
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354AL243_2.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       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    -       -      T      27           -
LGA    L      14      S      28           #
LGA    E      15      K      29          3.502
LGA    D      16      L      30           -
LGA    I      17      T      31           -
LGA    K      18      S      32           -
LGA    G      19      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    K      20      R      36          3.332
LGA    D      21      M      37          3.577
LGA    I      22      I      38          2.682
LGA    I      23      V      39          2.878
LGA    E      24      A      40          3.703
LGA    L      25      T      41          2.868
LGA    D      26      G      42          1.026
LGA    T      27      D      43          1.918
LGA    S      28      S      44          1.890
LGA    K      29      N      45          2.098
LGA    Q      47      R      46          3.216
LGA    V      48      Q      47          0.688
LGA    K      49      V      48          2.094
LGA    A      50      K      49          2.555
LGA    L      51      A      50          0.864
LGA    A      52      L      51          1.202
LGA    N      53      A      52          1.885
LGA    S      54      N      53          0.741
LGA    V      55      S      54          1.287
LGA    Q      56      V      55          2.202
LGA    V      57      Q      56          1.276
LGA    K      58      V      57          2.289
LGA    L      59      K      58          4.378
LGA    K      60      L      59          4.199
LGA    E      61      K      60          2.625
LGA    -       -      E      61           -
LGA    -       -      A      62           -
LGA    -       -      G      63           -
LGA    A      62      V      64          3.185
LGA    G      63      D      65          5.597
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    S      69      A      82          4.751
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    E      70      V      85          2.100
LGA    V      78      V      86          2.730
LGA    L      79      V      87          2.332
LGA    V      80      H      88          2.954
LGA    D      81      V      89          2.199
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)   47  122    5.0     34    2.80     8.82     19.645     1.173

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.417869 * X  +   0.908506 * Y  +  -0.001128 * Z  +  -4.723286
  Y_new =  -0.026078 * X  +  -0.010754 * Y  +   0.999602 * Z  + -33.288197
  Z_new =   0.908133 * X  +   0.417733 * Y  +   0.028186 * Z  + -77.094986 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.503425   -1.638168  [ DEG:    86.1399    -93.8601 ]
  Theta =  -1.138802   -2.002790  [ DEG:   -65.2486   -114.7514 ]
  Phi   =  -3.079266    0.062327  [ DEG:  -176.4289      3.5711 ]
 
# 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_2                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354AL243_2.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   34   2.80    8.82  19.645
REMARK  ---------------------------------------------------------- 
MOLECULE T0354AL243_2
REMARK Aligment from pdb entry: 1qf6A
ATOM      1  N   ILE     6      44.687  14.539  -3.676  1.00  0.00              
ATOM      2  CA  ILE     6      44.173  15.894  -3.661  1.00  0.00              
ATOM      3  C   ILE     6      44.063  16.231  -2.172  1.00  0.00              
ATOM      4  O   ILE     6      43.836  15.352  -1.373  1.00  0.00              
ATOM      5  N   SER     7      44.267  17.483  -1.785  1.00  0.00              
ATOM      6  CA  SER     7      44.155  17.848  -0.376  1.00  0.00              
ATOM      7  C   SER     7      42.730  17.629   0.137  1.00  0.00              
ATOM      8  O   SER     7      42.541  17.240   1.288  1.00  0.00              
ATOM      9  N   LYS     8      41.719  17.877  -0.689  1.00  0.00              
ATOM     10  CA  LYS     8      40.383  17.664  -0.190  1.00  0.00              
ATOM     11  C   LYS     8      40.161  16.175   0.079  1.00  0.00              
ATOM     12  O   LYS     8      39.758  15.793   1.167  1.00  0.00              
ATOM     13  N   LEU     9      40.453  15.316  -0.873  1.00  0.00              
ATOM     14  CA  LEU     9      40.271  13.893  -0.620  1.00  0.00              
ATOM     15  C   LEU     9      41.121  13.352   0.543  1.00  0.00              
ATOM     16  O   LEU     9      40.768  12.345   1.164  1.00  0.00              
ATOM     17  N   ALA    10      42.241  13.983   0.869  1.00  0.00              
ATOM     18  CA  ALA    10      43.018  13.408   1.956  1.00  0.00              
ATOM     19  C   ALA    10      42.338  13.771   3.267  1.00  0.00              
ATOM     20  O   ALA    10      42.225  12.939   4.183  1.00  0.00              
ATOM     21  N   ILE    11      41.876  15.016   3.350  1.00  0.00              
ATOM     22  CA  ILE    11      41.184  15.469   4.540  1.00  0.00              
ATOM     23  C   ILE    11      39.926  14.605   4.667  1.00  0.00              
ATOM     24  O   ILE    11      39.453  14.312   5.765  1.00  0.00              
ATOM     25  N   GLU    12      39.405  14.167   3.529  1.00  0.00              
ATOM     26  CA  GLU    12      38.223  13.336   3.565  1.00  0.00              
ATOM     27  C   GLU    12      38.574  12.099   4.349  1.00  0.00              
ATOM     28  O   GLU    12      37.896  11.707   5.303  1.00  0.00              
ATOM     29  N   ALA    13      39.689  11.508   3.944  1.00  0.00              
ATOM     30  CA  ALA    13      40.202  10.297   4.541  1.00  0.00              
ATOM     31  C   ALA    13      40.629  10.428   5.987  1.00  0.00              
ATOM     32  O   ALA    13      40.346   9.546   6.773  1.00  0.00              
ATOM     33  N   LEU    14      41.315  11.507   6.347  1.00  0.00              
ATOM     34  CA  LEU    14      41.764  11.680   7.733  1.00  0.00              
ATOM     35  C   LEU    14      40.590  11.798   8.681  1.00  0.00              
ATOM     36  O   LEU    14      40.578  11.227   9.782  1.00  0.00              
ATOM     37  N   GLU    15      39.615  12.590   8.264  1.00  0.00              
ATOM     38  CA  GLU    15      38.453  12.784   9.077  1.00  0.00              
ATOM     39  C   GLU    15      37.832  11.431   9.430  1.00  0.00              
ATOM     40  O   GLU    15      37.529  11.170  10.597  1.00  0.00              
ATOM     41  N   ASP    16      37.676  10.546   8.455  1.00  0.00              
ATOM     42  CA  ASP    16      37.081   9.260   8.777  1.00  0.00              
ATOM     43  C   ASP    16      38.046   8.330   9.542  1.00  0.00              
ATOM     44  O   ASP    16      37.619   7.459  10.300  1.00  0.00              
ATOM     45  N   ILE    17      39.348   8.509   9.364  1.00  0.00              
ATOM     46  CA  ILE    17      40.294   7.655  10.054  1.00  0.00              
ATOM     47  C   ILE    17      40.287   8.002  11.533  1.00  0.00              
ATOM     48  O   ILE    17      40.278   7.126  12.384  1.00  0.00              
ATOM     49  N   LYS    18      40.293   9.291  11.844  1.00  0.00              
ATOM     50  CA  LYS    18      40.301   9.725  13.234  1.00  0.00              
ATOM     51  C   LYS    18      38.901   9.965  13.776  1.00  0.00              
ATOM     52  O   LYS    18      38.729  10.373  14.938  1.00  0.00              
ATOM     53  N   GLY    19      37.905   9.729  12.927  1.00  0.00              
ATOM     54  CA  GLY    19      36.535   9.941  13.328  1.00  0.00              
ATOM     55  C   GLY    19      36.368  11.342  13.922  1.00  0.00              
ATOM     56  O   GLY    19      35.678  11.523  14.920  1.00  0.00              
ATOM     57  N   LYS    20      40.941  23.634  16.881  1.00  0.00              
ATOM     58  CA  LYS    20      41.201  24.301  18.173  1.00  0.00              
ATOM     59  C   LYS    20      41.911  23.270  19.051  1.00  0.00              
ATOM     60  O   LYS    20      41.418  22.146  19.217  1.00  0.00              
ATOM     61  N   ASP    21      43.068  23.642  19.592  1.00  0.00              
ATOM     62  CA  ASP    21      43.852  22.723  20.401  1.00  0.00              
ATOM     63  C   ASP    21      43.545  22.762  21.886  1.00  0.00              
ATOM     64  O   ASP    21      43.560  21.733  22.573  1.00  0.00              
ATOM     65  N   ILE    22      43.235  23.950  22.376  1.00  0.00              
ATOM     66  CA  ILE    22      42.979  24.111  23.780  1.00  0.00              
ATOM     67  C   ILE    22      41.854  25.068  24.087  1.00  0.00              
ATOM     68  O   ILE    22      41.774  26.153  23.513  1.00  0.00              
ATOM     69  N   ILE    23      40.970  24.661  24.987  1.00  0.00              
ATOM     70  CA  ILE    23      39.909  25.563  25.430  1.00  0.00              
ATOM     71  C   ILE    23      40.161  25.797  26.915  1.00  0.00              
ATOM     72  O   ILE    23      40.310  24.844  27.687  1.00  0.00              
ATOM     73  N   GLU    24      40.237  27.063  27.304  1.00  0.00              
ATOM     74  CA  GLU    24      40.472  27.398  28.689  1.00  0.00              
ATOM     75  C   GLU    24      39.214  28.027  29.264  1.00  0.00              
ATOM     76  O   GLU    24      38.813  29.099  28.831  1.00  0.00              
ATOM     77  N   LEU    25      38.579  27.372  30.235  1.00  0.00              
ATOM     78  CA  LEU    25      37.357  27.947  30.826  1.00  0.00              
ATOM     79  C   LEU    25      37.488  28.368  32.279  1.00  0.00              
ATOM     80  O   LEU    25      38.331  27.859  33.024  1.00  0.00              
ATOM     81  N   ASP    26      36.614  29.297  32.665  1.00  0.00              
ATOM     82  CA  ASP    26      36.539  29.813  34.025  1.00  0.00              
ATOM     83  C   ASP    26      35.268  29.222  34.614  1.00  0.00              
ATOM     84  O   ASP    26      34.469  28.629  33.886  1.00  0.00              
ATOM     85  N   THR    27      35.075  29.354  35.922  1.00  0.00              
ATOM     86  CA  THR    27      33.857  28.818  36.515  1.00  0.00              
ATOM     87  C   THR    27      32.891  29.955  36.839  1.00  0.00              
ATOM     88  O   THR    27      31.675  29.774  36.784  1.00  0.00              
ATOM     89  N   SER    28      33.454  31.130  37.131  1.00  0.00              
ATOM     90  CA  SER    28      32.694  32.341  37.455  1.00  0.00              
ATOM     91  C   SER    28      33.541  33.569  37.104  1.00  0.00              
ATOM     92  O   SER    28      34.768  33.464  37.012  1.00  0.00              
ATOM     93  N   LYS    29      32.894  34.722  36.920  1.00  0.00              
ATOM     94  CA  LYS    29      33.601  35.973  36.588  1.00  0.00              
ATOM     95  C   LYS    29      34.945  36.061  37.250  1.00  0.00              
ATOM     96  O   LYS    29      35.918  36.555  36.682  1.00  0.00              
ATOM     97  N   GLN    47      34.953  35.620  38.496  1.00  0.00              
ATOM     98  CA  GLN    47      36.143  35.621  39.314  1.00  0.00              
ATOM     99  C   GLN    47      37.371  35.283  38.465  1.00  0.00              
ATOM    100  O   GLN    47      38.176  36.162  38.154  1.00  0.00              
ATOM    101  N   VAL    48      37.484  34.025  38.051  1.00  0.00              
ATOM    102  CA  VAL    48      38.639  33.586  37.281  1.00  0.00              
ATOM    103  C   VAL    48      38.861  34.213  35.902  1.00  0.00              
ATOM    104  O   VAL    48      39.985  34.218  35.406  1.00  0.00              
ATOM    105  N   LYS    49      37.814  34.760  35.297  1.00  0.00              
ATOM    106  CA  LYS    49      37.932  35.309  33.952  1.00  0.00              
ATOM    107  C   LYS    49      39.194  36.106  33.624  1.00  0.00              
ATOM    108  O   LYS    49      39.928  35.742  32.713  1.00  0.00              
ATOM    109  N   ALA    50      39.465  37.186  34.339  1.00  0.00              
ATOM    110  CA  ALA    50      40.656  37.978  34.041  1.00  0.00              
ATOM    111  C   ALA    50      41.956  37.154  34.088  1.00  0.00              
ATOM    112  O   ALA    50      42.967  37.526  33.486  1.00  0.00              
ATOM    113  N   LEU    51      41.926  36.034  34.802  1.00  0.00              
ATOM    114  CA  LEU    51      43.093  35.158  34.903  1.00  0.00              
ATOM    115  C   LEU    51      43.135  34.301  33.647  1.00  0.00              
ATOM    116  O   LEU    51      44.192  34.114  33.038  1.00  0.00              
ATOM    117  N   ALA    52      41.963  33.790  33.273  1.00  0.00              
ATOM    118  CA  ALA    52      41.785  32.958  32.087  1.00  0.00              
ATOM    119  C   ALA    52      42.246  33.677  30.809  1.00  0.00              
ATOM    120  O   ALA    52      42.861  33.076  29.931  1.00  0.00              
ATOM    121  N   ASN    53      41.957  34.964  30.709  1.00  0.00              
ATOM    122  CA  ASN    53      42.368  35.698  29.537  1.00  0.00              
ATOM    123  C   ASN    53      43.867  35.777  29.431  1.00  0.00              
ATOM    124  O   ASN    53      44.437  35.355  28.429  1.00  0.00              
ATOM    125  N   SER    54      44.534  36.297  30.449  1.00  0.00              
ATOM    126  CA  SER    54      45.974  36.373  30.328  1.00  0.00              
ATOM    127  C   SER    54      46.564  34.971  30.271  1.00  0.00              
ATOM    128  O   SER    54      47.697  34.778  29.832  1.00  0.00              
ATOM    129  N   VAL    55      45.791  33.978  30.694  1.00  0.00              
ATOM    130  CA  VAL    55      46.290  32.617  30.633  1.00  0.00              
ATOM    131  C   VAL    55      46.254  32.193  29.171  1.00  0.00              
ATOM    132  O   VAL    55      47.261  31.738  28.629  1.00  0.00              
ATOM    133  N   GLN    56      45.105  32.375  28.522  1.00  0.00              
ATOM    134  CA  GLN    56      44.963  32.002  27.115  1.00  0.00              
ATOM    135  C   GLN    56      45.886  32.830  26.208  1.00  0.00              
ATOM    136  O   GLN    56      46.427  32.324  25.213  1.00  0.00              
ATOM    137  N   VAL    57      46.071  34.097  26.557  1.00  0.00              
ATOM    138  CA  VAL    57      46.946  34.963  25.782  1.00  0.00              
ATOM    139  C   VAL    57      48.330  34.338  25.815  1.00  0.00              
ATOM    140  O   VAL    57      48.989  34.216  24.793  1.00  0.00              
ATOM    141  N   LYS    58      48.745  33.914  27.003  1.00  0.00              
ATOM    142  CA  LYS    58      50.047  33.288  27.195  1.00  0.00              
ATOM    143  C   LYS    58      50.205  32.089  26.256  1.00  0.00              
ATOM    144  O   LYS    58      51.276  31.887  25.685  1.00  0.00              
ATOM    145  N   LEU    59      49.139  31.306  26.089  1.00  0.00              
ATOM    146  CA  LEU    59      49.179  30.134  25.208  1.00  0.00              
ATOM    147  C   LEU    59      49.246  30.496  23.724  1.00  0.00              
ATOM    148  O   LEU    59      49.835  29.770  22.919  1.00  0.00              
ATOM    149  N   LYS    60      48.621  31.612  23.372  1.00  0.00              
ATOM    150  CA  LYS    60      48.605  32.072  21.999  1.00  0.00              
ATOM    151  C   LYS    60      50.008  32.511  21.576  1.00  0.00              
ATOM    152  O   LYS    60      50.501  32.115  20.520  1.00  0.00              
ATOM    153  N   GLU    61      50.651  33.323  22.411  1.00  0.00              
ATOM    154  CA  GLU    61      51.995  33.805  22.120  1.00  0.00              
ATOM    155  C   GLU    61      52.939  32.622  22.077  1.00  0.00              
ATOM    156  O   GLU    61      54.082  32.763  21.668  1.00  0.00              
ATOM    157  N   ALA    62      52.463  31.467  22.531  1.00  0.00              
ATOM    158  CA  ALA    62      53.279  30.257  22.567  1.00  0.00              
ATOM    159  C   ALA    62      53.035  29.389  21.333  1.00  0.00              
ATOM    160  O   ALA    62      53.627  28.304  21.178  1.00  0.00              
ATOM    161  N   GLY    63      52.149  29.869  20.461  1.00  0.00              
ATOM    162  CA  GLY    63      51.835  29.148  19.242  1.00  0.00              
ATOM    163  C   GLY    63      50.817  28.032  19.381  1.00  0.00              
ATOM    164  O   GLY    63      50.908  27.012  18.698  1.00  0.00              
ATOM    165  N   SER    69      49.843  28.198  20.260  1.00  0.00              
ATOM    166  CA  SER    69      48.847  27.158  20.397  1.00  0.00              
ATOM    167  C   SER    69      47.506  27.740  20.081  1.00  0.00              
ATOM    168  O   SER    69      47.146  28.800  20.588  1.00  0.00              
ATOM    169  N   GLU    70      46.782  27.045  19.216  1.00  0.00              
ATOM    170  CA  GLU    70      45.449  27.453  18.818  1.00  0.00              
ATOM    171  C   GLU    70      44.591  27.232  20.052  1.00  0.00              
ATOM    172  O   GLU    70      44.226  26.093  20.368  1.00  0.00              
ATOM    173  N   VAL    78      44.292  28.323  20.755  1.00  0.00              
ATOM    174  CA  VAL    78      43.516  28.236  21.980  1.00  0.00              
ATOM    175  C   VAL    78      42.440  29.292  22.135  1.00  0.00              
ATOM    176  O   VAL    78      42.705  30.474  22.022  1.00  0.00              
ATOM    177  N   LEU    79      41.216  28.865  22.400  1.00  0.00              
ATOM    178  CA  LEU    79      40.152  29.835  22.575  1.00  0.00              
ATOM    179  C   LEU    79      39.665  29.808  24.036  1.00  0.00              
ATOM    180  O   LEU    79      39.714  28.776  24.712  1.00  0.00              
ATOM    181  N   VAL    80      39.234  30.959  24.540  1.00  0.00              
ATOM    182  CA  VAL    80      38.797  31.057  25.928  1.00  0.00              
ATOM    183  C   VAL    80      37.304  31.057  26.124  1.00  0.00              
ATOM    184  O   VAL    80      36.639  31.984  25.677  1.00  0.00              
ATOM    185  N   ASP    81      36.771  30.050  26.815  1.00  0.00              
ATOM    186  CA  ASP    81      35.324  30.014  27.056  1.00  0.00              
ATOM    187  C   ASP    81      34.912  30.696  28.363  1.00  0.00              
ATOM    188  O   ASP    81      35.012  30.097  29.436  1.00  0.00              
END
