
#######################################################
#                                                     #
#                        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 T0363AL243_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL243_4-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          2.266
LGA    I      13      I      13          1.681
LGA    N      14      N      14          0.926
LGA    I      15      I      15          1.280
LGA    E      16      E      16          2.909
LGA    I      17      I      17          3.310
LGA    A      18      A      18          3.361
LGA    Y      19      Y      19          2.411
LGA    A      20      A      20          2.770
LGA    F      21      F      21          4.929
LGA    P      22      P      22           -
LGA    -       -      E      23           -
LGA    E      23      R      24          4.263
LGA    R      24      Y      25          2.870
LGA    Y      25      -       -           -
LGA    Y      26      Y      26           #
LGA    L      27      L      27          3.446
LGA    K      28      K      28          2.523
LGA    S      29      S      29          1.452
LGA    F      30      F      30          2.408
LGA    Q      31      Q      31          2.382
LGA    V      32      V      32          2.122
LGA    D      33      D      33          3.663
LGA    E      34      E      34          4.023
LGA    G      35      G      35          2.363
LGA    I      36      I      36          1.555
LGA    T      37      T      37          1.341
LGA    V      38      V      38          1.276
LGA    Q      39      Q      39          1.174
LGA    T      40      T      40          0.933
LGA    A      41      A      41          0.917
LGA    I      42      I      42          0.676
LGA    T      43      T      43          1.300
LGA    Q      44      Q      44          1.727
LGA    I      47      S      45          1.762
LGA    L      48      G      46          2.667
LGA    S      49      -       -           -
LGA    Q      50      -       -           -
LGA    F      51      -       -           -
LGA    P      52      I      47          4.490
LGA    E      53      L      48           -
LGA    I      54      S      49          4.440
LGA    D      55      Q      50          2.583
LGA    L      56      F      51          3.851
LGA    -       -      P      52           -
LGA    -       -      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     36    2.70    77.78     54.766     1.285

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.079774 * X  +  -0.995106 * Y  +   0.058318 * Z  +  28.762348
  Y_new =   0.894703 * X  +   0.045686 * Y  +  -0.444319 * Z  +  16.236050
  Z_new =   0.439480 * X  +   0.087623 * Y  +   0.893968 * Z  +   7.079986 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.097703   -3.043889  [ DEG:     5.5980   -174.4020 ]
  Theta =  -0.455020   -2.686573  [ DEG:   -26.0707   -153.9293 ]
  Phi   =   1.481868   -1.659724  [ DEG:    84.9048    -95.0952 ]
 
# 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: T0363AL243_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL243_4-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   36   2.70   77.78  54.766
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL243_4-D1
REMARK Aligment from pdb entry: 2ax5A
ATOM      1  N   GLN    12      18.565   2.292   5.020  1.00  0.00              
ATOM      2  CA  GLN    12      17.576   2.255   6.133  1.00  0.00              
ATOM      3  C   GLN    12      17.257   3.659   6.659  1.00  0.00              
ATOM      4  O   GLN    12      16.106   3.955   6.981  1.00  0.00              
ATOM      5  N   ILE    13      18.279   4.514   6.743  1.00  0.00              
ATOM      6  CA  ILE    13      18.100   5.885   7.234  1.00  0.00              
ATOM      7  C   ILE    13      18.343   6.920   6.133  1.00  0.00              
ATOM      8  O   ILE    13      18.863   6.593   5.063  1.00  0.00              
ATOM      9  N   ASN    14      17.964   8.172   6.408  1.00  0.00              
ATOM     10  CA  ASN    14      18.139   9.263   5.449  1.00  0.00              
ATOM     11  C   ASN    14      18.309  10.604   6.165  1.00  0.00              
ATOM     12  O   ASN    14      17.542  10.934   7.072  1.00  0.00              
ATOM     13  N   ILE    15      19.315  11.372   5.748  1.00  0.00              
ATOM     14  CA  ILE    15      19.587  12.680   6.344  1.00  0.00              
ATOM     15  C   ILE    15      19.793  13.743   5.265  1.00  0.00              
ATOM     16  O   ILE    15      20.698  13.628   4.434  1.00  0.00              
ATOM     17  N   GLU    16      18.952  14.777   5.282  1.00  0.00              
ATOM     18  CA  GLU    16      19.045  15.861   4.305  1.00  0.00              
ATOM     19  C   GLU    16      20.036  16.928   4.773  1.00  0.00              
ATOM     20  O   GLU    16      19.717  17.750   5.634  1.00  0.00              
ATOM     21  N   ILE    17      21.240  16.905   4.198  1.00  0.00              
ATOM     22  CA  ILE    17      22.282  17.867   4.555  1.00  0.00              
ATOM     23  C   ILE    17      22.356  18.996   3.534  1.00  0.00              
ATOM     24  O   ILE    17      22.203  18.769   2.333  1.00  0.00              
ATOM     25  N   ALA    18      22.600  20.212   4.018  1.00  0.00              
ATOM     26  CA  ALA    18      22.701  21.375   3.147  1.00  0.00              
ATOM     27  C   ALA    18      24.091  22.001   3.233  1.00  0.00              
ATOM     28  O   ALA    18      24.405  22.706   4.194  1.00  0.00              
ATOM     29  N   TYR    19      24.918  21.738   2.223  1.00  0.00              
ATOM     30  CA  TYR    19      26.278  22.273   2.180  1.00  0.00              
ATOM     31  C   TYR    19      26.304  23.648   1.517  1.00  0.00              
ATOM     32  O   TYR    19      25.722  23.846   0.449  1.00  0.00              
ATOM     33  N   ALA    20      26.977  24.595   2.171  1.00  0.00              
ATOM     34  CA  ALA    20      27.080  25.962   1.667  1.00  0.00              
ATOM     35  C   ALA    20      28.488  26.524   1.872  1.00  0.00              
ATOM     36  O   ALA    20      29.347  25.877   2.476  1.00  0.00              
ATOM     37  N   PHE    21      32.529  21.269  -4.052  1.00  0.00              
ATOM     38  CA  PHE    21      33.259  20.017  -4.219  1.00  0.00              
ATOM     39  C   PHE    21      32.305  18.860  -4.519  1.00  0.00              
ATOM     40  O   PHE    21      32.599  18.002  -5.350  1.00  0.00              
ATOM     41  N   PRO    22      31.164  18.845  -3.830  1.00  0.00              
ATOM     42  CA  PRO    22      30.164  17.793  -4.015  1.00  0.00              
ATOM     43  C   PRO    22      29.587  17.811  -5.432  1.00  0.00              
ATOM     44  O   PRO    22      29.197  16.769  -5.961  1.00  0.00              
ATOM     45  N   GLU    23      29.526  18.999  -6.033  1.00  0.00              
ATOM     46  CA  GLU    23      28.988  19.136  -7.378  1.00  0.00              
ATOM     47  C   GLU    23      27.879  20.170  -7.449  1.00  0.00              
ATOM     48  O   GLU    23      26.824  19.918  -8.034  1.00  0.00              
ATOM     49  N   ARG    24      28.116  21.334  -6.843  1.00  0.00              
ATOM     50  CA  ARG    24      27.135  22.420  -6.823  1.00  0.00              
ATOM     51  C   ARG    24      25.807  21.954  -6.217  1.00  0.00              
ATOM     52  O   ARG    24      24.735  22.397  -6.632  1.00  0.00              
ATOM     53  N   TYR    25      25.886  21.060  -5.228  1.00  0.00              
ATOM     54  CA  TYR    25      24.693  20.541  -4.567  1.00  0.00              
ATOM     55  C   TYR    25      24.483  21.224  -3.217  1.00  0.00              
ATOM     56  O   TYR    25      25.093  20.842  -2.217  1.00  0.00              
ATOM     57  N   TYR    26      23.614  22.236  -3.197  1.00  0.00              
ATOM     58  CA  TYR    26      23.318  22.972  -1.967  1.00  0.00              
ATOM     59  C   TYR    26      22.737  22.042  -0.900  1.00  0.00              
ATOM     60  O   TYR    26      22.944  22.256   0.293  1.00  0.00              
ATOM     61  N   LEU    27      22.012  21.007  -1.340  1.00  0.00              
ATOM     62  CA  LEU    27      21.408  20.043  -0.423  1.00  0.00              
ATOM     63  C   LEU    27      21.526  18.620  -0.972  1.00  0.00              
ATOM     64  O   LEU    27      21.162  18.355  -2.120  1.00  0.00              
ATOM     65  N   LYS    28      22.045  17.709  -0.147  1.00  0.00              
ATOM     66  CA  LYS    28      22.219  16.317  -0.550  1.00  0.00              
ATOM     67  C   LYS    28      21.833  15.363   0.582  1.00  0.00              
ATOM     68  O   LYS    28      22.152  15.609   1.747  1.00  0.00              
ATOM     69  N   SER    29      21.142  14.276   0.231  1.00  0.00              
ATOM     70  CA  SER    29      20.708  13.285   1.216  1.00  0.00              
ATOM     71  C   SER    29      21.722  12.146   1.340  1.00  0.00              
ATOM     72  O   SER    29      22.310  11.715   0.346  1.00  0.00              
ATOM     73  N   PHE    30      21.917  11.664   2.570  1.00  0.00              
ATOM     74  CA  PHE    30      22.859  10.575   2.840  1.00  0.00              
ATOM     75  C   PHE    30      22.157   9.378   3.487  1.00  0.00              
ATOM     76  O   PHE    30      21.188   9.545   4.232  1.00  0.00              
ATOM     77  N   GLN    31      22.656   8.171   3.197  1.00  0.00              
ATOM     78  CA  GLN    31      22.084   6.940   3.749  1.00  0.00              
ATOM     79  C   GLN    31      23.181   6.021   4.300  1.00  0.00              
ATOM     80  O   GLN    31      24.137   5.690   3.595  1.00  0.00              
ATOM     81  N   VAL    32      23.034   5.613   5.565  1.00  0.00              
ATOM     82  CA  VAL    32      24.010   4.736   6.214  1.00  0.00              
ATOM     83  C   VAL    32      23.348   3.455   6.730  1.00  0.00              
ATOM     84  O   VAL    32      22.219   3.484   7.225  1.00  0.00              
ATOM     85  N   ASP    33      24.062   2.334   6.612  1.00  0.00              
ATOM     86  CA  ASP    33      23.550   1.042   7.068  1.00  0.00              
ATOM     87  C   ASP    33      24.642   0.240   7.776  1.00  0.00              
ATOM     88  O   ASP    33      25.508  -0.352   7.125  1.00  0.00              
ATOM     89  N   GLU    34      22.415   0.311  14.993  1.00  0.00              
ATOM     90  CA  GLU    34      21.327   1.165  15.468  1.00  0.00              
ATOM     91  C   GLU    34      21.859   2.486  16.028  1.00  0.00              
ATOM     92  O   GLU    34      21.480   3.556  15.551  1.00  0.00              
ATOM     93  N   GLY    35      22.743   2.441  17.048  1.00  0.00              
ATOM     94  CA  GLY    35      23.308   3.653  17.654  1.00  0.00              
ATOM     95  C   GLY    35      24.336   4.343  16.750  1.00  0.00              
ATOM     96  O   GLY    35      25.507   4.477  17.111  1.00  0.00              
ATOM     97  N   ILE    36      23.886   4.784  15.576  1.00  0.00              
ATOM     98  CA  ILE    36      24.760   5.465  14.624  1.00  0.00              
ATOM     99  C   ILE    36      25.000   6.911  15.049  1.00  0.00              
ATOM    100  O   ILE    36      24.067   7.712  15.104  1.00  0.00              
ATOM    101  N   THR    37      26.257   7.242  15.347  1.00  0.00              
ATOM    102  CA  THR    37      26.612   8.599  15.765  1.00  0.00              
ATOM    103  C   THR    37      26.849   9.497  14.556  1.00  0.00              
ATOM    104  O   THR    37      27.093   9.016  13.450  1.00  0.00              
ATOM    105  N   VAL    38      26.772  10.807  14.776  1.00  0.00              
ATOM    106  CA  VAL    38      26.977  11.783  13.705  1.00  0.00              
ATOM    107  C   VAL    38      28.352  11.628  13.057  1.00  0.00              
ATOM    108  O   VAL    38      28.501  11.827  11.848  1.00  0.00              
ATOM    109  N   GLN    39      29.348  11.250  13.862  1.00  0.00              
ATOM    110  CA  GLN    39      30.687  11.049  13.341  1.00  0.00              
ATOM    111  C   GLN    39      30.718  10.000  12.243  1.00  0.00              
ATOM    112  O   GLN    39      31.561  10.058  11.347  1.00  0.00              
ATOM    113  N   THR    40      29.779   9.053  12.304  1.00  0.00              
ATOM    114  CA  THR    40      29.687   7.998  11.298  1.00  0.00              
ATOM    115  C   THR    40      29.206   8.574   9.970  1.00  0.00              
ATOM    116  O   THR    40      29.735   8.239   8.910  1.00  0.00              
ATOM    117  N   ALA    41      28.206   9.456  10.043  1.00  0.00              
ATOM    118  CA  ALA    41      27.656  10.101   8.854  1.00  0.00              
ATOM    119  C   ALA    41      28.772  10.749   8.041  1.00  0.00              
ATOM    120  O   ALA    41      28.905  10.495   6.843  1.00  0.00              
ATOM    121  N   ILE    42      29.582  11.576   8.706  1.00  0.00              
ATOM    122  CA  ILE    42      30.699  12.245   8.042  1.00  0.00              
ATOM    123  C   ILE    42      31.643  11.212   7.425  1.00  0.00              
ATOM    124  O   ILE    42      32.145  11.400   6.317  1.00  0.00              
ATOM    125  N   THR    43      31.865  10.109   8.150  1.00  0.00              
ATOM    126  CA  THR    43      32.734   9.032   7.676  1.00  0.00              
ATOM    127  C   THR    43      32.224   8.470   6.354  1.00  0.00              
ATOM    128  O   THR    43      33.001   8.242   5.429  1.00  0.00              
ATOM    129  N   GLN    44      30.913   8.252   6.275  1.00  0.00              
ATOM    130  CA  GLN    44      30.292   7.718   5.064  1.00  0.00              
ATOM    131  C   GLN    44      30.568   8.625   3.864  1.00  0.00              
ATOM    132  O   GLN    44      30.795   8.146   2.753  1.00  0.00              
ATOM    133  N   ILE    47      30.550   9.937   4.102  1.00  0.00              
ATOM    134  CA  ILE    47      30.804  10.916   3.049  1.00  0.00              
ATOM    135  C   ILE    47      32.262  10.871   2.586  1.00  0.00              
ATOM    136  O   ILE    47      32.564  11.200   1.441  1.00  0.00              
ATOM    137  N   LEU    48      33.161  10.485   3.487  1.00  0.00              
ATOM    138  CA  LEU    48      34.587  10.425   3.172  1.00  0.00              
ATOM    139  C   LEU    48      35.044   9.017   2.760  1.00  0.00              
ATOM    140  O   LEU    48      36.193   8.834   2.355  1.00  0.00              
ATOM    141  N   SER    49      34.159   8.022   2.866  1.00  0.00              
ATOM    142  CA  SER    49      34.518   6.652   2.504  1.00  0.00              
ATOM    143  C   SER    49      34.021   6.288   1.103  1.00  0.00              
ATOM    144  O   SER    49      34.803   6.263   0.153  1.00  0.00              
ATOM    145  N   GLN    50      32.725   5.997   0.976  1.00  0.00              
ATOM    146  CA  GLN    50      32.149   5.627  -0.318  1.00  0.00              
ATOM    147  C   GLN    50      31.771   6.863  -1.135  1.00  0.00              
ATOM    148  O   GLN    50      32.037   6.922  -2.336  1.00  0.00              
ATOM    149  N   PHE    51      31.146   7.843  -0.481  1.00  0.00              
ATOM    150  CA  PHE    51      30.729   9.073  -1.153  1.00  0.00              
ATOM    151  C   PHE    51      31.917   9.764  -1.833  1.00  0.00              
ATOM    152  O   PHE    51      31.858  10.079  -3.023  1.00  0.00              
ATOM    153  N   PRO    52      32.994   9.993  -1.075  1.00  0.00              
ATOM    154  CA  PRO    52      34.189  10.641  -1.614  1.00  0.00              
ATOM    155  C   PRO    52      35.420   9.754  -1.441  1.00  0.00              
ATOM    156  O   PRO    52      35.575   9.091  -0.415  1.00  0.00              
ATOM    157  N   GLU    53      36.297   9.751  -2.446  1.00  0.00              
ATOM    158  CA  GLU    53      37.516   8.946  -2.395  1.00  0.00              
ATOM    159  C   GLU    53      38.588   9.508  -3.333  1.00  0.00              
ATOM    160  O   GLU    53      38.855   8.942  -4.395  1.00  0.00              
ATOM    161  N   ILE    54      39.201  10.626  -2.935  1.00  0.00              
ATOM    162  CA  ILE    54      40.241  11.259  -3.744  1.00  0.00              
ATOM    163  C   ILE    54      41.019  12.303  -2.939  1.00  0.00              
ATOM    164  O   ILE    54      40.432  13.071  -2.172  1.00  0.00              
ATOM    165  N   ASP    55      39.298  16.374  -2.670  1.00  0.00              
ATOM    166  CA  ASP    55      37.985  16.746  -2.139  1.00  0.00              
ATOM    167  C   ASP    55      37.877  16.390  -0.659  1.00  0.00              
ATOM    168  O   ASP    55      37.345  17.165   0.137  1.00  0.00              
ATOM    169  N   LEU    56      38.381  15.214  -0.293  1.00  0.00              
ATOM    170  CA  LEU    56      38.336  14.766   1.093  1.00  0.00              
ATOM    171  C   LEU    56      39.535  15.296   1.882  1.00  0.00              
ATOM    172  O   LEU    56      39.413  15.613   3.065  1.00  0.00              
END
