
#######################################################
#                                                     #
#                        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   36 (  144),  selected   36 , name T0335AL242_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL242_3-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          2.670
LGA    K       6      K       6          1.779
LGA    I       7      I       7          0.967
LGA    A       8      A       8          0.992
LGA    R       9      R       9          1.108
LGA    I      10      I      10          0.861
LGA    N      11      N      11          0.425
LGA    E      12      E      12          0.506
LGA    L      13      L      13          0.648
LGA    A      14      A      14          0.556
LGA    A      15      A      15          0.955
LGA    K      16      K      16          1.093
LGA    A      17      A      17          0.673
LGA    K      18      K      18          0.722
LGA    A      19      A      19          1.634
LGA    G      20      G      20          1.512
LGA    V      21      V      21          0.875
LGA    I      22      I      22          2.054
LGA    T      23      T      23          2.331
LGA    E      24      E      24          4.085
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    E      25      K      27          2.846
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    -       -      Q      30           -
LGA    E      26      Q      31          2.566
LGA    K      27      K      32          3.092
LGA    A      28      L      33           -
LGA    -       -      R      34           -
LGA    E      29      Q      35          5.466
LGA    Q      30      E      36          4.179
LGA    Q      31      Y      37           -
LGA    K      32      L      38           -
LGA    L      33      K      39           -
LGA    R      34      G      40           -
LGA    Q      35      -       -           -
LGA    E      36      -       -           -
LGA    Y      37      -       -           -
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     25    2.21    84.00     60.317     1.082

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.535031 * X  +  -0.754203 * Y  +  -0.380683 * Z  +   8.207874
  Y_new =   0.750907 * X  +   0.631022 * Y  +  -0.194808 * Z  + -35.448399
  Z_new =   0.387144 * X  +  -0.181629 * Y  +   0.903953 * Z  + -42.639954 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.198287    2.943305  [ DEG:   -11.3610    168.6390 ]
  Theta =  -0.397532   -2.744061  [ DEG:   -22.7769   -157.2231 ]
  Phi   =   0.951722   -2.189871  [ DEG:    54.5296   -125.4704 ]
 
# 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: T0335AL242_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL242_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   25   2.21   84.00  60.317
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL242_3-D1
REMARK Aligment from pdb entry: 1u6t_A
ATOM     17  N   ALA     5      -2.501 -10.277  -8.822  1.00  0.00              
ATOM     18  CA  ALA     5      -2.571 -10.757  -7.444  1.00  0.00              
ATOM     19  C   ALA     5      -1.939  -9.748  -6.489  1.00  0.00              
ATOM     20  O   ALA     5      -2.474  -9.477  -5.410  1.00  0.00              
ATOM     21  N   LYS     6      -0.793  -9.206  -6.886  1.00  0.00              
ATOM     22  CA  LYS     6      -0.092  -8.222  -6.069  1.00  0.00              
ATOM     23  C   LYS     6      -0.957  -6.966  -5.930  1.00  0.00              
ATOM     24  O   LYS     6      -1.138  -6.435  -4.832  1.00  0.00              
ATOM     25  N   ILE     7      -1.494  -6.501  -7.054  1.00  0.00              
ATOM     26  CA  ILE     7      -2.340  -5.317  -7.065  1.00  0.00              
ATOM     27  C   ILE     7      -3.485  -5.484  -6.064  1.00  0.00              
ATOM     28  O   ILE     7      -3.772  -4.581  -5.272  1.00  0.00              
ATOM     29  N   ALA     8      -4.123  -6.648  -6.089  1.00  0.00              
ATOM     30  CA  ALA     8      -5.231  -6.917  -5.184  1.00  0.00              
ATOM     31  C   ALA     8      -4.767  -6.992  -3.730  1.00  0.00              
ATOM     32  O   ALA     8      -5.454  -6.506  -2.833  1.00  0.00              
ATOM     33  N   ARG     9      -3.604  -7.590  -3.487  1.00  0.00              
ATOM     34  CA  ARG     9      -3.094  -7.687  -2.122  1.00  0.00              
ATOM     35  C   ARG     9      -2.810  -6.292  -1.559  1.00  0.00              
ATOM     36  O   ARG     9      -3.080  -6.020  -0.387  1.00  0.00              
ATOM     37  N   ILE    10      -2.278  -5.408  -2.400  1.00  0.00              
ATOM     38  CA  ILE    10      -1.973  -4.044  -1.974  1.00  0.00              
ATOM     39  C   ILE    10      -3.259  -3.295  -1.629  1.00  0.00              
ATOM     40  O   ILE    10      -3.348  -2.637  -0.593  1.00  0.00              
ATOM     41  N   ASN    11      -4.258  -3.401  -2.497  1.00  0.00              
ATOM     42  CA  ASN    11      -5.525  -2.725  -2.248  1.00  0.00              
ATOM     43  C   ASN    11      -6.180  -3.255  -0.978  1.00  0.00              
ATOM     44  O   ASN    11      -6.839  -2.510  -0.250  1.00  0.00              
ATOM     45  N   GLU    12      -5.984  -4.542  -0.708  1.00  0.00              
ATOM     46  CA  GLU    12      -6.542  -5.164   0.484  1.00  0.00              
ATOM     47  C   GLU    12      -5.985  -4.463   1.727  1.00  0.00              
ATOM     48  O   GLU    12      -6.739  -4.035   2.601  1.00  0.00              
ATOM     49  N   LEU    13      -4.663  -4.336   1.796  1.00  0.00              
ATOM     50  CA  LEU    13      -4.023  -3.687   2.937  1.00  0.00              
ATOM     51  C   LEU    13      -4.422  -2.214   3.055  1.00  0.00              
ATOM     52  O   LEU    13      -4.847  -1.765   4.119  1.00  0.00              
ATOM     53  N   ALA    14      -4.292  -1.470   1.962  1.00  0.00              
ATOM     54  CA  ALA    14      -4.633  -0.050   1.972  1.00  0.00              
ATOM     55  C   ALA    14      -6.084   0.173   2.396  1.00  0.00              
ATOM     56  O   ALA    14      -6.379   1.077   3.180  1.00  0.00              
ATOM     57  N   ALA    15      -6.983  -0.660   1.880  1.00  0.00              
ATOM     58  CA  ALA    15      -8.389  -0.536   2.220  1.00  0.00              
ATOM     59  C   ALA    15      -8.657  -0.792   3.690  1.00  0.00              
ATOM     60  O   ALA    15      -9.474  -0.108   4.306  1.00  0.00              
ATOM     61  N   LYS    16      -7.973  -1.781   4.256  1.00  0.00              
ATOM     62  CA  LYS    16      -8.148  -2.119   5.664  1.00  0.00              
ATOM     63  C   LYS    16      -7.746  -0.963   6.575  1.00  0.00              
ATOM     64  O   LYS    16      -8.455  -0.630   7.527  1.00  0.00              
ATOM     65  N   ALA    17      -6.597  -0.365   6.287  1.00  0.00              
ATOM     66  CA  ALA    17      -6.095   0.748   7.082  1.00  0.00              
ATOM     67  C   ALA    17      -7.075   1.909   7.039  1.00  0.00              
ATOM     68  O   ALA    17      -7.386   2.515   8.065  1.00  0.00              
ATOM     69  N   LYS    18      -7.567   2.206   5.843  1.00  0.00              
ATOM     70  CA  LYS    18      -8.527   3.285   5.651  1.00  0.00              
ATOM     71  C   LYS    18      -9.789   3.009   6.459  1.00  0.00              
ATOM     72  O   LYS    18     -10.261   3.866   7.207  1.00  0.00              
ATOM     73  N   ALA    19     -10.322   1.800   6.313  1.00  0.00              
ATOM     74  CA  ALA    19     -11.536   1.400   7.013  1.00  0.00              
ATOM     75  C   ALA    19     -11.427   1.520   8.528  1.00  0.00              
ATOM     76  O   ALA    19     -12.372   1.955   9.190  1.00  0.00              
ATOM     77  N   GLY    20     -10.278   1.137   9.076  1.00  0.00              
ATOM     78  CA  GLY    20     -10.077   1.186  10.518  1.00  0.00              
ATOM     79  C   GLY    20      -9.492   2.501  11.005  1.00  0.00              
ATOM     80  O   GLY    20      -9.108   2.624  12.168  1.00  0.00              
ATOM     81  N   VAL    21      -9.441   3.481  10.108  1.00  0.00              
ATOM     82  CA  VAL    21      -8.915   4.804  10.418  1.00  0.00              
ATOM     83  C   VAL    21      -7.531   4.742  11.052  1.00  0.00              
ATOM     84  O   VAL    21      -7.245   5.427  12.032  1.00  0.00              
ATOM     85  N   ILE    22      -6.677   3.903  10.487  1.00  0.00              
ATOM     86  CA  ILE    22      -5.315   3.781  10.969  1.00  0.00              
ATOM     87  C   ILE    22      -4.501   4.717  10.086  1.00  0.00              
ATOM     88  O   ILE    22      -4.572   4.625   8.859  1.00  0.00              
ATOM     89  N   THR    23      -3.760   5.635  10.702  1.00  0.00              
ATOM     90  CA  THR    23      -2.956   6.570   9.931  1.00  0.00              
ATOM     91  C   THR    23      -1.955   5.827   9.065  1.00  0.00              
ATOM     92  O   THR    23      -1.156   5.041   9.576  1.00  0.00              
ATOM     93  N   GLU    24      -1.984   6.075   7.758  1.00  0.00              
ATOM     94  CA  GLU    24      -1.071   5.392   6.853  1.00  0.00              
ATOM     95  C   GLU    24      -0.739   6.211   5.616  1.00  0.00              
ATOM     96  O   GLU    24      -1.381   7.220   5.317  1.00  0.00              
ATOM     97  N   GLU    25       0.272   5.752   4.891  1.00  0.00              
ATOM     98  CA  GLU    25       0.687   6.387   3.653  1.00  0.00              
ATOM     99  C   GLU    25       1.287   5.318   2.761  1.00  0.00              
ATOM    100  O   GLU    25       1.970   4.408   3.234  1.00  0.00              
ATOM    101  N   GLU    26       1.011   5.408   1.470  1.00  0.00              
ATOM    102  CA  GLU    26       1.562   4.441   0.547  1.00  0.00              
ATOM    103  C   GLU    26       2.880   4.983   0.030  1.00  0.00              
ATOM    104  O   GLU    26       3.054   6.192  -0.102  1.00  0.00              
ATOM    105  N   LYS    27       3.814   4.079  -0.232  1.00  0.00              
ATOM    106  CA  LYS    27       5.118   4.442  -0.770  1.00  0.00              
ATOM    107  C   LYS    27       5.232   3.555  -2.001  1.00  0.00              
ATOM    108  O   LYS    27       5.431   2.345  -1.883  1.00  0.00              
ATOM    109  N   ALA    28      14.195   5.604  -4.832  1.00  0.00              
ATOM    110  CA  ALA    28      14.417   5.698  -3.393  1.00  0.00              
ATOM    111  C   ALA    28      13.468   4.754  -2.655  1.00  0.00              
ATOM    112  O   ALA    28      13.898   3.956  -1.821  1.00  0.00              
ATOM    113  N   GLU    29      12.178   4.848  -2.962  1.00  0.00              
ATOM    114  CA  GLU    29      11.186   3.980  -2.326  1.00  0.00              
ATOM    115  C   GLU    29      11.514   2.510  -2.574  1.00  0.00              
ATOM    116  O   GLU    29      11.464   1.694  -1.655  1.00  0.00              
ATOM    117  N   GLN    30      11.847   2.177  -3.819  1.00  0.00              
ATOM    118  CA  GLN    30      12.158   0.796  -4.177  1.00  0.00              
ATOM    119  C   GLN    30      13.383   0.260  -3.438  1.00  0.00              
ATOM    120  O   GLN    30      13.322  -0.814  -2.836  1.00  0.00              
ATOM    121  N   GLN    31      14.486   1.006  -3.477  1.00  0.00              
ATOM    122  CA  GLN    31      15.705   0.582  -2.791  1.00  0.00              
ATOM    123  C   GLN    31      15.469   0.502  -1.282  1.00  0.00              
ATOM    124  O   GLN    31      15.854  -0.475  -0.635  1.00  0.00              
ATOM    125  N   LYS    32      14.833   1.529  -0.721  1.00  0.00              
ATOM    126  CA  LYS    32      14.573   1.549   0.716  1.00  0.00              
ATOM    127  C   LYS    32      13.815   0.305   1.160  1.00  0.00              
ATOM    128  O   LYS    32      14.200  -0.355   2.129  1.00  0.00              
ATOM    129  N   LEU    33      12.733  -0.018   0.457  1.00  0.00              
ATOM    130  CA  LEU    33      11.944  -1.189   0.815  1.00  0.00              
ATOM    131  C   LEU    33      12.791  -2.456   0.791  1.00  0.00              
ATOM    132  O   LEU    33      12.849  -3.202   1.771  1.00  0.00              
ATOM    133  N   ARG    34      13.451  -2.695  -0.335  1.00  0.00              
ATOM    134  CA  ARG    34      14.275  -3.888  -0.496  1.00  0.00              
ATOM    135  C   ARG    34      15.358  -4.055   0.569  1.00  0.00              
ATOM    136  O   ARG    34      15.640  -5.174   0.994  1.00  0.00              
ATOM    137  N   GLN    35      15.951  -2.952   1.011  1.00  0.00              
ATOM    138  CA  GLN    35      16.993  -3.021   2.031  1.00  0.00              
ATOM    139  C   GLN    35      16.425  -3.139   3.439  1.00  0.00              
ATOM    140  O   GLN    35      16.997  -3.820   4.293  1.00  0.00              
ATOM    141  N   GLU    36      15.295  -2.486   3.685  1.00  0.00              
ATOM    142  CA  GLU    36      14.710  -2.513   5.016  1.00  0.00              
ATOM    143  C   GLU    36      13.820  -3.698   5.347  1.00  0.00              
ATOM    144  O   GLU    36      13.334  -3.824   6.469  1.00  0.00              
ATOM    145  N   TYR    37      13.593  -4.567   4.370  1.00  0.00              
ATOM    146  CA  TYR    37      12.840  -5.778   4.647  1.00  0.00              
ATOM    147  C   TYR    37      13.941  -6.680   5.202  1.00  0.00              
ATOM    148  O   TYR    37      14.952  -6.911   4.538  1.00  0.00              
ATOM    149  N   LEU    38      13.773  -7.174   6.437  1.00  0.00              
ATOM    150  CA  LEU    38      14.778  -8.044   7.053  1.00  0.00              
ATOM    151  C   LEU    38      15.055  -9.307   6.250  1.00  0.00              
ATOM    152  O   LEU    38      14.187  -9.815   5.539  1.00  0.00              
ATOM    153  N   LYS    39      16.278  -9.803   6.383  1.00  0.00              
ATOM    154  CA  LYS    39      16.733 -10.999   5.686  1.00  0.00              
ATOM    155  C   LYS    39      15.763 -12.179   5.809  1.00  0.00              
ATOM    156  O   LYS    39      15.498 -12.878   4.828  1.00  0.00              
ATOM    157  N   GLY    40      15.229 -12.398   7.007  1.00  0.00              
ATOM    158  CA  GLY    40      14.318 -13.516   7.223  1.00  0.00              
ATOM    159  C   GLY    40      12.938 -13.371   6.588  1.00  0.00              
ATOM    160  O   GLY    40      12.095 -14.262   6.709  1.00  0.00              
END
