
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0349AL242_5
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349AL242_5.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A      23      M       1           -
LGA    D      24      R       2          2.889
LGA    I      25      E       3          0.838
LGA    G      26      L       4          2.710
LGA    H      27      L       5          3.283
LGA    L      28      R       6          4.148
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    V      29      L      13          2.282
LGA    L      30      S      14          3.814
LGA    -       -      A      15           -
LGA    -       -      V      16           -
LGA    D      31      G      17          2.981
LGA    -       -      A      18           -
LGA    Q      32      L      19          4.121
LGA    N      33      L      20          1.171
LGA    -       -      D      21           -
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    M      34      I      25          2.249
LGA    -       -      G      26           -
LGA    S      35      H      27          2.612
LGA    I      36      L      28          2.526
LGA    L      37      V      29          1.526
LGA    E      38      L      30          3.675
LGA    G      39      D      31          0.729
LGA    S      40      Q      32          4.012
LGA    L      41      N      33           -
LGA    G      42      M      34           -
LGA    -       -      S      35           -
LGA    -       -      I      36           -
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    V      43      L      41           #
LGA    I      44      G      42          3.089
LGA    P      45      V      43          4.093
LGA    R      46      I      44          4.104
LGA    R      47      P      45          3.337
LGA    V      48      R      46          1.339
LGA    L      49      R      47          1.116
LGA    V      50      V      48          1.528
LGA    H      51      L      49          0.769
LGA    E      52      V      50          0.518
LGA    D      53      H      51          2.607
LGA    D      54      E      52          4.159
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    -       -      L      55           -
LGA    -       -      A      56           -
LGA    -       -      G      57           -
LGA    -       -      A      58           -
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    -       -      L      61           -
LGA    -       -      L      62           -
LGA    -       -      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32   75    5.0     28    2.85     3.57     23.046     0.951

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.933672 * X  +   0.183158 * Y  +  -0.307750 * Z  +  -1.045190
  Y_new =   0.140365 * X  +   0.977726 * Y  +   0.156046 * Z  +   0.961433
  Z_new =   0.329477 * X  +   0.102498 * Y  +  -0.938584 * Z  +  -0.754683 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.032818   -0.108774  [ DEG:   173.7677     -6.2323 ]
  Theta =  -0.335749   -2.805844  [ DEG:   -19.2370   -160.7630 ]
  Phi   =   2.992373   -0.149219  [ DEG:   171.4504     -8.5496 ]
 
# 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: T0349AL242_5                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL242_5.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32   75   5.0   28   2.85    3.57  23.046
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL242_5
REMARK Aligment from pdb entry: 1ews_A
ATOM      1  N   ALA    23      10.629   3.137  -3.635  1.00  0.00              
ATOM      2  CA  ALA    23       9.298   3.174  -4.300  1.00  0.00              
ATOM      3  C   ALA    23       8.580   4.469  -3.854  1.00  0.00              
ATOM      4  O   ALA    23       8.471   4.701  -2.664  1.00  0.00              
ATOM      5  N   ASP    24       8.108   5.280  -4.781  1.00  0.00              
ATOM      6  CA  ASP    24       7.321   6.508  -4.446  1.00  0.00              
ATOM      7  C   ASP    24       6.021   6.104  -3.732  1.00  0.00              
ATOM      8  O   ASP    24       5.584   6.760  -2.807  1.00  0.00              
ATOM      9  N   ILE    25       5.457   5.023  -4.208  1.00  0.00              
ATOM     10  CA  ILE    25       4.188   4.479  -3.635  1.00  0.00              
ATOM     11  C   ILE    25       4.561   3.490  -2.508  1.00  0.00              
ATOM     12  O   ILE    25       5.707   3.441  -2.102  1.00  0.00              
ATOM     13  N   GLY    26       3.604   2.728  -2.031  1.00  0.00              
ATOM     14  CA  GLY    26       3.887   1.742  -0.935  1.00  0.00              
ATOM     15  C   GLY    26       2.739   0.738  -0.743  1.00  0.00              
ATOM     16  O   GLY    26       1.583   1.117  -0.729  1.00  0.00              
ATOM     17  N   HIS    27       3.098  -0.514  -0.594  1.00  0.00              
ATOM     18  CA  HIS    27       2.080  -1.591  -0.396  1.00  0.00              
ATOM     19  C   HIS    27       1.755  -1.792   1.094  1.00  0.00              
ATOM     20  O   HIS    27       2.625  -2.111   1.882  1.00  0.00              
ATOM     21  N   LEU    28       0.502  -1.595   1.423  1.00  0.00              
ATOM     22  CA  LEU    28       0.008  -1.749   2.830  1.00  0.00              
ATOM     23  C   LEU    28      -1.446  -2.254   2.805  1.00  0.00              
ATOM     24  O   LEU    28      -2.139  -2.074   1.822  1.00  0.00              
ATOM     25  N   VAL    29      -1.865  -2.870   3.886  1.00  0.00              
ATOM     26  CA  VAL    29      -3.272  -3.394   3.972  1.00  0.00              
ATOM     27  C   VAL    29      -4.216  -2.182   3.982  1.00  0.00              
ATOM     28  O   VAL    29      -5.300  -2.214   3.432  1.00  0.00              
ATOM     29  N   LEU    30      -3.738  -1.151   4.631  1.00  0.00              
ATOM     30  CA  LEU    30      -4.481   0.137   4.768  1.00  0.00              
ATOM     31  C   LEU    30      -3.463   1.265   4.561  1.00  0.00              
ATOM     32  O   LEU    30      -2.276   1.060   4.727  1.00  0.00              
ATOM     33  N   ASP    31      -3.948   2.427   4.215  1.00  0.00              
ATOM     34  CA  ASP    31      -3.046   3.587   3.982  1.00  0.00              
ATOM     35  C   ASP    31      -2.765   4.404   5.246  1.00  0.00              
ATOM     36  O   ASP    31      -3.260   4.120   6.320  1.00  0.00              
ATOM     37  N   GLN    32      -1.954   5.409   5.034  1.00  0.00              
ATOM     38  CA  GLN    32      -1.539   6.347   6.117  1.00  0.00              
ATOM     39  C   GLN    32      -2.573   7.492   6.138  1.00  0.00              
ATOM     40  O   GLN    32      -3.268   7.684   5.159  1.00  0.00              
ATOM     41  N   ASN    33      -2.664   8.223   7.227  1.00  0.00              
ATOM     42  CA  ASN    33      -3.517   9.448   7.296  1.00  0.00              
ATOM     43  C   ASN    33      -3.200  10.442   6.162  1.00  0.00              
ATOM     44  O   ASN    33      -4.049  11.218   5.772  1.00  0.00              
ATOM     45  N   MET    34      -1.982  10.381   5.673  1.00  0.00              
ATOM     46  CA  MET    34      -1.536  11.290   4.569  1.00  0.00              
ATOM     47  C   MET    34      -1.449  10.578   3.206  1.00  0.00              
ATOM     48  O   MET    34      -1.225  11.224   2.202  1.00  0.00              
ATOM     49  N   SER    35      -1.628   9.278   3.210  1.00  0.00              
ATOM     50  CA  SER    35      -1.562   8.485   1.940  1.00  0.00              
ATOM     51  C   SER    35      -2.948   7.915   1.569  1.00  0.00              
ATOM     52  O   SER    35      -3.797   7.767   2.425  1.00  0.00              
ATOM     53  N   ILE    36      -3.134   7.615   0.300  1.00  0.00              
ATOM     54  CA  ILE    36      -4.440   7.054  -0.194  1.00  0.00              
ATOM     55  C   ILE    36      -4.210   5.882  -1.169  1.00  0.00              
ATOM     56  O   ILE    36      -3.212   5.842  -1.862  1.00  0.00              
ATOM     57  N   LEU    37      -5.152   4.966  -1.187  1.00  0.00              
ATOM     58  CA  LEU    37      -5.077   3.767  -2.078  1.00  0.00              
ATOM     59  C   LEU    37      -4.872   4.141  -3.553  1.00  0.00              
ATOM     60  O   LEU    37      -5.204   5.231  -3.975  1.00  0.00              
ATOM     61  N   GLU    38      -4.323   3.204  -4.285  1.00  0.00              
ATOM     62  CA  GLU    38      -4.055   3.412  -5.741  1.00  0.00              
ATOM     63  C   GLU    38      -4.126   2.084  -6.522  1.00  0.00              
ATOM     64  O   GLU    38      -4.257   2.099  -7.730  1.00  0.00              
ATOM     65  N   GLY    39      -4.035   0.978  -5.821  1.00  0.00              
ATOM     66  CA  GLY    39      -4.094  -0.355  -6.501  1.00  0.00              
ATOM     67  C   GLY    39      -4.255  -1.510  -5.502  1.00  0.00              
ATOM     68  O   GLY    39      -4.739  -1.317  -4.403  1.00  0.00              
ATOM     69  N   SER    40      -3.838  -2.680  -5.929  1.00  0.00              
ATOM     70  CA  SER    40      -3.928  -3.907  -5.074  1.00  0.00              
ATOM     71  C   SER    40      -2.658  -4.766  -5.186  1.00  0.00              
ATOM     72  O   SER    40      -2.413  -5.385  -6.204  1.00  0.00              
ATOM     73  N   LEU    41      -1.893  -4.767  -4.121  1.00  0.00              
ATOM     74  CA  LEU    41      -0.617  -5.553  -4.065  1.00  0.00              
ATOM     75  C   LEU    41      -0.817  -6.896  -3.352  1.00  0.00              
ATOM     76  O   LEU    41      -1.914  -7.231  -2.945  1.00  0.00              
ATOM     77  N   GLY    42       0.267  -7.620  -3.224  1.00  0.00              
ATOM     78  CA  GLY    42       0.240  -8.953  -2.553  1.00  0.00              
ATOM     79  C   GLY    42       0.081 -10.059  -3.597  1.00  0.00              
ATOM     80  O   GLY    42       0.363  -9.859  -4.764  1.00  0.00              
ATOM     81  N   VAL    43      -0.370 -11.198  -3.137  1.00  0.00              
ATOM     82  CA  VAL    43      -0.576 -12.366  -4.041  1.00  0.00              
ATOM     83  C   VAL    43      -1.997 -12.341  -4.613  1.00  0.00              
ATOM     84  O   VAL    43      -2.173 -12.111  -5.794  1.00  0.00              
ATOM     85  N   ILE    44      -2.967 -12.571  -3.768  1.00  0.00              
ATOM     86  CA  ILE    44      -4.398 -12.568  -4.207  1.00  0.00              
ATOM     87  C   ILE    44      -4.968 -11.143  -4.053  1.00  0.00              
ATOM     88  O   ILE    44      -6.120 -10.969  -3.700  1.00  0.00              
ATOM     89  N   PRO    45      -4.131 -10.166  -4.325  1.00  0.00              
ATOM     90  CA  PRO    45      -4.521  -8.719  -4.223  1.00  0.00              
ATOM     91  C   PRO    45      -5.028  -8.360  -2.811  1.00  0.00              
ATOM     92  O   PRO    45      -5.712  -7.370  -2.622  1.00  0.00              
ATOM     93  N   ARG    46      -4.662  -9.188  -1.863  1.00  0.00              
ATOM     94  CA  ARG    46      -5.065  -8.991  -0.437  1.00  0.00              
ATOM     95  C   ARG    46      -4.572  -7.638   0.101  1.00  0.00              
ATOM     96  O   ARG    46      -5.268  -6.976   0.845  1.00  0.00              
ATOM     97  N   ARG    47      -3.380  -7.281  -0.302  1.00  0.00              
ATOM     98  CA  ARG    47      -2.773  -5.989   0.142  1.00  0.00              
ATOM     99  C   ARG    47      -3.179  -4.901  -0.867  1.00  0.00              
ATOM    100  O   ARG    47      -3.698  -5.204  -1.925  1.00  0.00              
ATOM    101  N   VAL    48      -2.924  -3.667  -0.505  1.00  0.00              
ATOM    102  CA  VAL    48      -3.273  -2.509  -1.393  1.00  0.00              
ATOM    103  C   VAL    48      -2.064  -1.655  -1.755  1.00  0.00              
ATOM    104  O   VAL    48      -1.205  -1.421  -0.929  1.00  0.00              
ATOM    105  N   LEU    49      -2.045  -1.208  -2.986  1.00  0.00              
ATOM    106  CA  LEU    49      -0.923  -0.354  -3.478  1.00  0.00              
ATOM    107  C   LEU    49      -1.359   1.063  -3.142  1.00  0.00              
ATOM    108  O   LEU    49      -2.053   1.710  -3.899  1.00  0.00              
ATOM    109  N   VAL    50      -0.926   1.488  -1.990  1.00  0.00              
ATOM    110  CA  VAL    50      -1.275   2.857  -1.525  1.00  0.00              
ATOM    111  C   VAL    50      -0.172   3.859  -1.878  1.00  0.00              
ATOM    112  O   VAL    50       0.959   3.703  -1.460  1.00  0.00              
ATOM    113  N   HIS    51      -0.543   4.859  -2.641  1.00  0.00              
ATOM    114  CA  HIS    51       0.431   5.913  -3.065  1.00  0.00              
ATOM    115  C   HIS    51       0.118   7.263  -2.404  1.00  0.00              
ATOM    116  O   HIS    51      -1.016   7.545  -2.061  1.00  0.00              
ATOM    117  N   GLU    52       1.154   8.052  -2.254  1.00  0.00              
ATOM    118  CA  GLU    52       1.047   9.412  -1.626  1.00  0.00              
ATOM    119  C   GLU    52      -0.053  10.306  -2.226  1.00  0.00              
ATOM    120  O   GLU    52      -0.384  10.198  -3.392  1.00  0.00              
ATOM    121  N   ASP    53      -0.577  11.162  -1.386  1.00  0.00              
ATOM    122  CA  ASP    53      -1.655  12.108  -1.806  1.00  0.00              
ATOM    123  C   ASP    53      -0.990  13.379  -2.363  1.00  0.00              
ATOM    124  O   ASP    53      -0.797  14.349  -1.655  1.00  0.00              
ATOM    125  N   ASP    54      -0.659  13.317  -3.629  1.00  0.00              
ATOM    126  CA  ASP    54      -0.001  14.473  -4.322  1.00  0.00              
ATOM    127  C   ASP    54      -0.820  14.912  -5.552  1.00  0.00              
ATOM    128  O   ASP    54      -1.542  14.073  -6.070  1.00  0.00              
END
