
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0363AL333_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL333_2-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          2.202
LGA    Q      12      Q      12          2.306
LGA    I      13      I      13          1.281
LGA    N      14      N      14          1.229
LGA    I      15      I      15          1.225
LGA    E      16      E      16          2.080
LGA    I      17      I      17          2.027
LGA    A      20      A      18          2.183
LGA    F      21      Y      19          1.882
LGA    P      22      A      20          1.471
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    E      23      R      24          2.702
LGA    R      24      Y      25          3.028
LGA    -       -      Y      26           -
LGA    Y      25      L      27          2.047
LGA    Y      26      K      28          1.378
LGA    S      29      S      29          1.038
LGA    F      30      F      30          2.006
LGA    Q      31      Q      31          2.265
LGA    V      32      V      32          1.656
LGA    D      33      D      33          0.836
LGA    E      34      E      34          0.602
LGA    G      35      G      35          1.504
LGA    I      36      I      36          1.303
LGA    T      37      T      37          1.753
LGA    V      38      V      38          1.852
LGA    Q      39      Q      39          2.284
LGA    T      40      T      40          1.291
LGA    A      41      A      41          1.494
LGA    I      42      I      42          2.596
LGA    T      43      T      43          1.609
LGA    Q      44      Q      44          2.420
LGA    L      48      S      45          3.943
LGA    -       -      G      46           -
LGA    S      49      I      47          3.985
LGA    Q      50      L      48          3.522
LGA    F      51      S      49          4.632
LGA    P      52      Q      50          3.826
LGA    E      53      F      51          2.850
LGA    I      54      P      52          3.858
LGA    -       -      E      53           -
LGA    D      55      I      54          1.682
LGA    -       -      D      55           -
LGA    L      56      L      56          2.610

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39   46    5.0     39    2.36    64.10     66.878     1.584

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.532533 * X  +   0.322573 * Y  +  -0.782531 * Z  +  14.476013
  Y_new =   0.295525 * X  +   0.937208 * Y  +   0.185221 * Z  +   4.922400
  Z_new =   0.793141 * X  +  -0.132621 * Y  +  -0.594423 * Z  +  -1.701536 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.922078    0.219514  [ DEG:  -167.4228     12.5772 ]
  Theta =  -0.915950   -2.225643  [ DEG:   -52.4801   -127.5199 ]
  Phi   =   2.634963   -0.506630  [ DEG:   150.9722    -29.0277 ]
 
# 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: T0363AL333_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL333_2-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39   46   5.0   39   2.36   64.10  66.878
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL333_2-D1
REMARK Aligment from pdb entry: 1j8c_A
ATOM     41  N   ASN    11      17.805   0.038   9.802  1.00  0.00              
ATOM     42  CA  ASN    11      16.850   1.156   9.602  1.00  0.00              
ATOM     43  C   ASN    11      17.640   2.295   8.965  1.00  0.00              
ATOM     44  O   ASN    11      17.858   3.331   9.561  1.00  0.00              
ATOM     45  N   GLN    12      18.118   2.080   7.770  1.00  0.00              
ATOM     46  CA  GLN    12      18.951   3.114   7.104  1.00  0.00              
ATOM     47  C   GLN    12      18.178   4.436   6.977  1.00  0.00              
ATOM     48  O   GLN    12      17.369   4.605   6.087  1.00  0.00              
ATOM     49  N   ILE    13      18.429   5.378   7.854  1.00  0.00              
ATOM     50  CA  ILE    13      17.709   6.685   7.762  1.00  0.00              
ATOM     51  C   ILE    13      18.352   7.542   6.666  1.00  0.00              
ATOM     52  O   ILE    13      19.545   7.479   6.441  1.00  0.00              
ATOM     53  N   ASN    14      17.574   8.333   5.977  1.00  0.00              
ATOM     54  CA  ASN    14      18.150   9.180   4.889  1.00  0.00              
ATOM     55  C   ASN    14      18.557  10.548   5.439  1.00  0.00              
ATOM     56  O   ASN    14      17.810  11.189   6.149  1.00  0.00              
ATOM     57  N   ILE    15      19.740  10.998   5.114  1.00  0.00              
ATOM     58  CA  ILE    15      20.201  12.326   5.617  1.00  0.00              
ATOM     59  C   ILE    15      20.577  13.237   4.443  1.00  0.00              
ATOM     60  O   ILE    15      21.521  12.981   3.722  1.00  0.00              
ATOM     61  N   GLU    16      19.844  14.302   4.250  1.00  0.00              
ATOM     62  CA  GLU    16      20.152  15.234   3.127  1.00  0.00              
ATOM     63  C   GLU    16      21.199  16.261   3.570  1.00  0.00              
ATOM     64  O   GLU    16      20.918  17.151   4.348  1.00  0.00              
ATOM     65  N   ILE    17      22.404  16.143   3.079  1.00  0.00              
ATOM     66  CA  ILE    17      23.469  17.110   3.473  1.00  0.00              
ATOM     67  C   ILE    17      23.691  18.137   2.361  1.00  0.00              
ATOM     68  O   ILE    17      23.893  17.791   1.212  1.00  0.00              
ATOM     69  N   ALA    20      23.659  19.401   2.696  1.00  0.00              
ATOM     70  CA  ALA    20      23.873  20.456   1.664  1.00  0.00              
ATOM     71  C   ALA    20      25.332  20.919   1.690  1.00  0.00              
ATOM     72  O   ALA    20      25.834  21.359   2.705  1.00  0.00              
ATOM     73  N   PHE    21      26.017  20.819   0.583  1.00  0.00              
ATOM     74  CA  PHE    21      27.446  21.248   0.545  1.00  0.00              
ATOM     75  C   PHE    21      27.639  22.354  -0.498  1.00  0.00              
ATOM     76  O   PHE    21      26.761  22.604  -1.301  1.00  0.00              
ATOM     77  N   PRO    22      28.789  22.983  -0.460  1.00  0.00              
ATOM     78  CA  PRO    22      29.091  24.070  -1.425  1.00  0.00              
ATOM     79  C   PRO    22      29.294  23.491  -2.829  1.00  0.00              
ATOM     80  O   PRO    22      30.358  23.595  -3.408  1.00  0.00              
ATOM     81  N   GLU    23      28.276  22.882  -3.376  1.00  0.00              
ATOM     82  CA  GLU    23      28.391  22.288  -4.741  1.00  0.00              
ATOM     83  C   GLU    23      27.025  21.759  -5.189  1.00  0.00              
ATOM     84  O   GLU    23      26.585  21.998  -6.296  1.00  0.00              
ATOM     85  N   ARG    24      26.352  21.040  -4.328  1.00  0.00              
ATOM     86  CA  ARG    24      25.012  20.488  -4.687  1.00  0.00              
ATOM     87  C   ARG    24      24.373  19.827  -3.462  1.00  0.00              
ATOM     88  O   ARG    24      24.943  19.811  -2.386  1.00  0.00              
ATOM     89  N   TYR    25      23.198  19.279  -3.617  1.00  0.00              
ATOM     90  CA  TYR    25      22.523  18.614  -2.465  1.00  0.00              
ATOM     91  C   TYR    25      22.590  17.094  -2.628  1.00  0.00              
ATOM     92  O   TYR    25      22.029  16.537  -3.553  1.00  0.00              
ATOM     93  N   TYR    26      23.277  16.420  -1.746  1.00  0.00              
ATOM     94  CA  TYR    26      23.383  14.935  -1.859  1.00  0.00              
ATOM     95  C   TYR    26      22.880  14.261  -0.580  1.00  0.00              
ATOM     96  O   TYR    26      23.224  14.655   0.518  1.00  0.00              
ATOM     97  N   SER    29      22.075  13.242  -0.716  1.00  0.00              
ATOM     98  CA  SER    29      21.553  12.531   0.486  1.00  0.00              
ATOM     99  C   SER    29      22.458  11.340   0.815  1.00  0.00              
ATOM    100  O   SER    29      23.089  10.775  -0.056  1.00  0.00              
ATOM    101  N   PHE    30      22.531  10.959   2.061  1.00  0.00              
ATOM    102  CA  PHE    30      23.401   9.808   2.438  1.00  0.00              
ATOM    103  C   PHE    30      22.599   8.764   3.219  1.00  0.00              
ATOM    104  O   PHE    30      21.662   9.084   3.923  1.00  0.00              
ATOM    105  N   GLN    31      22.974   7.520   3.106  1.00  0.00              
ATOM    106  CA  GLN    31      22.253   6.446   3.848  1.00  0.00              
ATOM    107  C   GLN    31      23.077   6.045   5.070  1.00  0.00              
ATOM    108  O   GLN    31      24.273   5.846   4.978  1.00  0.00              
ATOM    109  N   VAL    32      22.461   5.933   6.215  1.00  0.00              
ATOM    110  CA  VAL    32      23.229   5.554   7.427  1.00  0.00              
ATOM    111  C   VAL    32      22.368   4.659   8.316  1.00  0.00              
ATOM    112  O   VAL    32      21.164   4.803   8.348  1.00  0.00              
ATOM    113  N   ASP    33      23.008   3.754   9.005  1.00  0.00              
ATOM    114  CA  ASP    33      22.266   2.828   9.888  1.00  0.00              
ATOM    115  C   ASP    33      21.648   3.585  11.064  1.00  0.00              
ATOM    116  O   ASP    33      22.321   4.300  11.778  1.00  0.00              
ATOM    117  N   GLU    34      20.362   3.430  11.253  1.00  0.00              
ATOM    118  CA  GLU    34      19.651   4.128  12.376  1.00  0.00              
ATOM    119  C   GLU    34      20.464   4.085  13.680  1.00  0.00              
ATOM    120  O   GLU    34      20.244   4.873  14.571  1.00  0.00              
ATOM    121  N   GLY    35      21.390   3.175  13.811  1.00  0.00              
ATOM    122  CA  GLY    35      22.191   3.121  15.068  1.00  0.00              
ATOM    123  C   GLY    35      23.661   3.440  14.779  1.00  0.00              
ATOM    124  O   GLY    35      24.535   2.617  14.969  1.00  0.00              
ATOM    125  N   ILE    36      23.935   4.633  14.324  1.00  0.00              
ATOM    126  CA  ILE    36      25.346   5.019  14.026  1.00  0.00              
ATOM    127  C   ILE    36      25.673   6.366  14.676  1.00  0.00              
ATOM    128  O   ILE    36      24.800   7.175  14.924  1.00  0.00              
ATOM    129  N   THR    37      26.926   6.614  14.950  1.00  0.00              
ATOM    130  CA  THR    37      27.313   7.911  15.580  1.00  0.00              
ATOM    131  C   THR    37      27.826   8.877  14.508  1.00  0.00              
ATOM    132  O   THR    37      28.274   8.466  13.456  1.00  0.00              
ATOM    133  N   VAL    38      27.763  10.157  14.766  1.00  0.00              
ATOM    134  CA  VAL    38      28.248  11.144  13.757  1.00  0.00              
ATOM    135  C   VAL    38      29.735  10.935  13.468  1.00  0.00              
ATOM    136  O   VAL    38      30.178  11.146  12.368  1.00  0.00              
ATOM    137  N   GLN    39      30.511  10.543  14.444  1.00  0.00              
ATOM    138  CA  GLN    39      31.976  10.349  14.197  1.00  0.00              
ATOM    139  C   GLN    39      32.205   9.508  12.931  1.00  0.00              
ATOM    140  O   GLN    39      33.042   9.829  12.108  1.00  0.00              
ATOM    141  N   THR    40      31.460   8.449  12.763  1.00  0.00              
ATOM    142  CA  THR    40      31.629   7.602  11.543  1.00  0.00              
ATOM    143  C   THR    40      31.131   8.361  10.308  1.00  0.00              
ATOM    144  O   THR    40      31.825   8.482   9.318  1.00  0.00              
ATOM    145  N   ALA    41      29.931   8.875  10.366  1.00  0.00              
ATOM    146  CA  ALA    41      29.375   9.636   9.206  1.00  0.00              
ATOM    147  C   ALA    41      30.264  10.846   8.893  1.00  0.00              
ATOM    148  O   ALA    41      30.458  11.210   7.749  1.00  0.00              
ATOM    149  N   ILE    42      30.793  11.472   9.907  1.00  0.00              
ATOM    150  CA  ILE    42      31.662  12.664   9.693  1.00  0.00              
ATOM    151  C   ILE    42      32.842  12.290   8.794  1.00  0.00              
ATOM    152  O   ILE    42      33.171  12.995   7.858  1.00  0.00              
ATOM    153  N   THR    43      33.477  11.182   9.069  1.00  0.00              
ATOM    154  CA  THR    43      34.634  10.755   8.228  1.00  0.00              
ATOM    155  C   THR    43      34.140  10.246   6.870  1.00  0.00              
ATOM    156  O   THR    43      34.887  10.180   5.913  1.00  0.00              
ATOM    157  N   GLN    44      32.886   9.884   6.777  1.00  0.00              
ATOM    158  CA  GLN    44      32.345   9.381   5.479  1.00  0.00              
ATOM    159  C   GLN    44      32.355  10.498   4.432  1.00  0.00              
ATOM    160  O   GLN    44      32.868  10.334   3.343  1.00  0.00              
ATOM    161  N   LEU    48      31.789  11.632   4.753  1.00  0.00              
ATOM    162  CA  LEU    48      31.769  12.758   3.773  1.00  0.00              
ATOM    163  C   LEU    48      33.201  13.218   3.479  1.00  0.00              
ATOM    164  O   LEU    48      33.556  13.487   2.351  1.00  0.00              
ATOM    165  N   SER    49      34.028  13.309   4.482  1.00  0.00              
ATOM    166  CA  SER    49      35.433  13.754   4.246  1.00  0.00              
ATOM    167  C   SER    49      36.090  12.887   3.166  1.00  0.00              
ATOM    168  O   SER    49      36.646  13.387   2.209  1.00  0.00              
ATOM    169  N   GLN    50      36.037  11.591   3.318  1.00  0.00              
ATOM    170  CA  GLN    50      36.665  10.689   2.305  1.00  0.00              
ATOM    171  C   GLN    50      35.909  10.731   0.968  1.00  0.00              
ATOM    172  O   GLN    50      36.493  10.956  -0.073  1.00  0.00              
ATOM    173  N   PHE    51      34.621  10.494   0.985  1.00  0.00              
ATOM    174  CA  PHE    51      33.843  10.496  -0.295  1.00  0.00              
ATOM    175  C   PHE    51      33.674  11.915  -0.847  1.00  0.00              
ATOM    176  O   PHE    51      34.007  12.190  -1.984  1.00  0.00              
ATOM    177  N   PRO    52      33.157  12.817  -0.057  1.00  0.00              
ATOM    178  CA  PRO    52      32.966  14.217  -0.543  1.00  0.00              
ATOM    179  C   PRO    52      34.324  14.892  -0.758  1.00  0.00              
ATOM    180  O   PRO    52      34.500  15.673  -1.673  1.00  0.00              
ATOM    181  N   GLU    53      35.282  14.600   0.089  1.00  0.00              
ATOM    182  CA  GLU    53      36.640  15.219  -0.045  1.00  0.00              
ATOM    183  C   GLU    53      36.574  16.715   0.274  1.00  0.00              
ATOM    184  O   GLU    53      36.512  17.547  -0.609  1.00  0.00              
ATOM    185  N   ILE    54      36.587  17.057   1.534  1.00  0.00              
ATOM    186  CA  ILE    54      36.527  18.497   1.924  1.00  0.00              
ATOM    187  C   ILE    54      37.203  18.703   3.282  1.00  0.00              
ATOM    188  O   ILE    54      38.219  19.363   3.385  1.00  0.00              
ATOM    189  N   ASP    55      36.647  18.143   4.322  1.00  0.00              
ATOM    190  CA  ASP    55      37.255  18.302   5.676  1.00  0.00              
ATOM    191  C   ASP    55      36.608  17.326   6.662  1.00  0.00              
ATOM    192  O   ASP    55      35.768  16.527   6.297  1.00  0.00              
ATOM    193  N   LEU    56      36.991  17.385   7.910  1.00  0.00              
ATOM    194  CA  LEU    56      36.398  16.459   8.919  1.00  0.00              
ATOM    195  C   LEU    56      36.286  17.157  10.278  1.00  0.00              
ATOM    196  O   LEU    56      35.204  17.366  10.790  1.00  0.00              
END
