
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0307AL044_5
# Molecule2: number of CA atoms  132 ( 1005),  selected  132 , name T0307.pdb
# PARAMETERS: T0307AL044_5.T0307.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      18      M       1           -
LGA    T      19      G       2           -
LGA    -       -      L       3           -
LGA    -       -      G       4           -
LGA    -       -      R       5           -
LGA    -       -      Q       6           -
LGA    -       -      S       7           -
LGA    -       -      L       8           -
LGA    A      20      N       9           #
LGA    I      21      I      10          4.073
LGA    I      22      M      11          5.046
LGA    K      23      T      12          2.145
LGA    M      24      F      13          3.872
LGA    A      25      S      14          2.436
LGA    -       -      G      15           -
LGA    -       -      Q      16           -
LGA    -       -      E      17           -
LGA    K      26      L      18          1.394
LGA    S      27      T      19          1.966
LGA    G      33      A      20          1.369
LGA    K      34      I      21          0.689
LGA    K      36      I      22          1.328
LGA    P      37      K      23          1.470
LGA    A      38      M      24          0.793
LGA    E      39      A      25          1.689
LGA    I      40      K      26          1.962
LGA    A      41      S      27          1.343
LGA    M      48      M      28          1.365
LGA    R      49      V      29          1.968
LGA    F      50      M      30          1.137
LGA    G      51      A      31          1.254
LGA    -       -      D      32           -
LGA    -       -      G      33           -
LGA    I      52      K      34           #
LGA    Q      54      I      35          5.420
LGA    -       -      K      36           -
LGA    -       -      P      37           -
LGA    -       -      A      38           -
LGA    -       -      E      39           -
LGA    -       -      I      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      M      43           -
LGA    -       -      T      44           -
LGA    -       -      R      45           -
LGA    -       -      E      46           -
LGA    -       -      F      47           -
LGA    -       -      M      48           -
LGA    -       -      R      49           -
LGA    -       -      F      50           -
LGA    -       -      G      51           -
LGA    -       -      I      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    -       -      D      58           -
LGA    -       -      L      59           -
LGA    -       -      L      60           -
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      S      64           -
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      I      76           -
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    -       -      E      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      K      85           -
LGA    -       -      Y      86           -
LGA    -       -      V      87           -
LGA    -       -      A      88           -
LGA    -       -      S      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      G      92           -
LGA    -       -      V      93           -
LGA    D      55      I      94           #
LGA    Q      56      M      95          5.051
LGA    V      57      A      96          3.309
LGA    D      58      S      97           #
LGA    L      60      D      98          4.315
LGA    L      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      -       -           -
LGA    S      64      G      99           #
LGA    D      65      D     100           #
LGA    S      66      I     101           #
LGA    -       -      D     102           -
LGA    -       -      D     103           -
LGA    -       -      N     104           -
LGA    -       -      E     105           -
LGA    I      67      L     106          0.992
LGA    E      68      A     107          1.074
LGA    -       -      L     108           -
LGA    -       -      W     109           -
LGA    K      85      T     110           #
LGA    Y      86      L     111          4.554
LGA    V      87      I     112           -
LGA    A      88      S     113           -
LGA    S      89      T     114           -
LGA    D     103      L     115           -
LGA    N     104      C     116           -
LGA    -       -      G     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      T     120           -
LGA    -       -      M     121           -
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44  132    5.0     26    2.81     7.69     14.790     0.895

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.123832 * X  +   0.469756 * Y  +   0.874068 * Z  +  11.324538
  Y_new =   0.306806 * X  +  -0.819562 * Y  +   0.483929 * Z  +   4.721836
  Z_new =   0.943682 * X  +   0.328096 * Y  +  -0.042636 * Z  +  21.372414 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.700021   -1.441571  [ DEG:    97.4040    -82.5960 ]
  Theta =  -1.233588   -1.908005  [ DEG:   -70.6794   -109.3206 ]
  Phi   =   1.954417   -1.187176  [ DEG:   111.9799    -68.0201 ]
 
# 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: T0307AL044_5                                  
REMARK     2: T0307.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307AL044_5.T0307.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  132   5.0   26   2.81    7.69  14.790
REMARK  ---------------------------------------------------------- 
MOLECULE T0307AL044_5
REMARK Aligment from pdb entry: 1y41_A
ATOM      1  N   LEU    18      15.588  20.898  31.223  1.00  0.00              
ATOM      2  CA  LEU    18      14.995  22.192  31.502  1.00  0.00              
ATOM      3  C   LEU    18      13.522  22.064  31.831  1.00  0.00              
ATOM      4  O   LEU    18      12.963  22.883  32.560  1.00  0.00              
ATOM      5  N   THR    19      11.910  21.393  36.578  1.00  0.00              
ATOM      6  CA  THR    19      10.769  21.955  37.291  1.00  0.00              
ATOM      7  C   THR    19       9.611  20.959  37.354  1.00  0.00              
ATOM      8  O   THR    19       8.774  21.026  38.254  1.00  0.00              
ATOM      9  N   ALA    20       9.574  20.030  36.401  1.00  0.00              
ATOM     10  CA  ALA    20       8.521  19.018  36.362  1.00  0.00              
ATOM     11  C   ALA    20       8.870  17.883  37.312  1.00  0.00              
ATOM     12  O   ALA    20       8.022  17.383  38.050  1.00  0.00              
ATOM     13  N   ILE    21      10.140  17.508  37.296  1.00  0.00              
ATOM     14  CA  ILE    21      10.651  16.456  38.159  1.00  0.00              
ATOM     15  C   ILE    21      12.001  16.881  38.729  1.00  0.00              
ATOM     16  O   ILE    21      13.026  16.256  38.461  1.00  0.00              
ATOM     17  N   ILE    22      12.016  17.970  39.518  1.00  0.00              
ATOM     18  CA  ILE    22      13.247  18.490  40.115  1.00  0.00              
ATOM     19  C   ILE    22      13.895  17.492  41.069  1.00  0.00              
ATOM     20  O   ILE    22      15.089  17.579  41.354  1.00  0.00              
ATOM     21  N   LYS    23      13.100  16.547  41.562  1.00  0.00              
ATOM     22  CA  LYS    23      13.601  15.536  42.488  1.00  0.00              
ATOM     23  C   LYS    23      13.957  14.245  41.755  1.00  0.00              
ATOM     24  O   LYS    23      14.734  13.432  42.256  1.00  0.00              
ATOM     25  N   MET    24      13.381  14.056  40.571  1.00  0.00              
ATOM     26  CA  MET    24      13.638  12.858  39.780  1.00  0.00              
ATOM     27  C   MET    24      14.554  13.155  38.592  1.00  0.00              
ATOM     28  O   MET    24      15.007  12.237  37.908  1.00  0.00              
ATOM     29  N   ALA    25      17.405  15.046  38.929  1.00  0.00              
ATOM     30  CA  ALA    25      18.771  15.085  39.448  1.00  0.00              
ATOM     31  C   ALA    25      19.614  13.931  38.899  1.00  0.00              
ATOM     32  O   ALA    25      20.709  14.148  38.380  1.00  0.00              
ATOM     33  N   LYS    26      20.146  14.377  35.026  1.00  0.00              
ATOM     34  CA  LYS    26      21.075  15.425  34.622  1.00  0.00              
ATOM     35  C   LYS    26      22.521  14.998  34.861  1.00  0.00              
ATOM     36  O   LYS    26      23.436  15.466  34.182  1.00  0.00              
ATOM     37  N   SER    27      22.722  14.107  35.828  1.00  0.00              
ATOM     38  CA  SER    27      24.058  13.621  36.153  1.00  0.00              
ATOM     39  C   SER    27      24.261  12.196  35.645  1.00  0.00              
ATOM     40  O   SER    27      25.354  11.832  35.210  1.00  0.00              
ATOM     41  N   GLY    33      23.204  11.394  35.704  1.00  0.00              
ATOM     42  CA  GLY    33      23.287  10.020  35.248  1.00  0.00              
ATOM     43  C   GLY    33      22.864   9.864  33.802  1.00  0.00              
ATOM     44  O   GLY    33      23.678   9.516  32.945  1.00  0.00              
ATOM     45  N   LYS    34      21.590  10.124  33.526  1.00  0.00              
ATOM     46  CA  LYS    34      21.066  10.013  32.167  1.00  0.00              
ATOM     47  C   LYS    34      21.912  10.822  31.192  1.00  0.00              
ATOM     48  O   LYS    34      22.216  10.364  30.091  1.00  0.00              
ATOM     49  N   LYS    36      22.301  12.024  31.609  1.00  0.00              
ATOM     50  CA  LYS    36      23.124  12.888  30.775  1.00  0.00              
ATOM     51  C   LYS    36      24.451  12.212  30.456  1.00  0.00              
ATOM     52  O   LYS    36      25.034  12.431  29.394  1.00  0.00              
ATOM     53  N   PRO    37      24.916  11.378  31.382  1.00  0.00              
ATOM     54  CA  PRO    37      26.166  10.655  31.201  1.00  0.00              
ATOM     55  C   PRO    37      25.976   9.514  30.210  1.00  0.00              
ATOM     56  O   PRO    37      26.845   9.245  29.381  1.00  0.00              
ATOM     57  N   ALA    38      24.826   8.852  30.299  1.00  0.00              
ATOM     58  CA  ALA    38      24.506   7.745  29.405  1.00  0.00              
ATOM     59  C   ALA    38      24.664   8.175  27.949  1.00  0.00              
ATOM     60  O   ALA    38      25.060   7.383  27.095  1.00  0.00              
ATOM     61  N   GLU    39      24.355   9.440  27.680  1.00  0.00              
ATOM     62  CA  GLU    39      24.465   9.989  26.333  1.00  0.00              
ATOM     63  C   GLU    39      25.856   9.747  25.751  1.00  0.00              
ATOM     64  O   GLU    39      26.000   9.165  24.678  1.00  0.00              
ATOM     65  N   ILE    40      26.874  10.207  26.466  1.00  0.00              
ATOM     66  CA  ILE    40      28.257  10.054  26.024  1.00  0.00              
ATOM     67  C   ILE    40      28.637   8.584  25.881  1.00  0.00              
ATOM     68  O   ILE    40      29.551   8.241  25.131  1.00  0.00              
ATOM     69  N   ALA    41      27.935   7.718  26.605  1.00  0.00              
ATOM     70  CA  ALA    41      28.208   6.287  26.555  1.00  0.00              
ATOM     71  C   ALA    41      27.476   5.628  25.390  1.00  0.00              
ATOM     72  O   ALA    41      27.915   4.601  24.872  1.00  0.00              
ATOM     73  N   MET    48      26.357   6.221  24.983  1.00  0.00              
ATOM     74  CA  MET    48      25.569   5.680  23.882  1.00  0.00              
ATOM     75  C   MET    48      25.925   6.345  22.557  1.00  0.00              
ATOM     76  O   MET    48      25.979   5.687  21.518  1.00  0.00              
ATOM     77  N   ARG    49      26.171   7.651  22.598  1.00  0.00              
ATOM     78  CA  ARG    49      26.525   8.397  21.398  1.00  0.00              
ATOM     79  C   ARG    49      27.742   7.771  20.734  1.00  0.00              
ATOM     80  O   ARG    49      27.855   7.748  19.509  1.00  0.00              
ATOM     81  N   PHE    50      28.636   7.239  21.558  1.00  0.00              
ATOM     82  CA  PHE    50      29.833   6.581  21.060  1.00  0.00              
ATOM     83  C   PHE    50      29.460   5.348  20.242  1.00  0.00              
ATOM     84  O   PHE    50      30.269   4.830  19.473  1.00  0.00              
ATOM     85  N   GLY    51      28.222   4.886  20.418  1.00  0.00              
ATOM     86  CA  GLY    51      27.729   3.717  19.700  1.00  0.00              
ATOM     87  C   GLY    51      26.579   4.090  18.765  1.00  0.00              
ATOM     88  O   GLY    51      26.214   3.317  17.881  1.00  0.00              
ATOM     89  N   ILE    52      26.012   5.282  18.963  1.00  0.00              
ATOM     90  CA  ILE    52      24.907   5.756  18.133  1.00  0.00              
ATOM     91  C   ILE    52      25.228   5.572  16.655  1.00  0.00              
ATOM     92  O   ILE    52      24.385   5.138  15.870  1.00  0.00              
ATOM     93  N   GLN    54      26.458   5.906  16.287  1.00  0.00              
ATOM     94  CA  GLN    54      26.906   5.783  14.906  1.00  0.00              
ATOM     95  C   GLN    54      26.843   4.333  14.433  1.00  0.00              
ATOM     96  O   GLN    54      26.837   4.063  13.231  1.00  0.00              
ATOM     97  N   ASP    55      19.690   4.017  14.948  1.00  0.00              
ATOM     98  CA  ASP    55      18.941   5.198  15.367  1.00  0.00              
ATOM     99  C   ASP    55      18.336   5.907  14.160  1.00  0.00              
ATOM    100  O   ASP    55      19.047   6.276  13.226  1.00  0.00              
ATOM    101  N   GLN    56      17.020   6.091  14.182  1.00  0.00              
ATOM    102  CA  GLN    56      16.328   6.753  13.082  1.00  0.00              
ATOM    103  C   GLN    56      14.955   7.253  13.517  1.00  0.00              
ATOM    104  O   GLN    56      14.205   6.542  14.186  1.00  0.00              
ATOM    105  N   VAL    57      14.632   8.485  13.129  1.00  0.00              
ATOM    106  CA  VAL    57      13.351   9.091  13.472  1.00  0.00              
ATOM    107  C   VAL    57      13.040  10.268  12.553  1.00  0.00              
ATOM    108  O   VAL    57      13.825  10.595  11.662  1.00  0.00              
ATOM    109  N   ASP    58       9.550  10.730  11.372  1.00  0.00              
ATOM    110  CA  ASP    58       8.174  10.516  10.939  1.00  0.00              
ATOM    111  C   ASP    58       7.180  10.889  12.040  1.00  0.00              
ATOM    112  O   ASP    58       5.973  10.935  11.802  1.00  0.00              
ATOM    113  N   LEU    60       7.690  11.152  13.241  1.00  0.00              
ATOM    114  CA  LEU    60       6.836  11.517  14.366  1.00  0.00              
ATOM    115  C   LEU    60       7.663  11.820  15.613  1.00  0.00              
ATOM    116  O   LEU    60       7.310  12.696  16.403  1.00  0.00              
ATOM    117  N   LEU    61      15.616  16.020  18.600  1.00  0.00              
ATOM    118  CA  LEU    61      16.038  16.536  19.897  1.00  0.00              
ATOM    119  C   LEU    61      15.059  16.126  20.999  1.00  0.00              
ATOM    120  O   LEU    61      15.287  16.407  22.175  1.00  0.00              
ATOM    121  N   LYS    62      13.970  15.464  20.612  1.00  0.00              
ATOM    122  CA  LYS    62      12.982  15.034  21.583  1.00  0.00              
ATOM    123  C   LYS    62      13.212  13.617  22.059  1.00  0.00              
ATOM    124  O   LYS    62      13.421  13.379  23.249  1.00  0.00              
ATOM    125  N   ALA    63      13.161  12.670  21.130  1.00  0.00              
ATOM    126  CA  ALA    63      13.354  11.267  21.466  1.00  0.00              
ATOM    127  C   ALA    63      13.614  10.432  20.214  1.00  0.00              
ATOM    128  O   ALA    63      12.879  10.521  19.232  1.00  0.00              
ATOM    129  N   SER    64      14.668   9.621  20.260  1.00  0.00              
ATOM    130  CA  SER    64      15.029   8.769  19.131  1.00  0.00              
ATOM    131  C   SER    64      15.026   7.297  19.535  1.00  0.00              
ATOM    132  O   SER    64      15.328   6.959  20.680  1.00  0.00              
ATOM    133  N   ASP    65      14.684   6.427  18.591  1.00  0.00              
ATOM    134  CA  ASP    65      14.643   4.994  18.855  1.00  0.00              
ATOM    135  C   ASP    65      15.956   4.321  18.467  1.00  0.00              
ATOM    136  O   ASP    65      16.443   4.490  17.351  1.00  0.00              
ATOM    137  N   SER    66      16.522   3.557  19.396  1.00  0.00              
ATOM    138  CA  SER    66      17.778   2.856  19.152  1.00  0.00              
ATOM    139  C   SER    66      17.580   1.346  19.211  1.00  0.00              
ATOM    140  O   SER    66      17.633   0.743  20.283  1.00  0.00              
ATOM    141  N   ILE    67      17.350   0.743  18.052  1.00  0.00              
ATOM    142  CA  ILE    67      17.141  -0.697  17.965  1.00  0.00              
ATOM    143  C   ILE    67      18.465  -1.451  18.056  1.00  0.00              
ATOM    144  O   ILE    67      19.199  -1.553  17.073  1.00  0.00              
ATOM    145  N   GLU    68      18.765  -1.979  19.239  1.00  0.00              
ATOM    146  CA  GLU    68      20.002  -2.723  19.449  1.00  0.00              
ATOM    147  C   GLU    68      19.975  -3.475  20.776  1.00  0.00              
ATOM    148  O   GLU    68      19.472  -2.968  21.779  1.00  0.00              
ATOM    149  N   LYS    85      20.525  -4.686  20.774  1.00  0.00              
ATOM    150  CA  LYS    85      20.573  -5.509  21.979  1.00  0.00              
ATOM    151  C   LYS    85      22.015  -5.835  22.351  1.00  0.00              
ATOM    152  O   LYS    85      22.919  -5.728  21.523  1.00  0.00              
ATOM    153  N   TYR    86      22.223  -6.237  23.601  1.00  0.00              
ATOM    154  CA  TYR    86      23.557  -6.583  24.082  1.00  0.00              
ATOM    155  C   TYR    86      24.202  -7.638  23.186  1.00  0.00              
ATOM    156  O   TYR    86      23.633  -8.033  22.169  1.00  0.00              
ATOM    157  N   VAL    87      25.390  -8.091  23.573  1.00  0.00              
ATOM    158  CA  VAL    87      26.112  -9.101  22.805  1.00  0.00              
ATOM    159  C   VAL    87      25.263 -10.355  22.606  1.00  0.00              
ATOM    160  O   VAL    87      25.494 -11.130  21.676  1.00  0.00              
ATOM    161  N   ALA    88      24.282 -10.552  23.483  1.00  0.00              
ATOM    162  CA  ALA    88      23.402 -11.714  23.402  1.00  0.00              
ATOM    163  C   ALA    88      22.749 -11.819  22.026  1.00  0.00              
ATOM    164  O   ALA    88      22.706 -12.895  21.429  1.00  0.00              
ATOM    165  N   SER    89      22.236 -10.698  21.530  1.00  0.00              
ATOM    166  CA  SER    89      21.587 -10.690  20.234  1.00  0.00              
ATOM    167  C   SER    89      20.333 -11.539  20.221  1.00  0.00              
ATOM    168  O   SER    89      20.103 -12.312  19.290  1.00  0.00              
ATOM    169  N   ASP   103      19.524 -11.401  21.267  1.00  0.00              
ATOM    170  CA  ASP   103      18.290 -12.166  21.387  1.00  0.00              
ATOM    171  C   ASP   103      17.108 -11.424  20.767  1.00  0.00              
ATOM    172  O   ASP   103      16.290 -12.021  20.067  1.00  0.00              
ATOM    173  N   ASN   104      17.018 -10.123  21.030  1.00  0.00              
ATOM    174  CA  ASN   104      15.926  -9.316  20.494  1.00  0.00              
ATOM    175  C   ASN   104      16.222  -7.823  20.634  1.00  0.00              
ATOM    176  O   ASN   104      16.099  -7.261  21.722  1.00  0.00              
END
