
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0363AL257_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL257_1-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      Q      12          1.305
LGA    I      13      I      13          1.923
LGA    N      14      N      14          0.722
LGA    I      15      I      15          0.724
LGA    E      16      E      16          2.208
LGA    I      17      I      17          2.314
LGA    A      18      A      18          2.669
LGA    Y      19      Y      19          2.648
LGA    A      20      A      20          1.733
LGA    F      21      F      21          3.790
LGA    P      22      P      22          3.156
LGA    E      23      E      23           -
LGA    R      24      R      24          3.616
LGA    Y      25      Y      25          5.021
LGA    Y      26      Y      26           #
LGA    L      27      L      27           #
LGA    K      28      K      28          1.455
LGA    S      29      S      29          0.699
LGA    F      30      F      30          1.305
LGA    Q      31      Q      31          1.421
LGA    V      32      V      32          1.508
LGA    D      33      D      33          1.486
LGA    E      34      E      34          2.143
LGA    G      35      G      35          0.613
LGA    I      36      I      36          0.471
LGA    T      37      T      37          0.304
LGA    V      38      V      38          0.339
LGA    Q      39      Q      39          0.446
LGA    T      40      T      40          0.742
LGA    A      41      A      41          1.251
LGA    I      42      I      42          1.132
LGA    T      43      T      43          0.597
LGA    Q      44      Q      44          2.140
LGA    I      47      S      45          2.774
LGA    L      48      G      46          2.474
LGA    S      49      -       -           -
LGA    Q      50      I      47          5.587
LGA    F      51      L      48           #
LGA    P      52      S      49          2.233
LGA    E      53      Q      50          1.931
LGA    I      54      F      51          2.628
LGA    D      55      P      52          4.063
LGA    L      56      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     37    2.32    81.08     59.556     1.532

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.487473 * X  +  -0.852347 * Y  +  -0.189406 * Z  +  50.819447
  Y_new =   0.805535 * X  +   0.355327 * Y  +   0.474190 * Z  + -25.253624
  Z_new =  -0.336874 * X  +  -0.383728 * Y  +   0.859807 * Z  +  33.771400 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.419769    2.721823  [ DEG:   -24.0510    155.9490 ]
  Theta =   0.343594    2.797998  [ DEG:    19.6865    160.3135 ]
  Phi   =   1.026595   -2.114998  [ DEG:    58.8196   -121.1804 ]
 
# 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: T0363AL257_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL257_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   46   5.0   37   2.32   81.08  59.556
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL257_1-D1
REMARK Aligment from pdb entry: 1vjk_A
ATOM      1  N   GLN    12      17.808   1.449   9.151  1.00  0.00              
ATOM      2  CA  GLN    12      18.522   2.565   8.435  1.00  0.00              
ATOM      3  C   GLN    12      18.037   3.960   8.864  1.00  0.00              
ATOM      4  O   GLN    12      16.867   4.151   9.238  1.00  0.00              
ATOM      5  N   ILE    13      18.956   4.926   8.818  1.00  0.00              
ATOM      6  CA  ILE    13      18.668   6.333   9.106  1.00  0.00              
ATOM      7  C   ILE    13      19.015   7.109   7.823  1.00  0.00              
ATOM      8  O   ILE    13      20.168   7.068   7.383  1.00  0.00              
ATOM      9  N   ASN    14      18.037   7.782   7.218  1.00  0.00              
ATOM     10  CA  ASN    14      18.290   8.532   5.996  1.00  0.00              
ATOM     11  C   ASN    14      18.325  10.009   6.308  1.00  0.00              
ATOM     12  O   ASN    14      17.326  10.570   6.814  1.00  0.00              
ATOM     13  N   ILE    15      19.456  10.644   6.035  1.00  0.00              
ATOM     14  CA  ILE    15      19.614  12.070   6.301  1.00  0.00              
ATOM     15  C   ILE    15      19.746  12.821   4.992  1.00  0.00              
ATOM     16  O   ILE    15      20.218  12.270   3.970  1.00  0.00              
ATOM     17  N   GLU    16      19.334  14.072   4.988  1.00  0.00              
ATOM     18  CA  GLU    16      19.451  14.936   3.841  1.00  0.00              
ATOM     19  C   GLU    16      20.644  15.821   4.077  1.00  0.00              
ATOM     20  O   GLU    16      20.644  16.622   5.023  1.00  0.00              
ATOM     21  N   ILE    17      21.658  15.706   3.241  1.00  0.00              
ATOM     22  CA  ILE    17      22.856  16.524   3.342  1.00  0.00              
ATOM     23  C   ILE    17      22.776  17.681   2.377  1.00  0.00              
ATOM     24  O   ILE    17      22.524  17.459   1.192  1.00  0.00              
ATOM     25  N   ALA    18      22.957  18.909   2.881  1.00  0.00              
ATOM     26  CA  ALA    18      22.944  20.106   2.035  1.00  0.00              
ATOM     27  C   ALA    18      24.340  20.685   2.037  1.00  0.00              
ATOM     28  O   ALA    18      24.881  21.038   3.101  1.00  0.00              
ATOM     29  N   TYR    19      24.933  20.782   0.858  1.00  0.00              
ATOM     30  CA  TYR    19      26.260  21.380   0.700  1.00  0.00              
ATOM     31  C   TYR    19      26.140  22.833   0.342  1.00  0.00              
ATOM     32  O   TYR    19      25.217  23.237  -0.388  1.00  0.00              
ATOM     33  N   ALA    20      27.108  23.618   0.828  1.00  0.00              
ATOM     34  CA  ALA    20      27.121  25.047   0.589  1.00  0.00              
ATOM     35  C   ALA    20      28.408  25.517  -0.030  1.00  0.00              
ATOM     36  O   ALA    20      29.474  24.957   0.217  1.00  0.00              
ATOM     37  N   PHE    21      28.305  26.592  -0.811  1.00  0.00              
ATOM     38  CA  PHE    21      29.469  27.287  -1.353  1.00  0.00              
ATOM     39  C   PHE    21      30.389  26.300  -2.089  1.00  0.00              
ATOM     40  O   PHE    21      29.897  25.517  -2.912  1.00  0.00              
ATOM     41  N   PRO    22      31.700  26.317  -1.819  1.00  0.00              
ATOM     42  CA  PRO    22      32.588  25.499  -2.669  1.00  0.00              
ATOM     43  C   PRO    22      32.360  24.015  -2.490  1.00  0.00              
ATOM     44  O   PRO    22      32.731  23.224  -3.354  1.00  0.00              
ATOM     45  N   GLU    23      31.718  23.623  -1.392  1.00  0.00              
ATOM     46  CA  GLU    23      31.469  22.192  -1.140  1.00  0.00              
ATOM     47  C   GLU    23      30.421  21.620  -2.067  1.00  0.00              
ATOM     48  O   GLU    23      30.365  20.402  -2.239  1.00  0.00              
ATOM     49  N   ARG    24      29.636  22.487  -2.701  1.00  0.00              
ATOM     50  CA  ARG    24      28.744  22.048  -3.779  1.00  0.00              
ATOM     51  C   ARG    24      29.553  21.527  -4.954  1.00  0.00              
ATOM     52  O   ARG    24      29.118  20.574  -5.619  1.00  0.00              
ATOM     53  N   TYR    25      30.700  22.152  -5.257  1.00  0.00              
ATOM     54  CA  TYR    25      31.550  21.639  -6.311  1.00  0.00              
ATOM     55  C   TYR    25      32.279  20.405  -5.919  1.00  0.00              
ATOM     56  O   TYR    25      32.431  19.518  -6.745  1.00  0.00              
ATOM     57  N   TYR    26      32.747  20.325  -4.670  1.00  0.00              
ATOM     58  CA  TYR    26      33.434  19.106  -4.238  1.00  0.00              
ATOM     59  C   TYR    26      32.506  17.897  -4.229  1.00  0.00              
ATOM     60  O   TYR    26      32.923  16.792  -4.575  1.00  0.00              
ATOM     61  N   LEU    27      31.257  18.090  -3.790  1.00  0.00              
ATOM     62  CA  LEU    27      30.300  16.991  -3.770  1.00  0.00              
ATOM     63  C   LEU    27      29.724  16.697  -5.149  1.00  0.00              
ATOM     64  O   LEU    27      29.219  15.592  -5.393  1.00  0.00              
ATOM     65  N   LYS    28      22.148  15.786  -1.118  1.00  0.00              
ATOM     66  CA  LYS    28      22.081  14.356  -1.335  1.00  0.00              
ATOM     67  C   LYS    28      21.537  13.662  -0.118  1.00  0.00              
ATOM     68  O   LYS    28      21.782  14.100   1.013  1.00  0.00              
ATOM     69  N   SER    29      20.782  12.605  -0.338  1.00  0.00              
ATOM     70  CA  SER    29      20.289  11.764   0.723  1.00  0.00              
ATOM     71  C   SER    29      21.287  10.687   1.017  1.00  0.00              
ATOM     72  O   SER    29      21.732   9.971   0.093  1.00  0.00              
ATOM     73  N   PHE    30      21.623  10.506   2.283  1.00  0.00              
ATOM     74  CA  PHE    30      22.577   9.498   2.674  1.00  0.00              
ATOM     75  C   PHE    30      21.950   8.552   3.685  1.00  0.00              
ATOM     76  O   PHE    30      21.547   8.959   4.793  1.00  0.00              
ATOM     77  N   GLN    31      21.835   7.293   3.298  1.00  0.00              
ATOM     78  CA  GLN    31      21.336   6.240   4.174  1.00  0.00              
ATOM     79  C   GLN    31      22.494   5.711   5.018  1.00  0.00              
ATOM     80  O   GLN    31      23.554   5.364   4.492  1.00  0.00              
ATOM     81  N   VAL    32      22.281   5.674   6.332  1.00  0.00              
ATOM     82  CA  VAL    32      23.292   5.281   7.289  1.00  0.00              
ATOM     83  C   VAL    32      22.752   4.152   8.146  1.00  0.00              
ATOM     84  O   VAL    32      21.547   4.049   8.322  1.00  0.00              
ATOM     85  N   ASP    33      23.622   3.288   8.680  1.00  0.00              
ATOM     86  CA  ASP    33      23.164   2.215   9.559  1.00  0.00              
ATOM     87  C   ASP    33      22.599   2.744  10.867  1.00  0.00              
ATOM     88  O   ASP    33      22.944   3.841  11.321  1.00  0.00              
ATOM     89  N   GLU    34      21.725   1.944  11.462  1.00  0.00              
ATOM     90  CA  GLU    34      21.210   2.188  12.791  1.00  0.00              
ATOM     91  C   GLU    34      22.337   2.616  13.739  1.00  0.00              
ATOM     92  O   GLU    34      23.412   2.025  13.738  1.00  0.00              
ATOM     93  N   GLY    35      22.071   3.660  14.522  1.00  0.00              
ATOM     94  CA  GLY    35      23.017   4.137  15.522  1.00  0.00              
ATOM     95  C   GLY    35      24.027   5.134  14.982  1.00  0.00              
ATOM     96  O   GLY    35      24.922   5.591  15.714  1.00  0.00              
ATOM     97  N   ILE    36      23.904   5.485  13.710  1.00  0.00              
ATOM     98  CA  ILE    36      24.869   6.391  13.113  1.00  0.00              
ATOM     99  C   ILE    36      24.959   7.695  13.845  1.00  0.00              
ATOM    100  O   ILE    36      23.947   8.266  14.285  1.00  0.00              
ATOM    101  N   THR    37      26.196   8.180  13.932  1.00  0.00              
ATOM    102  CA  THR    37      26.515   9.446  14.563  1.00  0.00              
ATOM    103  C   THR    37      27.027  10.446  13.529  1.00  0.00              
ATOM    104  O   THR    37      27.407  10.079  12.405  1.00  0.00              
ATOM    105  N   VAL    38      27.096  11.719  13.900  1.00  0.00              
ATOM    106  CA  VAL    38      27.667  12.737  13.019  1.00  0.00              
ATOM    107  C   VAL    38      29.039  12.313  12.457  1.00  0.00              
ATOM    108  O   VAL    38      29.301  12.448  11.241  1.00  0.00              
ATOM    109  N   GLN    39      29.914  11.762  13.310  1.00  0.00              
ATOM    110  CA  GLN    39      31.228  11.354  12.807  1.00  0.00              
ATOM    111  C   GLN    39      31.131  10.281  11.693  1.00  0.00              
ATOM    112  O   GLN    39      31.967  10.255  10.775  1.00  0.00              
ATOM    113  N   THR    40      30.123   9.405  11.779  1.00  0.00              
ATOM    114  CA  THR    40      29.948   8.356  10.749  1.00  0.00              
ATOM    115  C   THR    40      29.497   8.979   9.463  1.00  0.00              
ATOM    116  O   THR    40      29.936   8.557   8.386  1.00  0.00              
ATOM    117  N   ALA    41      28.644   9.986   9.553  1.00  0.00              
ATOM    118  CA  ALA    41      28.216  10.703   8.351  1.00  0.00              
ATOM    119  C   ALA    41      29.391  11.418   7.675  1.00  0.00              
ATOM    120  O   ALA    41      29.530  11.344   6.440  1.00  0.00              
ATOM    121  N   ILE    42      30.257  12.054   8.464  1.00  0.00              
ATOM    122  CA  ILE    42      31.433  12.706   7.903  1.00  0.00              
ATOM    123  C   ILE    42      32.298  11.686   7.169  1.00  0.00              
ATOM    124  O   ILE    42      32.775  11.948   6.035  1.00  0.00              
ATOM    125  N   THR    43      32.513  10.504   7.774  1.00  0.00              
ATOM    126  CA  THR    43      33.280   9.474   7.062  1.00  0.00              
ATOM    127  C   THR    43      32.636   9.018   5.774  1.00  0.00              
ATOM    128  O   THR    43      33.353   8.739   4.788  1.00  0.00              
ATOM    129  N   GLN    44      31.314   8.941   5.751  1.00  0.00              
ATOM    130  CA  GLN    44      30.622   8.538   4.541  1.00  0.00              
ATOM    131  C   GLN    44      30.717   9.618   3.463  1.00  0.00              
ATOM    132  O   GLN    44      30.865   9.276   2.284  1.00  0.00              
ATOM    133  N   ILE    47      30.655  10.910   3.838  1.00  0.00              
ATOM    134  CA  ILE    47      30.833  11.983   2.852  1.00  0.00              
ATOM    135  C   ILE    47      32.208  11.859   2.193  1.00  0.00              
ATOM    136  O   ILE    47      32.319  11.941   0.951  1.00  0.00              
ATOM    137  N   LEU    48      33.226  11.614   3.012  1.00  0.00              
ATOM    138  CA  LEU    48      34.593  11.438   2.509  1.00  0.00              
ATOM    139  C   LEU    48      34.731  10.205   1.603  1.00  0.00              
ATOM    140  O   LEU    48      35.503  10.235   0.617  1.00  0.00              
ATOM    141  N   SER    49      33.995   9.143   1.916  1.00  0.00              
ATOM    142  CA  SER    49      34.019   7.933   1.112  1.00  0.00              
ATOM    143  C   SER    49      33.353   8.160  -0.242  1.00  0.00              
ATOM    144  O   SER    49      33.819   7.637  -1.265  1.00  0.00              
ATOM    145  N   GLN    50      32.256   8.914  -0.271  1.00  0.00              
ATOM    146  CA  GLN    50      31.548   9.161  -1.515  1.00  0.00              
ATOM    147  C   GLN    50      32.260  10.177  -2.395  1.00  0.00              
ATOM    148  O   GLN    50      32.153  10.148  -3.620  1.00  0.00              
ATOM    149  N   PHE    51      32.917  11.128  -1.748  1.00  0.00              
ATOM    150  CA  PHE    51      33.484  12.281  -2.437  1.00  0.00              
ATOM    151  C   PHE    51      34.890  12.498  -1.942  1.00  0.00              
ATOM    152  O   PHE    51      35.118  13.251  -0.963  1.00  0.00              
ATOM    153  N   PRO    52      35.843  11.868  -2.628  1.00  0.00              
ATOM    154  CA  PRO    52      37.219  11.802  -2.130  1.00  0.00              
ATOM    155  C   PRO    52      37.875  13.161  -1.928  1.00  0.00              
ATOM    156  O   PRO    52      38.802  13.267  -1.131  1.00  0.00              
ATOM    157  N   GLU    53      37.392  14.192  -2.617  1.00  0.00              
ATOM    158  CA  GLU    53      37.983  15.538  -2.436  1.00  0.00              
ATOM    159  C   GLU    53      37.765  16.068  -1.019  1.00  0.00              
ATOM    160  O   GLU    53      38.484  16.977  -0.579  1.00  0.00              
ATOM    161  N   ILE    54      36.808  15.495  -0.272  1.00  0.00              
ATOM    162  CA  ILE    54      36.609  15.896   1.121  1.00  0.00              
ATOM    163  C   ILE    54      37.614  15.279   2.092  1.00  0.00              
ATOM    164  O   ILE    54      37.689  15.694   3.256  1.00  0.00              
ATOM    165  N   ASP    55      38.370  14.279   1.649  1.00  0.00              
ATOM    166  CA  ASP    55      39.318  13.622   2.560  1.00  0.00              
ATOM    167  C   ASP    55      40.348  14.617   3.093  1.00  0.00              
ATOM    168  O   ASP    55      40.776  14.501   4.250  1.00  0.00              
ATOM    169  N   LEU    56      38.578  27.669  12.397  1.00  0.00              
ATOM    170  CA  LEU    56      39.880  27.243  11.859  1.00  0.00              
ATOM    171  C   LEU    56      39.783  26.018  10.940  1.00  0.00              
ATOM    172  O   LEU    56      40.723  25.708  10.204  1.00  0.00              
END
