
#######################################################
#                                                     #
#                        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 T0304AL243_3-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304AL243_3-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R      17           -
LGA    -       -      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    A      32      G      21          3.784
LGA    R      33      L      22          3.758
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    L      34      C      29           #
LGA    V      35      F      30          2.063
LGA    Q      36      -       -           -
LGA    E      37      G      31          3.521
LGA    G      38      A      32          1.722
LGA    N      39      R      33          1.508
LGA    R      40      L      34          1.176
LGA    L      41      -       -           -
LGA    H      42      V      35           #
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    Y      43      Y      43          1.517
LGA    L      44      L      44           #
LGA    A      45      -       -           -
LGA    D      46      -       -           -
LGA    R      47      A      45          6.211
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    A      48      L      62           #
LGA    G      49      D      63          3.219
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    I      50      F      66          2.357
LGA    L      53      P      67          2.575
LGA    F      54      L      68           #
LGA    S      55      L      69           -
LGA    -       -      M      70           -
LGA    -       -      K      71           -
LGA    -       -      Q      72           -
LGA    -       -      L      73           -
LGA    D      56      E      74           #
LGA    A      57      L      75          2.299
LGA    D      58      -       -           -
LGA    A      59      M      76          2.209
LGA    Y      60      L      77           #
LGA    H      61      T      78           -
LGA    -       -      S      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    L      62      V      90           #
LGA    D      63      -       -           -
LGA    Q      64      -       -           -
LGA    A      65      T      91           #
LGA    F      66      L      92          3.121
LGA    P      67      Y      93          1.792
LGA    L      68      A      94          3.920
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    L      69      T      98          3.308
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    M      70      V     114          5.847
LGA    K      71      Y     115          5.832
LGA    Q      72      -       -           -
LGA    L      73      P     116          2.310
LGA    E      74      T     117          2.447
LGA    L      75      -       -           -
LGA    M      76      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43  101    5.0     22    3.33     4.55     14.189     0.641

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.112184 * X  +   0.056382 * Y  +  -0.992087 * Z  +  82.806595
  Y_new =  -0.608482 * X  +  -0.793213 * Y  +   0.023726 * Z  +  64.181824
  Z_new =  -0.785598 * X  +   0.606328 * Y  +   0.123293 * Z  +  25.760809 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.370187   -1.771405  [ DEG:    78.5059   -101.4941 ]
  Theta =   0.903663    2.237930  [ DEG:    51.7761    128.2239 ]
  Phi   =  -1.753116    1.388477  [ DEG:  -100.4461     79.5539 ]
 
# 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: T0304AL243_3-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL243_3-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43  101   5.0   22   3.33    4.55  14.189
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL243_3-D1
REMARK Aligment from pdb entry: 2f96A
ATOM      1  N   ALA    32      43.229  27.026  41.638  1.00  0.00              
ATOM      2  CA  ALA    32      43.467  25.572  41.886  1.00  0.00              
ATOM      3  C   ALA    32      42.212  24.848  42.400  1.00  0.00              
ATOM      4  O   ALA    32      41.989  23.662  42.104  1.00  0.00              
ATOM      5  N   ARG    33      41.392  25.571  43.160  1.00  0.00              
ATOM      6  CA  ARG    33      40.078  25.079  43.543  1.00  0.00              
ATOM      7  C   ARG    33      39.273  24.684  42.302  1.00  0.00              
ATOM      8  O   ARG    33      38.716  23.616  42.241  1.00  0.00              
ATOM      9  N   LEU    34      39.196  25.577  41.330  1.00  0.00              
ATOM     10  CA  LEU    34      38.493  25.302  40.092  1.00  0.00              
ATOM     11  C   LEU    34      39.126  24.138  39.337  1.00  0.00              
ATOM     12  O   LEU    34      38.467  23.165  38.981  1.00  0.00              
ATOM     13  N   VAL    35      40.414  24.260  39.070  1.00  0.00              
ATOM     14  CA  VAL    35      41.090  23.368  38.144  1.00  0.00              
ATOM     15  C   VAL    35      41.262  21.988  38.728  1.00  0.00              
ATOM     16  O   VAL    35      41.052  20.990  38.023  1.00  0.00              
ATOM     17  N   GLN    36      41.643  21.927  40.009  1.00  0.00              
ATOM     18  CA  GLN    36      42.022  20.647  40.624  1.00  0.00              
ATOM     19  C   GLN    36      41.226  20.290  41.857  1.00  0.00              
ATOM     20  O   GLN    36      41.422  19.219  42.419  1.00  0.00              
ATOM     21  N   GLU    37      40.311  21.152  42.277  1.00  0.00              
ATOM     22  CA  GLU    37      39.610  20.940  43.532  1.00  0.00              
ATOM     23  C   GLU    37      40.486  20.972  44.778  1.00  0.00              
ATOM     24  O   GLU    37      40.116  20.364  45.798  1.00  0.00              
ATOM     25  N   GLY    38      41.628  21.670  44.704  1.00  0.00              
ATOM     26  CA  GLY    38      42.601  21.770  45.800  1.00  0.00              
ATOM     27  C   GLY    38      42.878  23.216  46.117  1.00  0.00              
ATOM     28  O   GLY    38      43.050  23.998  45.211  1.00  0.00              
ATOM     29  N   ASN    39      42.969  23.575  47.387  1.00  0.00              
ATOM     30  CA  ASN    39      43.345  24.955  47.772  1.00  0.00              
ATOM     31  C   ASN    39      44.735  25.112  48.397  1.00  0.00              
ATOM     32  O   ASN    39      45.190  26.235  48.587  1.00  0.00              
ATOM     33  N   ARG    40      45.371  24.007  48.769  1.00  0.00              
ATOM     34  CA  ARG    40      46.709  24.023  49.330  1.00  0.00              
ATOM     35  C   ARG    40      47.730  23.948  48.215  1.00  0.00              
ATOM     36  O   ARG    40      47.620  23.085  47.351  1.00  0.00              
ATOM     37  N   LEU    41      48.746  24.809  48.289  1.00  0.00              
ATOM     38  CA  LEU    41      49.687  25.040  47.172  1.00  0.00              
ATOM     39  C   LEU    41      50.388  23.793  46.721  1.00  0.00              
ATOM     40  O   LEU    41      50.444  23.519  45.528  1.00  0.00              
ATOM     41  N   HIS    42      50.949  23.059  47.677  1.00  0.00              
ATOM     42  CA  HIS    42      51.672  21.800  47.383  1.00  0.00              
ATOM     43  C   HIS    42      50.776  20.751  46.743  1.00  0.00              
ATOM     44  O   HIS    42      51.153  20.080  45.781  1.00  0.00              
ATOM     45  N   TYR    43      49.571  20.620  47.273  1.00  0.00              
ATOM     46  CA  TYR    43      48.590  19.687  46.746  1.00  0.00              
ATOM     47  C   TYR    43      48.054  20.087  45.381  1.00  0.00              
ATOM     48  O   TYR    43      47.728  19.236  44.549  1.00  0.00              
ATOM     49  N   LEU    44      47.965  21.384  45.140  1.00  0.00              
ATOM     50  CA  LEU    44      47.569  21.892  43.828  1.00  0.00              
ATOM     51  C   LEU    44      48.637  21.571  42.784  1.00  0.00              
ATOM     52  O   LEU    44      48.329  21.036  41.698  1.00  0.00              
ATOM     53  N   ALA    45      49.893  21.901  43.100  1.00  0.00              
ATOM     54  CA  ALA    45      51.032  21.568  42.214  1.00  0.00              
ATOM     55  C   ALA    45      51.181  20.064  41.951  1.00  0.00              
ATOM     56  O   ALA    45      51.537  19.642  40.849  1.00  0.00              
ATOM     57  N   ASP    46      50.907  19.258  42.965  1.00  0.00              
ATOM     58  CA  ASP    46      50.966  17.812  42.817  1.00  0.00              
ATOM     59  C   ASP    46      49.860  17.374  41.840  1.00  0.00              
ATOM     60  O   ASP    46      50.113  16.637  40.879  1.00  0.00              
ATOM     61  N   ARG    47      48.646  17.882  42.059  1.00  0.00              
ATOM     62  CA  ARG    47      47.517  17.630  41.153  1.00  0.00              
ATOM     63  C   ARG    47      47.826  18.063  39.714  1.00  0.00              
ATOM     64  O   ARG    47      47.424  17.396  38.768  1.00  0.00              
ATOM     65  N   ALA    48      48.544  19.175  39.563  1.00  0.00              
ATOM     66  CA  ALA    48      48.885  19.705  38.233  1.00  0.00              
ATOM     67  C   ALA    48      50.019  18.941  37.530  1.00  0.00              
ATOM     68  O   ALA    48      50.403  19.288  36.404  1.00  0.00              
ATOM     69  N   GLY    49      50.567  17.928  38.208  1.00  0.00              
ATOM     70  CA  GLY    49      51.693  17.143  37.694  1.00  0.00              
ATOM     71  C   GLY    49      53.063  17.761  37.948  1.00  0.00              
ATOM     72  O   GLY    49      54.059  17.227  37.481  1.00  0.00              
ATOM     73  N   ILE    50      53.120  18.889  38.658  1.00  0.00              
ATOM     74  CA  ILE    50      54.397  19.547  38.987  1.00  0.00              
ATOM     75  C   ILE    50      55.065  18.837  40.175  1.00  0.00              
ATOM     76  O   ILE    50      54.383  18.166  40.969  1.00  0.00              
ATOM     77  N   LEU    53      56.385  19.001  40.306  1.00  0.00              
ATOM     78  CA  LEU    53      57.101  18.618  41.534  1.00  0.00              
ATOM     79  C   LEU    53      56.883  19.703  42.605  1.00  0.00              
ATOM     80  O   LEU    53      56.862  20.906  42.298  1.00  0.00              
ATOM     81  N   PHE    54      56.689  19.291  43.853  1.00  0.00              
ATOM     82  CA  PHE    54      56.696  20.244  44.966  1.00  0.00              
ATOM     83  C   PHE    54      57.131  19.525  46.242  1.00  0.00              
ATOM     84  O   PHE    54      56.632  18.436  46.531  1.00  0.00              
ATOM     85  N   SER    55      58.052  20.144  46.991  1.00  0.00              
ATOM     86  CA  SER    55      58.658  19.527  48.184  1.00  0.00              
ATOM     87  C   SER    55      57.877  19.845  49.470  1.00  0.00              
ATOM     88  O   SER    55      57.591  21.013  49.766  1.00  0.00              
ATOM     89  N   ASP    56      61.369  32.721  46.717  1.00  0.00              
ATOM     90  CA  ASP    56      61.718  32.438  45.328  1.00  0.00              
ATOM     91  C   ASP    56      61.136  31.108  44.799  1.00  0.00              
ATOM     92  O   ASP    56      60.613  31.022  43.677  1.00  0.00              
ATOM     93  N   ALA    57      61.246  30.076  45.620  1.00  0.00              
ATOM     94  CA  ALA    57      60.709  28.762  45.281  1.00  0.00              
ATOM     95  C   ALA    57      59.200  28.855  45.118  1.00  0.00              
ATOM     96  O   ALA    57      58.649  28.311  44.173  1.00  0.00              
ATOM     97  N   ASP    58      58.550  29.552  46.040  1.00  0.00              
ATOM     98  CA  ASP    58      57.101  29.602  46.089  1.00  0.00              
ATOM     99  C   ASP    58      56.542  30.386  44.908  1.00  0.00              
ATOM    100  O   ASP    58      55.497  30.059  44.376  1.00  0.00              
ATOM    101  N   ALA    59      57.264  31.423  44.517  1.00  0.00              
ATOM    102  CA  ALA    59      56.851  32.309  43.442  1.00  0.00              
ATOM    103  C   ALA    59      57.004  31.617  42.068  1.00  0.00              
ATOM    104  O   ALA    59      56.152  31.716  41.204  1.00  0.00              
ATOM    105  N   TYR    60      58.102  30.907  41.898  1.00  0.00              
ATOM    106  CA  TYR    60      58.297  30.130  40.698  1.00  0.00              
ATOM    107  C   TYR    60      57.303  28.982  40.528  1.00  0.00              
ATOM    108  O   TYR    60      56.751  28.805  39.463  1.00  0.00              
ATOM    109  N   HIS    61      57.033  28.249  41.602  1.00  0.00              
ATOM    110  CA  HIS    61      55.986  27.203  41.568  1.00  0.00              
ATOM    111  C   HIS    61      54.577  27.756  41.320  1.00  0.00              
ATOM    112  O   HIS    61      53.789  27.174  40.563  1.00  0.00              
ATOM    113  N   LEU    62      54.269  28.883  41.955  1.00  0.00              
ATOM    114  CA  LEU    62      52.990  29.562  41.786  1.00  0.00              
ATOM    115  C   LEU    62      52.818  30.117  40.369  1.00  0.00              
ATOM    116  O   LEU    62      51.727  30.036  39.798  1.00  0.00              
ATOM    117  N   ASP    63      53.884  30.672  39.807  1.00  0.00              
ATOM    118  CA  ASP    63      53.844  31.128  38.422  1.00  0.00              
ATOM    119  C   ASP    63      53.594  29.978  37.443  1.00  0.00              
ATOM    120  O   ASP    63      52.815  30.129  36.529  1.00  0.00              
ATOM    121  N   GLN    64      54.229  28.829  37.665  1.00  0.00              
ATOM    122  CA  GLN    64      53.991  27.632  36.872  1.00  0.00              
ATOM    123  C   GLN    64      52.551  27.126  37.021  1.00  0.00              
ATOM    124  O   GLN    64      51.883  26.795  36.042  1.00  0.00              
ATOM    125  N   ALA    65      52.058  27.055  38.255  1.00  0.00              
ATOM    126  CA  ALA    65      50.643  26.726  38.507  1.00  0.00              
ATOM    127  C   ALA    65      49.679  27.712  37.779  1.00  0.00              
ATOM    128  O   ALA    65      48.729  27.318  37.135  1.00  0.00              
ATOM    129  N   PHE    66      49.903  29.006  37.939  1.00  0.00              
ATOM    130  CA  PHE    66      49.080  30.026  37.275  1.00  0.00              
ATOM    131  C   PHE    66      49.040  29.844  35.758  1.00  0.00              
ATOM    132  O   PHE    66      47.968  29.674  35.192  1.00  0.00              
ATOM    133  N   PRO    67      50.207  29.836  35.112  1.00  0.00              
ATOM    134  CA  PRO    67      50.304  29.724  33.623  1.00  0.00              
ATOM    135  C   PRO    67      49.721  28.415  33.094  1.00  0.00              
ATOM    136  O   PRO    67      49.087  28.398  32.042  1.00  0.00              
ATOM    137  N   LEU    68      49.949  27.329  33.829  1.00  0.00              
ATOM    138  CA  LEU    68      49.373  26.006  33.480  1.00  0.00              
ATOM    139  C   LEU    68      47.857  26.020  33.488  1.00  0.00              
ATOM    140  O   LEU    68      47.247  25.428  32.615  1.00  0.00              
ATOM    141  N   LEU    69      47.230  26.680  34.473  1.00  0.00              
ATOM    142  CA  LEU    69      45.765  26.712  34.544  1.00  0.00              
ATOM    143  C   LEU    69      45.201  27.568  33.391  1.00  0.00              
ATOM    144  O   LEU    69      44.333  27.121  32.633  1.00  0.00              
ATOM    145  N   MET    70      45.705  28.787  33.245  1.00  0.00              
ATOM    146  CA  MET    70      45.338  29.652  32.118  1.00  0.00              
ATOM    147  C   MET    70      45.581  28.946  30.769  1.00  0.00              
ATOM    148  O   MET    70      44.770  29.020  29.822  1.00  0.00              
ATOM    149  N   LYS    71      46.710  28.275  30.648  1.00  0.00              
ATOM    150  CA  LYS    71      46.986  27.548  29.398  1.00  0.00              
ATOM    151  C   LYS    71      46.062  26.342  29.118  1.00  0.00              
ATOM    152  O   LYS    71      45.690  26.055  27.919  1.00  0.00              
ATOM    153  N   GLN    72      45.686  25.632  30.186  1.00  0.00              
ATOM    154  CA  GLN    72      44.690  24.576  30.066  1.00  0.00              
ATOM    155  C   GLN    72      43.338  25.124  29.624  1.00  0.00              
ATOM    156  O   GLN    72      42.643  24.517  28.793  1.00  0.00              
ATOM    157  N   LEU    73      42.941  26.234  30.221  1.00  0.00              
ATOM    158  CA  LEU    73      41.699  26.920  29.849  1.00  0.00              
ATOM    159  C   LEU    73      41.689  27.207  28.326  1.00  0.00              
ATOM    160  O   LEU    73      40.710  26.906  27.640  1.00  0.00              
ATOM    161  N   GLU    74      42.797  27.749  27.806  1.00  0.00              
ATOM    162  CA  GLU    74      42.961  27.961  26.376  1.00  0.00              
ATOM    163  C   GLU    74      42.924  26.667  25.559  1.00  0.00              
ATOM    164  O   GLU    74      42.276  26.591  24.515  1.00  0.00              
ATOM    165  N   LEU    75      43.663  25.659  26.016  1.00  0.00              
ATOM    166  CA  LEU    75      43.710  24.370  25.338  1.00  0.00              
ATOM    167  C   LEU    75      42.337  23.731  25.290  1.00  0.00              
ATOM    168  O   LEU    75      42.038  23.077  24.337  1.00  0.00              
ATOM    169  N   MET    76      41.521  23.925  26.325  1.00  0.00              
ATOM    170  CA  MET    76      40.152  23.389  26.389  1.00  0.00              
ATOM    171  C   MET    76      39.106  24.220  25.627  1.00  0.00              
ATOM    172  O   MET    76      37.922  23.900  25.678  1.00  0.00              
END
