
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0363AL381_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL381_1-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    Q      12      Q      12          1.391
LGA    I      13      I      13          1.913
LGA    N      14      N      14          0.969
LGA    I      15      I      15          1.018
LGA    E      16      E      16          1.956
LGA    I      17      I      17          1.884
LGA    A      18      A      18          2.025
LGA    Y      19      Y      19          1.742
LGA    A      20      A      20          1.349
LGA    F      21      F      21          3.595
LGA    R      24      P      22           -
LGA    -       -      E      23           -
LGA    Y      25      R      24          5.611
LGA    Y      26      Y      25          2.647
LGA    -       -      Y      26           -
LGA    L      27      L      27          1.140
LGA    K      28      K      28          1.037
LGA    S      29      S      29          0.531
LGA    F      30      F      30          1.725
LGA    Q      31      Q      31          1.722
LGA    V      32      V      32          1.609
LGA    D      33      D      33          1.400
LGA    E      34      E      34          1.819
LGA    G      35      G      35          0.392
LGA    I      36      I      36          0.666
LGA    T      37      T      37          0.426
LGA    V      38      V      38          0.449
LGA    Q      39      Q      39          0.813
LGA    T      40      T      40          0.693
LGA    A      41      A      41          1.258
LGA    I      42      I      42          1.450
LGA    T      43      T      43          0.631
LGA    Q      44      Q      44          1.875
LGA    S      45      S      45          2.907
LGA    G      46      G      46          2.969
LGA    I      47      I      47          5.332
LGA    L      48      L      48          5.656
LGA    S      49      S      49          1.683
LGA    Q      50      Q      50          2.814
LGA    F      51      F      51          3.219
LGA    P      52      -       -           -
LGA    E      53      P      52          3.204
LGA    I      54      E      53          3.224
LGA    D      55      I      54           #
LGA    L      56      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     39    2.38    92.31     68.058     1.572

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.532993 * X  +  -0.819490 * Y  +  -0.210605 * Z  +  48.388214
  Y_new =   0.791152 * X  +   0.394432 * Y  +   0.467443 * Z  + -26.529062
  Z_new =  -0.299996 * X  +  -0.415764 * Y  +   0.858570 * Z  +  34.298550 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.450970    2.690623  [ DEG:   -25.8386    154.1613 ]
  Theta =   0.304688    2.836905  [ DEG:    17.4573    162.5426 ]
  Phi   =   0.977945   -2.163647  [ DEG:    56.0321   -123.9679 ]
 
# 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: T0363AL381_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL381_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   46   5.0   39   2.38   92.31  68.058
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL381_1-D1
REMARK Aligment from pdb entry: 1vjkA
ATOM      1  N   GLN    12      17.595   1.832   8.679  1.00  0.00              
ATOM      2  CA  GLN    12      18.384   2.931   8.015  1.00  0.00              
ATOM      3  C   GLN    12      17.934   4.337   8.446  1.00  0.00              
ATOM      4  O   GLN    12      16.755   4.567   8.770  1.00  0.00              
ATOM      5  N   ILE    13      18.890   5.266   8.460  1.00  0.00              
ATOM      6  CA  ILE    13      18.642   6.679   8.759  1.00  0.00              
ATOM      7  C   ILE    13      19.078   7.461   7.507  1.00  0.00              
ATOM      8  O   ILE    13      20.247   7.382   7.119  1.00  0.00              
ATOM      9  N   ASN    14      18.155   8.182   6.871  1.00  0.00              
ATOM     10  CA  ASN    14      18.493   8.941   5.675  1.00  0.00              
ATOM     11  C   ASN    14      18.570  10.410   6.015  1.00  0.00              
ATOM     12  O   ASN    14      17.572  11.001   6.485  1.00  0.00              
ATOM     13  N   ILE    15      19.737  11.005   5.805  1.00  0.00              
ATOM     14  CA  ILE    15      19.937  12.419   6.103  1.00  0.00              
ATOM     15  C   ILE    15      20.157  13.185   4.815  1.00  0.00              
ATOM     16  O   ILE    15      20.654  12.632   3.806  1.00  0.00              
ATOM     17  N   GLU    16      19.794  14.451   4.814  1.00  0.00              
ATOM     18  CA  GLU    16      19.997  15.328   3.689  1.00  0.00              
ATOM     19  C   GLU    16      21.211  16.162   3.994  1.00  0.00              
ATOM     20  O   GLU    16      21.198  16.947   4.953  1.00  0.00              
ATOM     21  N   ILE    17      22.257  16.021   3.204  1.00  0.00              
ATOM     22  CA  ILE    17      23.480  16.790   3.374  1.00  0.00              
ATOM     23  C   ILE    17      23.489  17.964   2.427  1.00  0.00              
ATOM     24  O   ILE    17      23.283  17.770   1.228  1.00  0.00              
ATOM     25  N   ALA    18      23.693  19.175   2.960  1.00  0.00              
ATOM     26  CA  ALA    18      23.765  20.385   2.136  1.00  0.00              
ATOM     27  C   ALA    18      25.181  20.910   2.212  1.00  0.00              
ATOM     28  O   ALA    18      25.685  21.224   3.305  1.00  0.00              
ATOM     29  N   TYR    19      25.830  21.002   1.063  1.00  0.00              
ATOM     30  CA  TYR    19      27.185  21.551   0.976  1.00  0.00              
ATOM     31  C   TYR    19      27.137  23.012   0.639  1.00  0.00              
ATOM     32  O   TYR    19      26.266  23.464  -0.126  1.00  0.00              
ATOM     33  N   ALA    20      28.112  23.751   1.182  1.00  0.00              
ATOM     34  CA  ALA    20      28.190  25.182   0.969  1.00  0.00              
ATOM     35  C   ALA    20      29.522  25.612   0.418  1.00  0.00              
ATOM     36  O   ALA    20      30.553  25.007   0.703  1.00  0.00              
ATOM     37  N   PHE    21      29.496  26.702  -0.348  1.00  0.00              
ATOM     38  CA  PHE    21      30.710  27.359  -0.824  1.00  0.00              
ATOM     39  C   PHE    21      31.624  26.349  -1.534  1.00  0.00              
ATOM     40  O   PHE    21      31.141  25.599  -2.393  1.00  0.00              
ATOM     41  N   ARG    24      30.843  17.837  -5.657  1.00  0.00              
ATOM     42  CA  ARG    24      30.274  17.747  -7.005  1.00  0.00              
ATOM     43  C   ARG    24      28.771  17.967  -7.104  1.00  0.00              
ATOM     44  O   ARG    24      28.204  17.864  -8.205  1.00  0.00              
ATOM     45  N   TYR    25      28.109  18.198  -5.976  1.00  0.00              
ATOM     46  CA  TYR    25      26.663  18.459  -5.868  1.00  0.00              
ATOM     47  C   TYR    25      26.422  19.474  -4.772  1.00  0.00              
ATOM     48  O   TYR    25      27.239  19.626  -3.838  1.00  0.00              
ATOM     49  N   TYR    26      25.276  20.131  -4.823  1.00  0.00              
ATOM     50  CA  TYR    26      24.923  21.102  -3.811  1.00  0.00              
ATOM     51  C   TYR    26      24.343  20.409  -2.588  1.00  0.00              
ATOM     52  O   TYR    26      24.454  20.900  -1.467  1.00  0.00              
ATOM     53  N   LEU    27      23.760  19.228  -2.794  1.00  0.00              
ATOM     54  CA  LEU    27      23.137  18.469  -1.721  1.00  0.00              
ATOM     55  C   LEU    27      23.065  17.023  -2.120  1.00  0.00              
ATOM     56  O   LEU    27      23.109  16.687  -3.309  1.00  0.00              
ATOM     57  N   LYS    28      22.950  16.151  -1.127  1.00  0.00              
ATOM     58  CA  LYS    28      22.839  14.728  -1.372  1.00  0.00              
ATOM     59  C   LYS    28      22.213  14.037  -0.193  1.00  0.00              
ATOM     60  O   LYS    28      22.422  14.447   0.955  1.00  0.00              
ATOM     61  N   SER    29      21.430  13.014  -0.466  1.00  0.00              
ATOM     62  CA  SER    29      20.856  12.175   0.557  1.00  0.00              
ATOM     63  C   SER    29      21.798  11.056   0.877  1.00  0.00              
ATOM     64  O   SER    29      22.257  10.338  -0.038  1.00  0.00              
ATOM     65  N   PHE    30      22.067  10.842   2.153  1.00  0.00              
ATOM     66  CA  PHE    30      22.963   9.791   2.569  1.00  0.00              
ATOM     67  C   PHE    30      22.254   8.855   3.534  1.00  0.00              
ATOM     68  O   PHE    30      21.816   9.259   4.629  1.00  0.00              
ATOM     69  N   GLN    31      22.109   7.607   3.120  1.00  0.00              
ATOM     70  CA  GLN    31      21.531   6.561   3.953  1.00  0.00              
ATOM     71  C   GLN    31      22.627   5.973   4.840  1.00  0.00              
ATOM     72  O   GLN    31      23.696   5.594   4.356  1.00  0.00              
ATOM     73  N   VAL    32      22.353   5.923   6.141  1.00  0.00              
ATOM     74  CA  VAL    32      23.302   5.476   7.136  1.00  0.00              
ATOM     75  C   VAL    32      22.681   4.356   7.948  1.00  0.00              
ATOM     76  O   VAL    32      21.465   4.297   8.067  1.00  0.00              
ATOM     77  N   ASP    33      23.491   3.450   8.505  1.00  0.00              
ATOM     78  CA  ASP    33      22.953   2.381   9.343  1.00  0.00              
ATOM     79  C   ASP    33      22.348   2.911  10.634  1.00  0.00              
ATOM     80  O   ASP    33      22.713   3.987  11.122  1.00  0.00              
ATOM     81  N   GLU    34      21.418   2.137  11.174  1.00  0.00              
ATOM     82  CA  GLU    34      20.851   2.380  12.483  1.00  0.00              
ATOM     83  C   GLU    34      21.949   2.748  13.488  1.00  0.00              
ATOM     84  O   GLU    34      22.999   2.115  13.525  1.00  0.00              
ATOM     85  N   GLY    35      21.688   3.790  14.276  1.00  0.00              
ATOM     86  CA  GLY    35      22.604   4.213  15.327  1.00  0.00              
ATOM     87  C   GLY    35      23.675   5.178  14.851  1.00  0.00              
ATOM     88  O   GLY    35      24.552   5.588  15.631  1.00  0.00              
ATOM     89  N   ILE    36      23.624   5.554  13.581  1.00  0.00              
ATOM     90  CA  ILE    36      24.650   6.431  13.045  1.00  0.00              
ATOM     91  C   ILE    36      24.756   7.719  13.803  1.00  0.00              
ATOM     92  O   ILE    36      23.748   8.321  14.207  1.00  0.00              
ATOM     93  N   THR    37      26.006   8.153  13.956  1.00  0.00              
ATOM     94  CA  THR    37      26.343   9.396  14.622  1.00  0.00              
ATOM     95  C   THR    37      26.940  10.391  13.630  1.00  0.00              
ATOM     96  O   THR    37      27.358  10.028  12.519  1.00  0.00              
ATOM     97  N   VAL    38      27.041  11.654  14.027  1.00  0.00              
ATOM     98  CA  VAL    38      27.691  12.664  13.191  1.00  0.00              
ATOM     99  C   VAL    38      29.069  12.195  12.685  1.00  0.00              
ATOM    100  O   VAL    38      29.392  12.339  11.485  1.00  0.00              
ATOM    101  N   GLN    39      29.883  11.597  13.566  1.00  0.00              
ATOM    102  CA  GLN    39      31.202  11.146  13.117  1.00  0.00              
ATOM    103  C   GLN    39      31.115  10.095  11.981  1.00  0.00              
ATOM    104  O   GLN    39      31.991  10.051  11.101  1.00  0.00              
ATOM    105  N   THR    40      30.071   9.258  12.005  1.00  0.00              
ATOM    106  CA  THR    40      29.904   8.233  10.950  1.00  0.00              
ATOM    107  C   THR    40      29.537   8.894   9.656  1.00  0.00              
ATOM    108  O   THR    40      30.009   8.472   8.592  1.00  0.00              
ATOM    109  N   ALA    41      28.721   9.932   9.724  1.00  0.00              
ATOM    110  CA  ALA    41      28.376  10.684   8.518  1.00  0.00              
ATOM    111  C   ALA    41      29.607  11.364   7.908  1.00  0.00              
ATOM    112  O   ALA    41      29.800  11.304   6.680  1.00  0.00              
ATOM    113  N   ILE    42      30.460  11.952   8.747  1.00  0.00              
ATOM    114  CA  ILE    42      31.684  12.567   8.252  1.00  0.00              
ATOM    115  C   ILE    42      32.543  11.525   7.540  1.00  0.00              
ATOM    116  O   ILE    42      33.082  11.787   6.433  1.00  0.00              
ATOM    117  N   THR    43      32.684  10.327   8.134  1.00  0.00              
ATOM    118  CA  THR    43      33.443   9.279   7.439  1.00  0.00              
ATOM    119  C   THR    43      32.842   8.870   6.115  1.00  0.00              
ATOM    120  O   THR    43      33.592   8.578   5.158  1.00  0.00              
ATOM    121  N   GLN    44      31.521   8.844   6.030  1.00  0.00              
ATOM    122  CA  GLN    44      30.870   8.488   4.783  1.00  0.00              
ATOM    123  C   GLN    44      31.057   9.580   3.730  1.00  0.00              
ATOM    124  O   GLN    44      31.246   9.252   2.553  1.00  0.00              
ATOM    125  N   SER    45      31.027  10.868   4.125  1.00  0.00              
ATOM    126  CA  SER    45      31.292  11.949   3.167  1.00  0.00              
ATOM    127  C   SER    45      32.689  11.782   2.569  1.00  0.00              
ATOM    128  O   SER    45      32.861  11.879   1.335  1.00  0.00              
ATOM    129  N   GLY    46      33.658  11.484   3.429  1.00  0.00              
ATOM    130  CA  GLY    46      35.040  11.262   2.985  1.00  0.00              
ATOM    131  C   GLY    46      35.172  10.040   2.066  1.00  0.00              
ATOM    132  O   GLY    46      35.989  10.056   1.116  1.00  0.00              
ATOM    133  N   ILE    47      32.738   8.877   0.058  1.00  0.00              
ATOM    134  CA  ILE    47      32.098   9.171  -1.212  1.00  0.00              
ATOM    135  C   ILE    47      32.888  10.173  -2.041  1.00  0.00              
ATOM    136  O   ILE    47      32.837  10.168  -3.269  1.00  0.00              
ATOM    137  N   LEU    48      33.551  11.086  -1.348  1.00  0.00              
ATOM    138  CA  LEU    48      34.193  12.227  -1.990  1.00  0.00              
ATOM    139  C   LEU    48      35.582  12.381  -1.428  1.00  0.00              
ATOM    140  O   LEU    48      35.793  13.109  -0.426  1.00  0.00              
ATOM    141  N   SER    49      36.541  11.726  -2.081  1.00  0.00              
ATOM    142  CA  SER    49      37.888  11.598  -1.522  1.00  0.00              
ATOM    143  C   SER    49      38.586  12.927  -1.266  1.00  0.00              
ATOM    144  O   SER    49      39.479  12.983  -0.426  1.00  0.00              
ATOM    145  N   GLN    50      38.176  13.987  -1.958  1.00  0.00              
ATOM    146  CA  GLN    50      38.809  15.306  -1.726  1.00  0.00              
ATOM    147  C   GLN    50      38.546  15.821  -0.311  1.00  0.00              
ATOM    148  O   GLN    50      39.278  16.694   0.177  1.00  0.00              
ATOM    149  N   PHE    51      37.534  15.274   0.381  1.00  0.00              
ATOM    150  CA  PHE    51      37.286  15.660   1.770  1.00  0.00              
ATOM    151  C   PHE    51      38.221  14.989   2.775  1.00  0.00              
ATOM    152  O   PHE    51      38.258  15.382   3.949  1.00  0.00              
ATOM    153  N   PRO    52      38.958  13.967   2.349  1.00  0.00              
ATOM    154  CA  PRO    52      39.837  13.259   3.291  1.00  0.00              
ATOM    155  C   PRO    52      40.878  14.205   3.887  1.00  0.00              
ATOM    156  O   PRO    52      41.248  14.054   5.060  1.00  0.00              
ATOM    157  N   GLU    53      41.307  15.179   3.083  1.00  0.00              
ATOM    158  CA  GLU    53      42.386  16.121   3.411  1.00  0.00              
ATOM    159  C   GLU    53      41.851  17.369   4.148  1.00  0.00              
ATOM    160  O   GLU    53      42.635  18.239   4.579  1.00  0.00              
ATOM    161  N   ILE    54      40.532  17.455   4.298  1.00  0.00              
ATOM    162  CA  ILE    54      39.892  18.593   4.945  1.00  0.00              
ATOM    163  C   ILE    54      39.659  18.282   6.414  1.00  0.00              
ATOM    164  O   ILE    54      39.132  17.225   6.767  1.00  0.00              
ATOM    165  N   ASP    55      40.014  19.220   7.278  1.00  0.00              
ATOM    166  CA  ASP    55      39.849  18.999   8.709  1.00  0.00              
ATOM    167  C   ASP    55      38.447  19.426   9.153  1.00  0.00              
ATOM    168  O   ASP    55      38.063  20.589   8.993  1.00  0.00              
ATOM    169  N   LEU    56      39.182  27.166  13.331  1.00  0.00              
ATOM    170  CA  LEU    56      40.490  26.698  12.846  1.00  0.00              
ATOM    171  C   LEU    56      40.389  25.493  11.901  1.00  0.00              
ATOM    172  O   LEU    56      41.350  25.158  11.203  1.00  0.00              
END
