
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0363AL316_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL316_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          3.545
LGA    Q      12      Q      12          0.944
LGA    I      13      I      13          1.460
LGA    N      14      N      14          0.406
LGA    I      15      I      15          1.073
LGA    E      16      E      16          1.276
LGA    I      17      I      17          1.337
LGA    A      18      A      18          1.657
LGA    Y      19      Y      19          1.710
LGA    A      20      A      20          2.407
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    F      21      Y      25          2.211
LGA    P      22      Y      26          4.071
LGA    E      23      L      27          2.551
LGA    R      24      K      28          1.255
LGA    S      29      S      29          1.047
LGA    F      30      F      30          1.083
LGA    Q      31      Q      31          1.337
LGA    V      32      V      32          0.566
LGA    D      33      D      33          2.653
LGA    E      34      E      34          3.821
LGA    G      35      G      35          2.565
LGA    I      36      I      36          0.504
LGA    T      37      T      37          0.659
LGA    V      38      V      38          0.879
LGA    Q      39      Q      39          1.235
LGA    T      40      T      40          0.993
LGA    A      41      A      41          1.794
LGA    I      42      I      42          2.027
LGA    T      43      T      43          2.485
LGA    Q      44      Q      44          2.709
LGA    S      45      S      45          4.320
LGA    -       -      G      46           -
LGA    -       -      I      47           -
LGA    G      46      L      48          3.878
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    I      54      I      54          4.790
LGA    D      55      D      55          2.310
LGA    L      56      L      56          1.858

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   46    5.0     35    2.29    85.71     61.781     1.462

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.517073 * X  +  -0.207656 * Y  +  -0.830370 * Z  +  26.625801
  Y_new =  -0.522714 * X  +  -0.691606 * Y  +   0.498449 * Z  +  15.757357
  Z_new =  -0.677795 * X  +   0.691781 * Y  +   0.249066 * Z  +   8.694853 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.225209   -1.916384  [ DEG:    70.1993   -109.8007 ]
  Theta =   0.744759    2.396834  [ DEG:    42.6715    137.3285 ]
  Phi   =  -2.350769    0.790823  [ DEG:  -134.6892     45.3108 ]
 
# 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: T0363AL316_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL316_2-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   46   5.0   35   2.29   85.71  61.781
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL316_2-D1
REMARK Aligment from pdb entry: 1ryj_A
ATOM      5  N   ASN    11      12.374  -0.516  13.439  1.00  0.00              
ATOM      6  CA  ASN    11      13.103  -0.727  12.198  1.00  0.00              
ATOM      7  C   ASN    11      14.244   0.278  12.116  1.00  0.00              
ATOM      8  O   ASN    11      14.019   1.487  12.171  1.00  0.00              
ATOM      9  N   GLN    12      17.141   2.343  10.307  1.00  0.00              
ATOM     10  CA  GLN    12      17.382   2.880   8.985  1.00  0.00              
ATOM     11  C   GLN    12      17.130   4.372   8.953  1.00  0.00              
ATOM     12  O   GLN    12      15.980   4.813   8.990  1.00  0.00              
ATOM     13  N   ILE    13      18.200   5.146   8.901  1.00  0.00              
ATOM     14  CA  ILE    13      18.089   6.596   8.980  1.00  0.00              
ATOM     15  C   ILE    13      18.430   7.244   7.644  1.00  0.00              
ATOM     16  O   ILE    13      19.451   6.933   7.036  1.00  0.00              
ATOM     17  N   ASN    14      17.570   8.135   7.188  1.00  0.00              
ATOM     18  CA  ASN    14      17.840   8.901   5.986  1.00  0.00              
ATOM     19  C   ASN    14      17.978  10.374   6.332  1.00  0.00              
ATOM     20  O   ASN    14      17.105  10.958   6.975  1.00  0.00              
ATOM     21  N   ILE    15      19.083  10.963   5.917  1.00  0.00              
ATOM     22  CA  ILE    15      19.389  12.339   6.260  1.00  0.00              
ATOM     23  C   ILE    15      19.968  13.065   5.060  1.00  0.00              
ATOM     24  O   ILE    15      20.318  12.439   4.056  1.00  0.00              
ATOM     25  N   GLU    16      20.063  14.379   5.153  1.00  0.00              
ATOM     26  CA  GLU    16      20.623  15.157   4.071  1.00  0.00              
ATOM     27  C   GLU    16      21.766  16.029   4.565  1.00  0.00              
ATOM     28  O   GLU    16      21.664  16.690   5.601  1.00  0.00              
ATOM     29  N   ILE    17      22.866  15.987   3.838  1.00  0.00              
ATOM     30  CA  ILE    17      23.995  16.853   4.106  1.00  0.00              
ATOM     31  C   ILE    17      24.097  17.887   2.997  1.00  0.00              
ATOM     32  O   ILE    17      24.249  17.535   1.832  1.00  0.00              
ATOM     33  N   ALA    18      23.990  19.157   3.346  1.00  0.00              
ATOM     34  CA  ALA    18      24.031  20.210   2.345  1.00  0.00              
ATOM     35  C   ALA    18      25.419  20.844   2.314  1.00  0.00              
ATOM     36  O   ALA    18      25.986  21.191   3.350  1.00  0.00              
ATOM     37  N   TYR    19      25.981  20.929   1.118  1.00  0.00              
ATOM     38  CA  TYR    19      27.288  21.535   0.907  1.00  0.00              
ATOM     39  C   TYR    19      27.262  22.333  -0.402  1.00  0.00              
ATOM     40  O   TYR    19      26.184  22.645  -0.907  1.00  0.00              
ATOM     41  N   ALA    20      28.430  22.668  -0.950  1.00  0.00              
ATOM     42  CA  ALA    20      28.513  23.367  -2.237  1.00  0.00              
ATOM     43  C   ALA    20      27.888  22.526  -3.344  1.00  0.00              
ATOM     44  O   ALA    20      27.392  23.048  -4.341  1.00  0.00              
ATOM     45  N   PHE    21      27.919  21.212  -3.142  1.00  0.00              
ATOM     46  CA  PHE    21      27.338  20.254  -4.080  1.00  0.00              
ATOM     47  C   PHE    21      25.810  20.266  -3.982  1.00  0.00              
ATOM     48  O   PHE    21      25.110  19.688  -4.814  1.00  0.00              
ATOM     49  N   PRO    22      25.301  20.959  -2.973  1.00  0.00              
ATOM     50  CA  PRO    22      23.874  21.011  -2.742  1.00  0.00              
ATOM     51  C   PRO    22      23.459  20.063  -1.640  1.00  0.00              
ATOM     52  O   PRO    22      24.299  19.606  -0.862  1.00  0.00              
ATOM     53  N   GLU    23      22.170  19.775  -1.562  1.00  0.00              
ATOM     54  CA  GLU    23      21.666  18.806  -0.605  1.00  0.00              
ATOM     55  C   GLU    23      21.953  17.393  -1.083  1.00  0.00              
ATOM     56  O   GLU    23      21.492  16.975  -2.148  1.00  0.00              
ATOM     57  N   ARG    24      22.723  16.669  -0.294  1.00  0.00              
ATOM     58  CA  ARG    24      23.092  15.303  -0.615  1.00  0.00              
ATOM     59  C   ARG    24      22.248  14.348   0.220  1.00  0.00              
ATOM     60  O   ARG    24      22.247  14.424   1.448  1.00  0.00              
ATOM     61  N   SER    29      21.512  13.473  -0.448  1.00  0.00              
ATOM     62  CA  SER    29      20.631  12.539   0.237  1.00  0.00              
ATOM     63  C   SER    29      21.273  11.162   0.338  1.00  0.00              
ATOM     64  O   SER    29      21.629  10.551  -0.672  1.00  0.00              
ATOM     65  N   PHE    30      21.440  10.694   1.564  1.00  0.00              
ATOM     66  CA  PHE    30      21.976   9.366   1.808  1.00  0.00              
ATOM     67  C   PHE    30      21.304   8.747   3.026  1.00  0.00              
ATOM     68  O   PHE    30      21.010   9.440   4.006  1.00  0.00              
ATOM     69  N   GLN    31      21.033   7.454   2.957  1.00  0.00              
ATOM     70  CA  GLN    31      20.420   6.755   4.072  1.00  0.00              
ATOM     71  C   GLN    31      21.305   5.605   4.541  1.00  0.00              
ATOM     72  O   GLN    31      21.907   4.893   3.739  1.00  0.00              
ATOM     73  N   VAL    32      21.392   5.451   5.852  1.00  0.00              
ATOM     74  CA  VAL    32      22.243   4.446   6.463  1.00  0.00              
ATOM     75  C   VAL    32      21.388   3.492   7.292  1.00  0.00              
ATOM     76  O   VAL    32      20.556   3.930   8.090  1.00  0.00              
ATOM     77  N   ASP    33      21.588   2.195   7.092  1.00  0.00              
ATOM     78  CA  ASP    33      20.800   1.195   7.791  1.00  0.00              
ATOM     79  C   ASP    33      21.005   1.228   9.294  1.00  0.00              
ATOM     80  O   ASP    33      20.090   0.915  10.058  1.00  0.00              
ATOM     81  N   GLU    34      22.203   1.591   9.721  1.00  0.00              
ATOM     82  CA  GLU    34      22.507   1.686  11.139  1.00  0.00              
ATOM     83  C   GLU    34      22.611   3.145  11.569  1.00  0.00              
ATOM     84  O   GLU    34      23.377   3.914  10.990  1.00  0.00              
ATOM     85  N   GLY    35      21.816   3.550  12.571  1.00  0.00              
ATOM     86  CA  GLY    35      21.878   4.901  13.141  1.00  0.00              
ATOM     87  C   GLY    35      23.229   5.167  13.804  1.00  0.00              
ATOM     88  O   GLY    35      23.551   4.586  14.842  1.00  0.00              
ATOM     89  N   ILE    36      24.011   6.048  13.198  1.00  0.00              
ATOM     90  CA  ILE    36      25.392   6.263  13.608  1.00  0.00              
ATOM     91  C   ILE    36      25.626   7.692  14.079  1.00  0.00              
ATOM     92  O   ILE    36      24.727   8.535  14.039  1.00  0.00              
ATOM     93  N   THR    37      26.843   7.948  14.524  1.00  0.00              
ATOM     94  CA  THR    37      27.244   9.248  15.024  1.00  0.00              
ATOM     95  C   THR    37      27.789  10.102  13.879  1.00  0.00              
ATOM     96  O   THR    37      28.204   9.563  12.849  1.00  0.00              
ATOM     97  N   VAL    38      27.769  11.428  14.049  1.00  0.00              
ATOM     98  CA  VAL    38      28.309  12.350  13.047  1.00  0.00              
ATOM     99  C   VAL    38      29.717  11.926  12.641  1.00  0.00              
ATOM    100  O   VAL    38      30.028  11.826  11.454  1.00  0.00              
ATOM    101  N   GLN    39      30.542  11.640  13.641  1.00  0.00              
ATOM    102  CA  GLN    39      31.941  11.290  13.428  1.00  0.00              
ATOM    103  C   GLN    39      32.100  10.049  12.556  1.00  0.00              
ATOM    104  O   GLN    39      33.092   9.918  11.846  1.00  0.00              
ATOM    105  N   THR    40      31.132   9.144  12.606  1.00  0.00              
ATOM    106  CA  THR    40      31.209   7.913  11.822  1.00  0.00              
ATOM    107  C   THR    40      31.172   8.229  10.335  1.00  0.00              
ATOM    108  O   THR    40      32.123   7.959   9.605  1.00  0.00              
ATOM    109  N   ALA    41      30.072   8.826   9.896  1.00  0.00              
ATOM    110  CA  ALA    41      29.896   9.170   8.492  1.00  0.00              
ATOM    111  C   ALA    41      30.918  10.218   8.065  1.00  0.00              
ATOM    112  O   ALA    41      31.474  10.150   6.964  1.00  0.00              
ATOM    113  N   ILE    42      31.184  11.168   8.953  1.00  0.00              
ATOM    114  CA  ILE    42      32.157  12.217   8.688  1.00  0.00              
ATOM    115  C   ILE    42      33.549  11.619   8.513  1.00  0.00              
ATOM    116  O   ILE    42      34.304  12.037   7.643  1.00  0.00              
ATOM    117  N   THR    43      33.874  10.639   9.356  1.00  0.00              
ATOM    118  CA  THR    43      35.162   9.976   9.292  1.00  0.00              
ATOM    119  C   THR    43      35.314   9.070   8.078  1.00  0.00              
ATOM    120  O   THR    43      36.406   8.953   7.523  1.00  0.00              
ATOM    121  N   GLN    44      34.227   8.420   7.667  1.00  0.00              
ATOM    122  CA  GLN    44      34.265   7.522   6.511  1.00  0.00              
ATOM    123  C   GLN    44      34.564   8.287   5.225  1.00  0.00              
ATOM    124  O   GLN    44      35.344   7.836   4.389  1.00  0.00              
ATOM    125  N   SER    45      33.943   9.447   5.071  1.00  0.00              
ATOM    126  CA  SER    45      34.229  10.319   3.936  1.00  0.00              
ATOM    127  C   SER    45      35.421  11.211   4.260  1.00  0.00              
ATOM    128  O   SER    45      35.952  11.902   3.390  1.00  0.00              
ATOM    129  N   GLY    46      35.830  11.148   5.524  1.00  0.00              
ATOM    130  CA  GLY    46      36.861  12.009   6.099  1.00  0.00              
ATOM    131  C   GLY    46      36.735  13.444   5.605  1.00  0.00              
ATOM    132  O   GLY    46      37.544  13.922   4.804  1.00  0.00              
ATOM    133  N   ILE    54      35.691  14.116   6.055  1.00  0.00              
ATOM    134  CA  ILE    54      35.515  15.522   5.754  1.00  0.00              
ATOM    135  C   ILE    54      36.134  16.342   6.873  1.00  0.00              
ATOM    136  O   ILE    54      35.657  16.314   8.009  1.00  0.00              
ATOM    137  N   ASP    55      37.223  17.061   6.572  1.00  0.00              
ATOM    138  CA  ASP    55      37.993  17.784   7.579  1.00  0.00              
ATOM    139  C   ASP    55      37.170  18.837   8.308  1.00  0.00              
ATOM    140  O   ASP    55      36.906  19.919   7.775  1.00  0.00              
ATOM    141  N   LEU    56      36.778  18.512   9.537  1.00  0.00              
ATOM    142  CA  LEU    56      36.067  19.448  10.406  1.00  0.00              
ATOM    143  C   LEU    56      36.989  20.622  10.756  1.00  0.00              
ATOM    144  O   LEU    56      36.564  21.645  11.287  1.00  0.00              
END
