  C   ALA    62      51.664  30.850  25.191  1.00  0.00              
ATOM    160  O   ALA    62      52.213  29.825  24.792  1.00  0.00              
ATOM    161  N   GLY    63      51.039  31.686  24.366  1.00  0.00              
ATOM    162  CA  GLY    63      51.013  31.390  22.942  1.00  0.00              
ATOM    163  C   GLY    63      49.928  30.425  22.486  1.00  0.00              
ATOM    164  O   GLY    63      49.998  29.875  21.379  1.00  0.00              
ATOM    165  N   SER    69      48.920  30.217  23.327  1.00  0.00              
ATOM    166  CA  SER    69      47.833  29.308  22.989  1.00  0.00              
ATOM    167  C   SER    69      46.625  30.139  22.533  1.00  0.00              
ATOM    168  O   SER    69      46.330  31.156  23.133  1.00  0.00              
ATOM    169  N   GLU    70      45.955  29.714  21.460  1.00  0.00              
ATOM    170  CA  GLU    70      44.767  30.428  20.954  1.00  0.00              
ATOM    171  C   GLU    70      43.644  30.042  21.899  1.00  0.00              
ATOM    172  O   GLU    70      43.109  28.937  21.813  1.00  0.00              
ATOM    173  N   VAL    78      43.274  30.938  22.798  1.00  0.00              
ATOM    174  CA  VAL    78      42.255  30.589  23.772  1.00  0.00              
ATOM    175  C   VAL    78      41.185  31.640  23.801  1.00  0.00              
ATOM    176  O   VAL    78      41.438  32.789  23.469  1.00  0.00              
ATOM    177  N   LEU    79      39.978  31.233  24.176  1.00  0.00              
ATOM    178  CA  LEU    79      38.855  32.142  24.259  1.00  0.00              
ATOM    179  C   LEU    79      38.098  31.864  25.548  1.00  0.00              
ATOM    180  O   LEU    79      38.026  30.718  25.997  1.00  0.00              
ATOM    181  N   VAL    80      37.536  32.909  26.143  1.00  0.00              
ATOM    182  CA  VAL    80      36.757  32.762  27.367  1.00  0.00              
ATOM    183  C   VAL    80      35.262  32.769  27.043  1.00  0.00              
ATOM    184  O   VAL    80      34.788  33.626  26.302  1.00  0.00              
ATOM    185  N   ASP    81      34.513  31.812  27.587  1.00  0.00              
ATOM    186  CA  ASP    81      33.074  31.783  27.355  1.00  0.00              
ATOM    187  C   ASP    81      32.380  32.106  28.689  1.00  0.00              
ATOM    188  O   ASP    81      32.138  31.215  29.501  1.00  0.00              
END
