
#######################################################
#                                                     #
#                        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 T0363AL381_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL381_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    E      16      N      14          0.923
LGA    I      17      I      15          1.368
LGA    A      18      E      16          1.425
LGA    Y      19      I      17          1.350
LGA    A      20      A      18          1.637
LGA    F      21      Y      19          1.970
LGA    P      22      A      20          3.059
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    E      23      Y      25          2.628
LGA    R      24      Y      26          4.143
LGA    Y      25      L      27          2.657
LGA    Y      26      K      28          1.307
LGA    L      27      S      29          1.152
LGA    K      28      F      30          1.166
LGA    Q      31      Q      31          1.681
LGA    V      32      V      32          0.348
LGA    D      33      D      33          2.368
LGA    E      34      E      34          3.220
LGA    G      35      G      35          2.349
LGA    I      36      I      36          0.753
LGA    T      37      T      37          0.853
LGA    V      38      V      38          1.113
LGA    Q      39      Q      39          1.215
LGA    T      40      T      40          0.888
LGA    A      41      A      41          1.701
LGA    I      42      I      42          1.829
LGA    T      43      T      43          2.093
LGA    Q      44      Q      44          2.240
LGA    S      45      S      45          3.819
LGA    -       -      G      46           -
LGA    -       -      I      47           -
LGA    E      53      L      48          3.730
LGA    I      54      S      49           #
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    D      55      I      54          3.204
LGA    L      56      D      55          2.483
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32   46    5.0     31    2.18    54.84     55.487     1.357

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.577483 * X  +  -0.203380 * Y  +  -0.790664 * Z  +  26.843121
  Y_new =  -0.515396 * X  +  -0.660267 * Y  +   0.546272 * Z  +  15.789470
  Z_new =  -0.633151 * X  +   0.722968 * Y  +   0.276472 * Z  +   8.478958 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.205543   -1.936049  [ DEG:    69.0725   -110.9275 ]
  Theta =   0.685617    2.455976  [ DEG:    39.2830    140.7170 ]
  Phi   =  -2.412944    0.728649  [ DEG:  -138.2515     41.7485 ]
 
# 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_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL381_3-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32   46   5.0   31   2.18   54.84  55.487
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL381_3-D1
REMARK Aligment from pdb entry: 1ryjA
ATOM      1  N   GLU    16      17.361   8.589   7.687  1.00  0.00              
ATOM      2  CA  GLU    16      17.603   9.306   6.449  1.00  0.00              
ATOM      3  C   GLU    16      17.830  10.779   6.742  1.00  0.00              
ATOM      4  O   GLU    16      17.023  11.425   7.411  1.00  0.00              
ATOM      5  N   ILE    17      18.938  11.301   6.250  1.00  0.00              
ATOM      6  CA  ILE    17      19.329  12.669   6.534  1.00  0.00              
ATOM      7  C   ILE    17      19.877  13.331   5.284  1.00  0.00              
ATOM      8  O   ILE    17      20.142  12.659   4.283  1.00  0.00              
ATOM      9  N   ALA    18      20.040  14.640   5.330  1.00  0.00              
ATOM     10  CA  ALA    18      20.578  15.358   4.196  1.00  0.00              
ATOM     11  C   ALA    18      21.787  16.186   4.602  1.00  0.00              
ATOM     12  O   ALA    18      21.773  16.880   5.621  1.00  0.00              
ATOM     13  N   TYR    19      22.843  16.068   3.821  1.00  0.00              
ATOM     14  CA  TYR    19      24.025  16.884   4.002  1.00  0.00              
ATOM     15  C   TYR    19      24.118  17.879   2.857  1.00  0.00              
ATOM     16  O   TYR    19      24.190  17.486   1.698  1.00  0.00              
ATOM     17  N   ALA    20      24.091  19.162   3.171  1.00  0.00              
ATOM     18  CA  ALA    20      24.130  20.182   2.138  1.00  0.00              
ATOM     19  C   ALA    20      25.543  20.745   2.014  1.00  0.00              
ATOM     20  O   ALA    20      26.181  21.093   3.008  1.00  0.00              
ATOM     21  N   PHE    21      26.043  20.767   0.788  1.00  0.00              
ATOM     22  CA  PHE    21      27.365  21.301   0.490  1.00  0.00              
ATOM     23  C   PHE    21      27.306  22.062  -0.840  1.00  0.00              
ATOM     24  O   PHE    21      26.219  22.413  -1.297  1.00  0.00              
ATOM     25  N   PRO    22      28.458  22.322  -1.458  1.00  0.00              
ATOM     26  CA  PRO    22      28.506  22.979  -2.769  1.00  0.00              
ATOM     27  C   PRO    22      27.782  22.139  -3.815  1.00  0.00              
ATOM     28  O   PRO    22      27.259  22.656  -4.801  1.00  0.00              
ATOM     29  N   GLU    23      27.760  20.832  -3.574  1.00  0.00              
ATOM     30  CA  GLU    23      27.084  19.877  -4.450  1.00  0.00              
ATOM     31  C   GLU    23      25.566  19.968  -4.272  1.00  0.00              
ATOM     32  O   GLU    23      24.795  19.403  -5.048  1.00  0.00              
ATOM     33  N   ARG    24      25.146  20.715  -3.260  1.00  0.00              
ATOM     34  CA  ARG    24      23.738  20.845  -2.957  1.00  0.00              
ATOM     35  C   ARG    24      23.337  19.951  -1.806  1.00  0.00              
ATOM     36  O   ARG    24      24.195  19.474  -1.059  1.00  0.00              
ATOM     37  N   TYR    25      22.042  19.730  -1.651  1.00  0.00              
ATOM     38  CA  TYR    25      21.543  18.815  -0.640  1.00  0.00              
ATOM     39  C   TYR    25      21.736  17.376  -1.087  1.00  0.00              
ATOM     40  O   TYR    25      21.199  16.951  -2.113  1.00  0.00              
ATOM     41  N   TYR    26      22.512  16.638  -0.318  1.00  0.00              
ATOM     42  CA  TYR    26      22.796  15.246  -0.614  1.00  0.00              
ATOM     43  C   TYR    26      21.952  14.359   0.293  1.00  0.00              
ATOM     44  O   TYR    26      22.021  14.470   1.516  1.00  0.00              
ATOM     45  N   LEU    27      21.140  13.503  -0.308  1.00  0.00              
ATOM     46  CA  LEU    27      20.253  12.634   0.451  1.00  0.00              
ATOM     47  C   LEU    27      20.832  11.230   0.562  1.00  0.00              
ATOM     48  O   LEU    27      21.103  10.573  -0.446  1.00  0.00              
ATOM     49  N   LYS    28      21.043  10.790   1.791  1.00  0.00              
ATOM     50  CA  LYS    28      21.526   9.444   2.047  1.00  0.00              
ATOM     51  C   LYS    28      20.891   8.895   3.319  1.00  0.00              
ATOM     52  O   LYS    28      20.684   9.629   4.290  1.00  0.00              
ATOM     53  N   GLN    31      20.555   7.615   3.304  1.00  0.00              
ATOM     54  CA  GLN    31      19.969   6.980   4.471  1.00  0.00              
ATOM     55  C   GLN    31      20.822   5.801   4.929  1.00  0.00              
ATOM     56  O   GLN    31      21.344   5.038   4.118  1.00  0.00              
ATOM     57  N   VAL    32      20.971   5.680   6.237  1.00  0.00              
ATOM     58  CA  VAL    32      21.804   4.652   6.833  1.00  0.00              
ATOM     59  C   VAL    32      20.950   3.766   7.736  1.00  0.00              
ATOM     60  O   VAL    32      20.184   4.268   8.562  1.00  0.00              
ATOM     61  N   ASP    33      21.075   2.456   7.566  1.00  0.00              
ATOM     62  CA  ASP    33      20.279   1.517   8.337  1.00  0.00              
ATOM     63  C   ASP    33      20.565   1.583   9.825  1.00  0.00              
ATOM     64  O   ASP    33      19.680   1.337  10.645  1.00  0.00              
ATOM     65  N   GLU    34      21.801   1.897  10.177  1.00  0.00              
ATOM     66  CA  GLU    34      22.185   2.017  11.573  1.00  0.00              
ATOM     67  C   GLU    34      22.383   3.481  11.952  1.00  0.00              
ATOM     68  O   GLU    34      23.153   4.194  11.310  1.00  0.00              
ATOM     69  N   GLY    35      21.663   3.954  12.981  1.00  0.00              
ATOM     70  CA  GLY    35      21.822   5.316  13.504  1.00  0.00              
ATOM     71  C   GLY    35      23.217   5.533  14.087  1.00  0.00              
ATOM     72  O   GLY    35      23.566   4.966  15.124  1.00  0.00              
ATOM     73  N   ILE    36      24.008   6.356  13.414  1.00  0.00              
ATOM     74  CA  ILE    36      25.417   6.513  13.745  1.00  0.00              
ATOM     75  C   ILE    36      25.745   7.942  14.157  1.00  0.00              
ATOM     76  O   ILE    36      24.887   8.827  14.139  1.00  0.00              
ATOM     77  N   THR    37      26.995   8.149  14.530  1.00  0.00              
ATOM     78  CA  THR    37      27.485   9.441  14.968  1.00  0.00              
ATOM     79  C   THR    37      28.009  10.234  13.769  1.00  0.00              
ATOM     80  O   THR    37      28.341   9.646  12.737  1.00  0.00              
ATOM     81  N   VAL    38      28.062  11.563  13.899  1.00  0.00              
ATOM     82  CA  VAL    38      28.591  12.428  12.842  1.00  0.00              
ATOM     83  C   VAL    38      29.953  11.922  12.376  1.00  0.00              
ATOM     84  O   VAL    38      30.195  11.773  11.177  1.00  0.00              
ATOM     85  N   GLN    39      30.816  11.624  13.339  1.00  0.00              
ATOM     86  CA  GLN    39      32.182  11.200  13.065  1.00  0.00              
ATOM     87  C   GLN    39      32.234   9.928  12.225  1.00  0.00              
ATOM     88  O   GLN    39      33.179   9.727  11.469  1.00  0.00              
ATOM     89  N   THR    40      31.228   9.074  12.354  1.00  0.00              
ATOM     90  CA  THR    40      31.203   7.818  11.606  1.00  0.00              
ATOM     91  C   THR    40      31.101   8.093  10.113  1.00  0.00              
ATOM     92  O   THR    40      31.997   7.755   9.344  1.00  0.00              
ATOM     93  N   ALA    41      30.009   8.732   9.714  1.00  0.00              
ATOM     94  CA  ALA    41      29.775   9.044   8.311  1.00  0.00              
ATOM     95  C   ALA    41      30.822  10.027   7.799  1.00  0.00              
ATOM     96  O   ALA    41      31.314   9.900   6.673  1.00  0.00              
ATOM     97  N   ILE    42      31.181  10.987   8.642  1.00  0.00              
ATOM     98  CA  ILE    42      32.188  11.979   8.293  1.00  0.00              
ATOM     99  C   ILE    42      33.538  11.306   8.065  1.00  0.00              
ATOM    100  O   ILE    42      34.265  11.662   7.144  1.00  0.00              
ATOM    101  N   THR    43      33.860  10.337   8.920  1.00  0.00              
ATOM    102  CA  THR    43      35.109   9.608   8.809  1.00  0.00              
ATOM    103  C   THR    43      35.151   8.662   7.618  1.00  0.00              
ATOM    104  O   THR    43      36.206   8.474   7.010  1.00  0.00              
ATOM    105  N   GLN    44      34.014   8.055   7.285  1.00  0.00              
ATOM    106  CA  GLN    44      33.946   7.124   6.156  1.00  0.00              
ATOM    107  C   GLN    44      34.212   7.835   4.834  1.00  0.00              
ATOM    108  O   GLN    44      34.923   7.322   3.972  1.00  0.00              
ATOM    109  N   SER    45      33.641   9.020   4.676  1.00  0.00              
ATOM    110  CA  SER    45      33.907   9.844   3.501  1.00  0.00              
ATOM    111  C   SER    45      35.156  10.684   3.734  1.00  0.00              
ATOM    112  O   SER    45      35.673  11.323   2.817  1.00  0.00              
ATOM    113  N   GLU    53      35.630  10.637   4.977  1.00  0.00              
ATOM    114  CA  GLU    53      36.731  11.462   5.470  1.00  0.00              
ATOM    115  C   GLU    53      36.648  12.886   4.938  1.00  0.00              
ATOM    116  O   GLU    53      37.434  13.300   4.082  1.00  0.00              
ATOM    117  N   ILE    54      35.663  13.622   5.421  1.00  0.00              
ATOM    118  CA  ILE    54      35.539  15.026   5.086  1.00  0.00              
ATOM    119  C   ILE    54      36.257  15.845   6.145  1.00  0.00              
ATOM    120  O   ILE    54      35.841  15.874   7.304  1.00  0.00              
ATOM    121  N   ASP    55      37.361  16.501   5.765  1.00  0.00              
ATOM    122  CA  ASP    55      38.219  17.212   6.707  1.00  0.00              
ATOM    123  C   ASP    55      37.488  18.326   7.445  1.00  0.00              
ATOM    124  O   ASP    55      37.248  19.403   6.893  1.00  0.00              
ATOM    125  N   LEU    56      37.147  18.056   8.702  1.00  0.00              
ATOM    126  CA  LEU    56      36.530  19.051   9.578  1.00  0.00              
ATOM    127  C   LEU    56      37.525  20.186   9.842  1.00  0.00              
ATOM    128  O   LEU    56      37.179  21.244  10.363  1.00  0.00              
END
