
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0335AL243_2
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335AL243_2.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I       2      M       1           -
LGA    S       3      I       2           -
LGA    N       4      S       3           -
LGA    A       5      N       4           -
LGA    K       6      A       5           -
LGA    I       7      K       6           -
LGA    A       8      I       7           -
LGA    R       9      A       8           -
LGA    I      10      R       9           -
LGA    N      11      I      10           -
LGA    E      12      N      11           -
LGA    L      13      E      12           -
LGA    A      14      L      13           -
LGA    A      15      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    K      16      G      20           #
LGA    A      17      V      21          3.583
LGA    K      18      I      22          5.831
LGA    A      19      T      23          3.349
LGA    G      20      E      24          3.079
LGA    V      21      E      25          1.560
LGA    I      22      E      26          0.885
LGA    T      23      K      27          1.666
LGA    E      24      A      28          1.576
LGA    E      25      E      29          0.762
LGA    E      26      Q      30          0.538
LGA    K      27      Q      31          1.611
LGA    A      28      K      32          1.201
LGA    E      29      L      33          0.600
LGA    Q      30      R      34          0.456
LGA    Q      31      Q      35          0.629
LGA    K      32      E      36          0.371
LGA    L      33      Y      37          0.192
LGA    R      34      L      38          0.605
LGA    Q      35      K      39          0.706
LGA    E      36      G      40          0.854
LGA    Y      37      F      41          1.680
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      R      42          3.156
LGA    F      41      -       -           -
LGA    R      42      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   42    5.0     22    2.09     9.09     48.099     1.003

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.905822 * X  +   0.182682 * Y  +   0.382248 * Z  + -47.251518
  Y_new =  -0.316373 * X  +   0.891760 * Y  +   0.323531 * Z  + -65.231651
  Z_new =  -0.281770 * X  +  -0.413994 * Y  +   0.865572 * Z  + -11.761514 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.446129    2.695463  [ DEG:   -25.5613    154.4387 ]
  Theta =   0.285639    2.855954  [ DEG:    16.3659    163.6341 ]
  Phi   =  -0.336021    2.805572  [ DEG:   -19.2526    160.7474 ]
 
# 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: T0335AL243_2                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL243_2.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   42   5.0   22   2.09    9.09  48.099
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL243_2
REMARK Aligment from pdb entry: 2ayuA
ATOM      1  N   ILE     2     -20.579  14.464  24.279  1.00  0.00              
ATOM      2  CA  ILE     2     -20.773  13.032  24.471  1.00  0.00              
ATOM      3  C   ILE     2     -20.295  12.557  25.859  1.00  0.00              
ATOM      4  O   ILE     2     -19.462  13.208  26.502  1.00  0.00              
ATOM      5  N   SER     3     -20.838  11.419  26.340  1.00  0.00              
ATOM      6  CA  SER     3     -20.516  10.805  27.636  1.00  0.00              
ATOM      7  C   SER     3     -19.047  10.428  27.768  1.00  0.00              
ATOM      8  O   SER     3     -18.364  10.249  26.760  1.00  0.00              
ATOM      9  N   ASN     4     -18.569  10.317  29.010  1.00  0.00              
ATOM     10  CA  ASN     4     -17.181   9.918  29.296  1.00  0.00              
ATOM     11  C   ASN     4     -17.010   8.608  28.525  1.00  0.00              
ATOM     12  O   ASN     4     -16.103   8.431  27.694  1.00  0.00              
ATOM     13  N   ALA     5     -17.934   7.709  28.847  1.00  0.00              
ATOM     14  CA  ALA     5     -18.074   6.384  28.285  1.00  0.00              
ATOM     15  C   ALA     5     -17.778   6.434  26.791  1.00  0.00              
ATOM     16  O   ALA     5     -16.733   5.967  26.341  1.00  0.00              
ATOM     17  N   LYS     6     -18.700   7.026  26.036  1.00  0.00              
ATOM     18  CA  LYS     6     -18.572   7.148  24.583  1.00  0.00              
ATOM     19  C   LYS     6     -17.299   7.857  24.131  1.00  0.00              
ATOM     20  O   LYS     6     -16.615   7.389  23.214  1.00  0.00              
ATOM     21  N   ILE     7     -17.013   8.997  24.760  1.00  0.00              
ATOM     22  CA  ILE     7     -15.828   9.792  24.453  1.00  0.00              
ATOM     23  C   ILE     7     -14.612   8.887  24.372  1.00  0.00              
ATOM     24  O   ILE     7     -13.836   8.943  23.413  1.00  0.00              
ATOM     25  N   ALA     8     -14.452   8.061  25.398  1.00  0.00              
ATOM     26  CA  ALA     8     -13.336   7.129  25.479  1.00  0.00              
ATOM     27  C   ALA     8     -13.182   6.271  24.222  1.00  0.00              
ATOM     28  O   ALA     8     -12.101   6.226  23.622  1.00  0.00              
ATOM     29  N   ARG     9     -14.266   5.590  23.849  1.00  0.00              
ATOM     30  CA  ARG     9     -14.309   4.736  22.662  1.00  0.00              
ATOM     31  C   ARG     9     -13.626   5.445  21.474  1.00  0.00              
ATOM     32  O   ARG     9     -12.757   4.879  20.796  1.00  0.00              
ATOM     33  N   ILE    10     -14.041   6.686  21.226  1.00  0.00              
ATOM     34  CA  ILE    10     -13.489   7.495  20.144  1.00  0.00              
ATOM     35  C   ILE    10     -11.999   7.726  20.362  1.00  0.00              
ATOM     36  O   ILE    10     -11.222   7.718  19.411  1.00  0.00              
ATOM     37  N   ASN    11     -11.603   7.943  21.613  1.00  0.00              
ATOM     38  CA  ASN    11     -10.194   8.139  21.909  1.00  0.00              
ATOM     39  C   ASN    11      -9.399   6.960  21.345  1.00  0.00              
ATOM     40  O   ASN    11      -8.320   7.143  20.773  1.00  0.00              
ATOM     41  N   GLU    12      -9.938   5.750  21.505  1.00  0.00              
ATOM     42  CA  GLU    12      -9.271   4.536  21.016  1.00  0.00              
ATOM     43  C   GLU    12      -9.415   4.414  19.505  1.00  0.00              
ATOM     44  O   GLU    12      -8.531   3.898  18.816  1.00  0.00              
ATOM     45  N   LEU    13     -10.542   4.888  18.995  1.00  0.00              
ATOM     46  CA  LEU    13     -10.775   4.862  17.565  1.00  0.00              
ATOM     47  C   LEU    13      -9.683   5.737  16.951  1.00  0.00              
ATOM     48  O   LEU    13      -9.107   5.421  15.911  1.00  0.00              
ATOM     49  N   ALA    14      -9.402   6.839  17.637  1.00  0.00              
ATOM     50  CA  ALA    14      -8.396   7.802  17.218  1.00  0.00              
ATOM     51  C   ALA    14      -7.008   7.138  17.221  1.00  0.00              
ATOM     52  O   ALA    14      -6.111   7.528  16.459  1.00  0.00              
ATOM     53  N   ALA    15      -6.848   6.133  18.084  1.00  0.00              
ATOM     54  CA  ALA    15      -5.589   5.383  18.202  1.00  0.00              
ATOM     55  C   ALA    15      -5.509   4.409  17.037  1.00  0.00              
ATOM     56  O   ALA    15      -4.474   4.266  16.387  1.00  0.00              
ATOM     57  N   LYS    16      -6.622   3.729  16.796  1.00  0.00              
ATOM     58  CA  LYS    16      -6.704   2.779  15.705  1.00  0.00              
ATOM     59  C   LYS    16      -6.376   3.491  14.404  1.00  0.00              
ATOM     60  O   LYS    16      -5.814   2.889  13.492  1.00  0.00              
ATOM     61  N   ALA    17      -6.726   4.776  14.328  1.00  0.00              
ATOM     62  CA  ALA    17      -6.468   5.577  13.135  1.00  0.00              
ATOM     63  C   ALA    17      -4.971   5.673  12.878  1.00  0.00              
ATOM     64  O   ALA    17      -4.526   5.452  11.749  1.00  0.00              
ATOM     65  N   LYS    18      -4.196   5.989  13.922  1.00  0.00              
ATOM     66  CA  LYS    18      -2.737   6.122  13.786  1.00  0.00              
ATOM     67  C   LYS    18      -2.059   4.814  13.401  1.00  0.00              
ATOM     68  O   LYS    18      -0.940   4.824  12.886  1.00  0.00              
ATOM     69  N   ALA    19      -2.740   3.695  13.657  1.00  0.00              
ATOM     70  CA  ALA    19      -2.232   2.368  13.308  1.00  0.00              
ATOM     71  C   ALA    19      -2.367   2.239  11.799  1.00  0.00              
ATOM     72  O   ALA    19      -1.403   1.894  11.106  1.00  0.00              
ATOM     73  N   GLY    20      -2.590   4.537   9.720  1.00  0.00              
ATOM     74  CA  GLY    20      -1.551   5.427   9.232  1.00  0.00              
ATOM     75  C   GLY    20      -0.187   4.763   9.023  1.00  0.00              
ATOM     76  O   GLY    20       0.482   4.984   8.009  1.00  0.00              
ATOM     77  N   VAL    21       0.227   3.944   9.975  1.00  0.00              
ATOM     78  CA  VAL    21       1.512   3.292   9.853  1.00  0.00              
ATOM     79  C   VAL    21       1.520   2.325   8.657  1.00  0.00              
ATOM     80  O   VAL    21       2.546   2.144   7.987  1.00  0.00              
ATOM     81  N   ILE    22       0.370   1.715   8.384  1.00  0.00              
ATOM     82  CA  ILE    22       0.235   0.777   7.262  1.00  0.00              
ATOM     83  C   ILE    22       0.263   1.561   5.942  1.00  0.00              
ATOM     84  O   ILE    22       0.994   1.235   4.992  1.00  0.00              
ATOM     85  N   THR    23      -0.577   2.593   5.912  1.00  0.00              
ATOM     86  CA  THR    23      -0.730   3.463   4.762  1.00  0.00              
ATOM     87  C   THR    23       0.599   4.051   4.315  1.00  0.00              
ATOM     88  O   THR    23       0.744   4.467   3.157  1.00  0.00              
ATOM     89  N   GLU    24       1.568   4.092   5.229  1.00  0.00              
ATOM     90  CA  GLU    24       2.866   4.604   4.856  1.00  0.00              
ATOM     91  C   GLU    24       3.567   3.533   4.036  1.00  0.00              
ATOM     92  O   GLU    24       4.125   3.816   2.964  1.00  0.00              
ATOM     93  N   GLU    25       3.524   2.295   4.524  1.00  0.00              
ATOM     94  CA  GLU    25       4.157   1.198   3.798  1.00  0.00              
ATOM     95  C   GLU    25       3.534   1.107   2.408  1.00  0.00              
ATOM     96  O   GLU    25       4.224   0.950   1.396  1.00  0.00              
ATOM     97  N   GLU    26       2.215   1.213   2.369  1.00  0.00              
ATOM     98  CA  GLU    26       1.510   1.163   1.104  1.00  0.00              
ATOM     99  C   GLU    26       2.161   2.120   0.115  1.00  0.00              
ATOM    100  O   GLU    26       2.583   1.727  -0.968  1.00  0.00              
ATOM    101  N   LYS    27       2.218   3.388   0.503  1.00  0.00              
ATOM    102  CA  LYS    27       2.800   4.419  -0.340  1.00  0.00              
ATOM    103  C   LYS    27       4.174   4.040  -0.819  1.00  0.00              
ATOM    104  O   LYS    27       4.563   4.368  -1.938  1.00  0.00              
ATOM    105  N   ALA    28       4.908   3.340   0.032  1.00  0.00              
ATOM    106  CA  ALA    28       6.251   2.919  -0.322  1.00  0.00              
ATOM    107  C   ALA    28       6.283   1.892  -1.452  1.00  0.00              
ATOM    108  O   ALA    28       6.993   2.071  -2.449  1.00  0.00              
ATOM    109  N   GLU    29       5.516   0.820  -1.299  1.00  0.00              
ATOM    110  CA  GLU    29       5.473  -0.214  -2.323  1.00  0.00              
ATOM    111  C   GLU    29       4.899   0.313  -3.634  1.00  0.00              
ATOM    112  O   GLU    29       5.159  -0.236  -4.714  1.00  0.00              
ATOM    113  N   GLN    30       4.128   1.392  -3.517  1.00  0.00              
ATOM    114  CA  GLN    30       3.509   2.056  -4.658  1.00  0.00              
ATOM    115  C   GLN    30       4.562   2.863  -5.401  1.00  0.00              
ATOM    116  O   GLN    30       4.713   2.753  -6.612  1.00  0.00              
ATOM    117  N   GLN    31       5.280   3.688  -4.655  1.00  0.00              
ATOM    118  CA  GLN    31       6.308   4.521  -5.239  1.00  0.00              
ATOM    119  C   GLN    31       7.269   3.626  -5.990  1.00  0.00              
ATOM    120  O   GLN    31       7.772   3.987  -7.061  1.00  0.00              
ATOM    121  N   LYS    32       7.524   2.457  -5.405  1.00  0.00              
ATOM    122  CA  LYS    32       8.417   1.466  -5.998  1.00  0.00              
ATOM    123  C   LYS    32       7.794   0.946  -7.274  1.00  0.00              
ATOM    124  O   LYS    32       8.389   1.056  -8.348  1.00  0.00              
ATOM    125  N   LEU    33       6.589   0.382  -7.135  1.00  0.00              
ATOM    126  CA  LEU    33       5.840  -0.163  -8.262  1.00  0.00              
ATOM    127  C   LEU    33       5.852   0.818  -9.427  1.00  0.00              
ATOM    128  O   LEU    33       5.912   0.414 -10.591  1.00  0.00              
ATOM    129  N   ARG    34       5.789   2.106  -9.104  1.00  0.00              
ATOM    130  CA  ARG    34       5.797   3.164 -10.106  1.00  0.00              
ATOM    131  C   ARG    34       7.139   3.232 -10.804  1.00  0.00              
ATOM    132  O   ARG    34       7.216   3.263 -12.034  1.00  0.00              
ATOM    133  N   GLN    35       8.201   3.253 -10.013  1.00  0.00              
ATOM    134  CA  GLN    35       9.535   3.315 -10.577  1.00  0.00              
ATOM    135  C   GLN    35       9.753   2.085 -11.464  1.00  0.00              
ATOM    136  O   GLN    35      10.474   2.131 -12.460  1.00  0.00              
ATOM    137  N   GLU    36       9.107   0.986 -11.094  1.00  0.00              
ATOM    138  CA  GLU    36       9.224  -0.249 -11.842  1.00  0.00              
ATOM    139  C   GLU    36       8.787  -0.058 -13.272  1.00  0.00              
ATOM    140  O   GLU    36       9.455  -0.518 -14.207  1.00  0.00              
ATOM    141  N   TYR    37       7.651   0.608 -13.444  1.00  0.00              
ATOM    142  CA  TYR    37       7.133   0.839 -14.775  1.00  0.00              
ATOM    143  C   TYR    37       7.760   2.015 -15.476  1.00  0.00              
ATOM    144  O   TYR    37       7.746   2.084 -16.708  1.00  0.00              
ATOM    145  N   LEU    38       8.329   2.932 -14.700  1.00  0.00              
ATOM    146  CA  LEU    38       8.982   4.068 -15.315  1.00  0.00              
ATOM    147  C   LEU    38      10.013   3.430 -16.217  1.00  0.00              
ATOM    148  O   LEU    38      10.259   3.880 -17.336  1.00  0.00              
ATOM    149  N   LYS    39      10.597   2.353 -15.703  1.00  0.00              
ATOM    150  CA  LYS    39      11.613   1.603 -16.413  1.00  0.00              
ATOM    151  C   LYS    39      11.073   1.064 -17.721  1.00  0.00              
ATOM    152  O   LYS    39      11.718   1.176 -18.764  1.00  0.00              
ATOM    153  N   GLY    40       9.882   0.486 -17.666  1.00  0.00              
ATOM    154  CA  GLY    40       9.267  -0.071 -18.857  1.00  0.00              
ATOM    155  C   GLY    40       8.881   1.005 -19.881  1.00  0.00              
ATOM    156  O   GLY    40       8.719   0.704 -21.073  1.00  0.00              
ATOM    157  N   PHE    41       8.742   2.253 -19.427  1.00  0.00              
ATOM    158  CA  PHE    41       8.384   3.341 -20.338  1.00  0.00              
ATOM    159  C   PHE    41       9.631   3.906 -21.004  1.00  0.00              
ATOM    160  O   PHE    41       9.652   4.085 -22.225  1.00  0.00              
ATOM    161  N   ARG    42      10.663   4.170 -20.191  1.00  0.00              
ATOM    162  CA  ARG    42      11.936   4.749 -20.653  1.00  0.00              
ATOM    163  C   ARG    42      12.319   4.350 -22.066  1.00  0.00              
ATOM    164  O   ARG    42      12.583   5.210 -22.902  1.00  0.00              
END
