
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0363AL044_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL044_3-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           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    I      13      I      15          0.271
LGA    N      14      E      16          1.507
LGA    I      15      I      17          1.592
LGA    E      16      A      18          1.918
LGA    I      17      Y      19          1.994
LGA    A      18      A      20          1.179
LGA    Y      19      F      21          3.155
LGA    A      20      P      22          4.135
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    F      21      Y      25           #
LGA    P      22      Y      26          3.567
LGA    E      23      L      27           -
LGA    Q      31      K      28           -
LGA    -       -      S      29           -
LGA    -       -      F      30           -
LGA    -       -      Q      31           -
LGA    -       -      V      32           -
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    V      32      G      35          1.023
LGA    D      33      I      36          0.214
LGA    V      38      T      37          0.329
LGA    Q      39      V      38          0.749
LGA    T      40      Q      39          1.067
LGA    A      41      T      40          0.317
LGA    I      42      A      41          1.107
LGA    T      43      I      42          1.674
LGA    Q      44      T      43          0.827
LGA    S      45      Q      44          1.318
LGA    G      46      S      45          2.695
LGA    I      47      G      46          3.150
LGA    L      48      -       -           -
LGA    S      49      I      47          5.621
LGA    Q      50      L      48          5.634
LGA    F      51      S      49          1.754
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    P      52      L      56          3.687
LGA    E      53      -       -           -
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   31   46    5.0     25    2.53    12.00     41.319     0.950

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.495684 * X  +  -0.839258 * Y  +  -0.223480 * Z  +  50.520538
  Y_new =   0.804118 * X  +   0.346257 * Y  +   0.483218 * Z  + -25.197790
  Z_new =  -0.328163 * X  +  -0.419228 * Y  +   0.846497 * Z  +  35.416920 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.459841    2.681752  [ DEG:   -26.3469    153.6531 ]
  Theta =   0.334358    2.807234  [ DEG:    19.1573    160.8427 ]
  Phi   =   1.018382   -2.123211  [ DEG:    58.3490   -121.6510 ]
 
# 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: T0363AL044_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL044_3-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31   46   5.0   25   2.53   12.00  41.319
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL044_3-D1
REMARK Aligment from pdb entry: 1vjk_A
ATOM      1  N   ILE    13      20.032  10.205   6.113  1.00  0.00              
ATOM      2  CA  ILE    13      20.173  11.635   6.368  1.00  0.00              
ATOM      3  C   ILE    13      20.350  12.371   5.056  1.00  0.00              
ATOM      4  O   ILE    13      20.862  11.810   4.058  1.00  0.00              
ATOM      5  N   ASN    14      19.932  13.619   5.021  1.00  0.00              
ATOM      6  CA  ASN    14      20.088  14.471   3.870  1.00  0.00              
ATOM      7  C   ASN    14      21.266  15.365   4.138  1.00  0.00              
ATOM      8  O   ASN    14      21.228  16.176   5.074  1.00  0.00              
ATOM      9  N   ILE    15      22.311  15.245   3.342  1.00  0.00              
ATOM     10  CA  ILE    15      23.501  16.071   3.478  1.00  0.00              
ATOM     11  C   ILE    15      23.451  17.216   2.497  1.00  0.00              
ATOM     12  O   ILE    15      23.244  16.978   1.306  1.00  0.00              
ATOM     13  N   GLU    16      23.607  18.450   2.993  1.00  0.00              
ATOM     14  CA  GLU    16      23.620  19.637   2.133  1.00  0.00              
ATOM     15  C   GLU    16      25.012  20.224   2.179  1.00  0.00              
ATOM     16  O   GLU    16      25.511  20.592   3.258  1.00  0.00              
ATOM     17  N   ILE    17      25.647  20.311   1.022  1.00  0.00              
ATOM     18  CA  ILE    17      26.977  20.914   0.906  1.00  0.00              
ATOM     19  C   ILE    17      26.862  22.361   0.527  1.00  0.00              
ATOM     20  O   ILE    17      25.966  22.752  -0.243  1.00  0.00              
ATOM     21  N   ALA    18      27.808  23.158   1.039  1.00  0.00              
ATOM     22  CA  ALA    18      27.823  24.584   0.783  1.00  0.00              
ATOM     23  C   ALA    18      29.130  25.053   0.206  1.00  0.00              
ATOM     24  O   ALA    18      30.189  24.502   0.499  1.00  0.00              
ATOM     25  N   TYR    19      29.050  26.118  -0.590  1.00  0.00              
ATOM     26  CA  TYR    19      30.231  26.813  -1.097  1.00  0.00              
ATOM     27  C   TYR    19      31.182  25.822  -1.787  1.00  0.00              
ATOM     28  O   TYR    19      30.725  25.027  -2.618  1.00  0.00              
ATOM     29  N   ALA    20      32.482  25.850  -1.468  1.00  0.00              
ATOM     30  CA  ALA    20      33.405  25.026  -2.275  1.00  0.00              
ATOM     31  C   ALA    20      33.178  23.544  -2.088  1.00  0.00              
ATOM     32  O   ALA    20      33.585  22.745  -2.928  1.00  0.00              
ATOM     33  N   PHE    21      32.497  23.161  -1.009  1.00  0.00              
ATOM     34  CA  PHE    21      32.246  21.732  -0.750  1.00  0.00              
ATOM     35  C   PHE    21      31.236  21.144  -1.707  1.00  0.00              
ATOM     36  O   PHE    21      31.193  19.922  -1.868  1.00  0.00              
ATOM     37  N   PRO    22      30.471  21.999  -2.381  1.00  0.00              
ATOM     38  CA  PRO    22      29.622  21.543  -3.486  1.00  0.00              
ATOM     39  C   PRO    22      30.476  21.011  -4.624  1.00  0.00              
ATOM     40  O   PRO    22      30.071  20.049  -5.293  1.00  0.00              
ATOM     41  N   GLU    23      31.630  21.639  -4.892  1.00  0.00              
ATOM     42  CA  GLU    23      32.522  21.118  -5.908  1.00  0.00              
ATOM     43  C   GLU    23      33.242  19.893  -5.474  1.00  0.00              
ATOM     44  O   GLU    23      33.429  18.997  -6.283  1.00  0.00              
ATOM     45  N   GLN    31      33.664  19.830  -4.207  1.00  0.00              
ATOM     46  CA  GLN    31      34.340  18.620  -3.736  1.00  0.00              
ATOM     47  C   GLN    31      33.418  17.406  -3.747  1.00  0.00              
ATOM     48  O   GLN    31      33.853  16.300  -4.064  1.00  0.00              
ATOM     49  N   VAL    32      22.365   3.335  14.773  1.00  0.00              
ATOM     50  CA  VAL    32      23.271   3.828  15.802  1.00  0.00              
ATOM     51  C   VAL    32      24.295   4.824  15.288  1.00  0.00              
ATOM     52  O   VAL    32      25.160   5.294  16.046  1.00  0.00              
ATOM     53  N   ASP    33      24.217   5.160  14.008  1.00  0.00              
ATOM     54  CA  ASP    33      25.200   6.063  13.436  1.00  0.00              
ATOM     55  C   ASP    33      25.256   7.377  14.155  1.00  0.00              
ATOM     56  O   ASP    33      24.226   7.947  14.551  1.00  0.00              
ATOM     57  N   VAL    38      26.487   7.869  14.283  1.00  0.00              
ATOM     58  CA  VAL    38      26.775   9.145  14.909  1.00  0.00              
ATOM     59  C   VAL    38      27.321  10.134  13.884  1.00  0.00              
ATOM     60  O   VAL    38      27.744   9.757  12.779  1.00  0.00              
ATOM     61  N   GLN    39      27.370  11.412  14.242  1.00  0.00              
ATOM     62  CA  GLN    39      27.969  12.423  13.371  1.00  0.00              
ATOM     63  C   GLN    39      29.362  12.000  12.865  1.00  0.00              
ATOM     64  O   GLN    39      29.668  12.122  11.658  1.00  0.00              
ATOM     65  N   THR    40      30.208  11.464  13.756  1.00  0.00              
ATOM     66  CA  THR    40      31.541  11.057  13.307  1.00  0.00              
ATOM     67  C   THR    40      31.491   9.970  12.203  1.00  0.00              
ATOM     68  O   THR    40      32.361   9.937  11.317  1.00  0.00              
ATOM     69  N   ALA    41      30.484   9.090  12.263  1.00  0.00              
ATOM     70  CA  ALA    41      30.353   8.028  11.239  1.00  0.00              
ATOM     71  C   ALA    41      29.947   8.633   9.930  1.00  0.00              
ATOM     72  O   ALA    41      30.428   8.201   8.874  1.00  0.00              
ATOM     73  N   ILE    42      29.087   9.637   9.976  1.00  0.00              
ATOM     74  CA  ILE    42      28.700  10.337   8.751  1.00  0.00              
ATOM     75  C   ILE    42      29.896  11.051   8.110  1.00  0.00              
ATOM     76  O   ILE    42      30.081  10.963   6.882  1.00  0.00              
ATOM     77  N   THR    43      30.728  11.700   8.923  1.00  0.00              
ATOM     78  CA  THR    43      31.921  12.352   8.398  1.00  0.00              
ATOM     79  C   THR    43      32.818  11.328   7.709  1.00  0.00              
ATOM     80  O   THR    43      33.336  11.580   6.590  1.00  0.00              
ATOM     81  N   GLN    44      33.016  10.155   8.336  1.00  0.00              
ATOM     82  CA  GLN    44      33.814   9.121   7.665  1.00  0.00              
ATOM     83  C   GLN    44      33.220   8.646   6.359  1.00  0.00              
ATOM     84  O   GLN    44      33.974   8.359   5.404  1.00  0.00              
ATOM     85  N   SER    45      31.901   8.562   6.288  1.00  0.00              
ATOM     86  CA  SER    45      31.255   8.141   5.059  1.00  0.00              
ATOM     87  C   SER    45      31.386   9.209   3.972  1.00  0.00              
ATOM     88  O   SER    45      31.579   8.854   2.803  1.00  0.00              
ATOM     89  N   GLY    46      31.303  10.504   4.329  1.00  0.00              
ATOM     90  CA  GLY    46      31.513  11.567   3.337  1.00  0.00              
ATOM     91  C   GLY    46      32.912  11.442   2.731  1.00  0.00              
ATOM     92  O   GLY    46      33.069  11.511   1.493  1.00  0.00              
ATOM     93  N   ILE    47      33.900  11.212   3.590  1.00  0.00              
ATOM     94  CA  ILE    47      35.286  11.038   3.140  1.00  0.00              
ATOM     95  C   ILE    47      35.463   9.795   2.255  1.00  0.00              
ATOM     96  O   ILE    47      36.271   9.818   1.298  1.00  0.00              
ATOM     97  N   LEU    48      34.721   8.733   2.554  1.00  0.00              
ATOM     98  CA  LEU    48      34.781   7.513   1.765  1.00  0.00              
ATOM     99  C   LEU    48      34.165   7.722   0.385  1.00  0.00              
ATOM    100  O   LEU    48      34.671   7.189  -0.614  1.00  0.00              
ATOM    101  N   SER    49      33.066   8.469   0.306  1.00  0.00              
ATOM    102  CA  SER    49      32.403   8.698  -0.966  1.00  0.00              
ATOM    103  C   SER    49      33.142   9.707  -1.831  1.00  0.00              
ATOM    104  O   SER    49      33.080   9.664  -3.058  1.00  0.00              
ATOM    105  N   GLN    50      33.770  10.669  -1.171  1.00  0.00              
ATOM    106  CA  GLN    50      34.356  11.817  -1.853  1.00  0.00              
ATOM    107  C   GLN    50      35.742  12.047  -1.309  1.00  0.00              
ATOM    108  O   GLN    50      35.930  12.813  -0.331  1.00  0.00              
ATOM    109  N   PHE    51      36.723  11.414  -1.951  1.00  0.00              
ATOM    110  CA  PHE    51      38.079  11.362  -1.402  1.00  0.00              
ATOM    111  C   PHE    51      38.721  12.726  -1.192  1.00  0.00              
ATOM    112  O   PHE    51      39.618  12.846  -0.362  1.00  0.00              
ATOM    113  N   PRO    52      35.703  20.246  11.932  1.00  0.00              
ATOM    114  CA  PRO    52      35.636  20.687  13.305  1.00  0.00              
ATOM    115  C   PRO    52      34.523  19.986  14.052  1.00  0.00              
ATOM    116  O   PRO    52      33.579  19.405  13.474  1.00  0.00              
ATOM    117  N   GLU    53      34.643  20.036  15.371  1.00  0.00              
ATOM    118  CA  GLU    53      33.594  19.551  16.238  1.00  0.00              
ATOM    119  C   GLU    53      32.841  20.756  16.758  1.00  0.00              
ATOM    120  O   GLU    53      33.443  21.642  17.411  1.00  0.00              
ATOM    121  N   LEU    56      31.543  20.803  16.485  1.00  0.00              
ATOM    122  CA  LEU    56      30.740  21.984  16.750  1.00  0.00              
ATOM    123  C   LEU    56      31.245  23.166  15.950  1.00  0.00              
ATOM    124  O   LEU    56      31.785  23.017  14.837  1.00  0.00              
END
