
#######################################################
#                                                     #
#                        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   36 (  144),  selected   36 , name T0350AL381_4-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350AL381_4-D1.T0350_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    D      14      P      11          2.021
LGA    R      15      V      12          1.746
LGA    Y      16      W      13          2.057
LGA    D      17      D      14          2.294
LGA    T      18      R      15          2.146
LGA    Q      19      Y      16          1.944
LGA    I      20      D      17          1.748
LGA    H      21      T      18          1.663
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    S      36      M      47          2.660
LGA    Y      37      N      48          4.292
LGA    T      38      K      49          2.305
LGA    N      39      L      50           #
LGA    L      40      L      51           -
LGA    A      41      E      52          2.628
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    E      42      Q      55           #
LGA    M      43      V      56          3.409
LGA    V      44      H      57          3.736
LGA    G      45      L      58          2.024
LGA    -       -      K      59           -
LGA    -       -      F      60           -
LGA    -       -      E      61           -
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    -       -      V      71           -
LGA    -       -      K      72           -
LGA    -       -      V      73           -
LGA    E      46      I      74          2.960
LGA    M      47      E      75          4.233
LGA    N      48      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    K      49      E      80           #
LGA    L      50      V      81          3.470
LGA    L      51      I      82          4.268
LGA    E      52      R      83          2.847
LGA    P      53      E      84          3.726
LGA    S      54      -       -           -
LGA    Q      55      -       -           -
LGA    V      56      -       -           -
LGA    H      57      -       -           -
LGA    L      58      I      85          3.888
LGA    K      59      P      86          2.572
LGA    F      60      P      87          3.416
LGA    -       -      K      88           -
LGA    E      61      R      89          2.148
LGA    L      62      W      90          2.185
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    H      63      Y      94          4.930
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   91    5.0     27    3.01     3.70     18.850     0.869

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.584950 * X  +   0.740317 * Y  +  -0.331308 * Z  +  18.896696
  Y_new =  -0.552073 * X  +  -0.064176 * Y  +   0.831322 * Z  +  21.264093
  Z_new =   0.594180 * X  +   0.669188 * Y  +   0.446249 * Z  + -41.872593 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.982666   -2.158926  [ DEG:    56.3026   -123.6974 ]
  Theta =  -0.636246   -2.505347  [ DEG:   -36.4542   -143.5458 ]
  Phi   =  -2.385101    0.756491  [ DEG:  -136.6562     43.3438 ]
 
# 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: T0350AL381_4-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL381_4-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   91   5.0   27   3.01    3.70  18.850
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL381_4-D1
REMARK Aligment from pdb entry: 1ww1A
ATOM      1  N   ASP    14       8.358  -4.766 -10.151  1.00  0.00              
ATOM      2  CA  ASP    14       7.454  -5.780 -10.662  1.00  0.00              
ATOM      3  C   ASP    14       6.910  -5.458 -12.041  1.00  0.00              
ATOM      4  O   ASP    14       6.280  -6.301 -12.677  1.00  0.00              
ATOM      5  N   ARG    15       7.149  -4.237 -12.507  1.00  0.00              
ATOM      6  CA  ARG    15       6.657  -3.815 -13.809  1.00  0.00              
ATOM      7  C   ARG    15       7.124  -4.709 -14.984  1.00  0.00              
ATOM      8  O   ARG    15       6.323  -5.108 -15.846  1.00  0.00              
ATOM      9  N   TYR    16       8.415  -5.030 -15.011  1.00  0.00              
ATOM     10  CA  TYR    16       8.965  -5.866 -16.073  1.00  0.00              
ATOM     11  C   TYR    16       8.149  -7.154 -16.237  1.00  0.00              
ATOM     12  O   TYR    16       7.860  -7.569 -17.359  1.00  0.00              
ATOM     13  N   ASP    17       7.770  -7.777 -15.122  1.00  0.00              
ATOM     14  CA  ASP    17       6.978  -9.000 -15.183  1.00  0.00              
ATOM     15  C   ASP    17       5.564  -8.775 -15.710  1.00  0.00              
ATOM     16  O   ASP    17       5.019  -9.599 -16.458  1.00  0.00              
ATOM     17  N   THR    18       4.960  -7.658 -15.321  1.00  0.00              
ATOM     18  CA  THR    18       3.619  -7.333 -15.784  1.00  0.00              
ATOM     19  C   THR    18       3.605  -7.221 -17.316  1.00  0.00              
ATOM     20  O   THR    18       2.784  -7.828 -17.995  1.00  0.00              
ATOM     21  N   GLN    19       4.536  -6.446 -17.849  1.00  0.00              
ATOM     22  CA  GLN    19       4.627  -6.237 -19.287  1.00  0.00              
ATOM     23  C   GLN    19       4.940  -7.538 -20.040  1.00  0.00              
ATOM     24  O   GLN    19       4.362  -7.817 -21.099  1.00  0.00              
ATOM     25  N   ILE    20       5.849  -8.338 -19.493  1.00  0.00              
ATOM     26  CA  ILE    20       6.223  -9.598 -20.116  1.00  0.00              
ATOM     27  C   ILE    20       5.058 -10.579 -20.161  1.00  0.00              
ATOM     28  O   ILE    20       4.745 -11.129 -21.211  1.00  0.00              
ATOM     29  N   HIS    21       4.407 -10.808 -19.029  1.00  0.00              
ATOM     30  CA  HIS    21       3.282 -11.719 -19.018  1.00  0.00              
ATOM     31  C   HIS    21       2.181 -11.254 -19.976  1.00  0.00              
ATOM     32  O   HIS    21       1.550 -12.076 -20.635  1.00  0.00              
ATOM     89  N   SER    36       2.354   5.940 -15.723  1.00  0.00              
ATOM     90  CA  SER    36       2.610   7.325 -15.323  1.00  0.00              
ATOM     91  C   SER    36       3.538   7.352 -14.105  1.00  0.00              
ATOM     92  O   SER    36       3.479   6.491 -13.222  1.00  0.00              
ATOM     93  N   TYR    37       4.384   8.361 -14.045  1.00  0.00              
ATOM     94  CA  TYR    37       5.318   8.470 -12.952  1.00  0.00              
ATOM     95  C   TYR    37       5.627   9.935 -12.825  1.00  0.00              
ATOM     96  O   TYR    37       5.417  10.687 -13.750  1.00  0.00              
ATOM     97  N   THR    38       6.132  10.365 -11.677  1.00  0.00              
ATOM     98  CA  THR    38       6.419  11.790 -11.569  1.00  0.00              
ATOM     99  C   THR    38       7.551  12.286 -12.451  1.00  0.00              
ATOM    100  O   THR    38       8.602  11.658 -12.572  1.00  0.00              
ATOM    101  N   ASN    39       7.310  13.429 -13.079  1.00  0.00              
ATOM    102  CA  ASN    39       8.277  14.052 -13.964  1.00  0.00              
ATOM    103  C   ASN    39       9.665  14.109 -13.331  1.00  0.00              
ATOM    104  O   ASN    39       9.809  14.389 -12.140  1.00  0.00              
ATOM    105  N   LEU    40      10.689  13.830 -14.128  1.00  0.00              
ATOM    106  CA  LEU    40      12.048  13.895 -13.621  1.00  0.00              
ATOM    107  C   LEU    40      12.541  12.739 -12.776  1.00  0.00              
ATOM    108  O   LEU    40      13.481  12.888 -12.002  1.00  0.00              
ATOM    109  N   ALA    41      11.920  11.575 -12.909  1.00  0.00              
ATOM    110  CA  ALA    41      12.373  10.428 -12.148  1.00  0.00              
ATOM    111  C   ALA    41      13.325   9.600 -12.997  1.00  0.00              
ATOM    112  O   ALA    41      12.901   8.811 -13.836  1.00  0.00              
ATOM    113  N   GLU    42      14.618   9.776 -12.774  1.00  0.00              
ATOM    114  CA  GLU    42      15.602   9.042 -13.548  1.00  0.00              
ATOM    115  C   GLU    42      15.444   7.515 -13.498  1.00  0.00              
ATOM    116  O   GLU    42      15.653   6.838 -14.513  1.00  0.00              
ATOM    117  N   MET    43      15.067   6.964 -12.344  1.00  0.00              
ATOM    118  CA  MET    43      14.927   5.504 -12.230  1.00  0.00              
ATOM    119  C   MET    43      13.853   4.914 -13.155  1.00  0.00              
ATOM    120  O   MET    43      14.085   3.896 -13.817  1.00  0.00              
ATOM    121  N   VAL    44      12.687   5.548 -13.201  1.00  0.00              
ATOM    122  CA  VAL    44      11.610   5.063 -14.052  1.00  0.00              
ATOM    123  C   VAL    44      12.009   5.125 -15.509  1.00  0.00              
ATOM    124  O   VAL    44      11.773   4.184 -16.265  1.00  0.00              
ATOM    125  N   GLY    45      12.595   6.247 -15.910  1.00  0.00              
ATOM    126  CA  GLY    45      13.021   6.415 -17.295  1.00  0.00              
ATOM    127  C   GLY    45      14.046   5.342 -17.664  1.00  0.00              
ATOM    128  O   GLY    45      13.885   4.595 -18.630  1.00  0.00              
ATOM    129  N   GLU    46      15.099   5.248 -16.881  1.00  0.00              
ATOM    130  CA  GLU    46      16.102   4.256 -17.180  1.00  0.00              
ATOM    131  C   GLU    46      15.524   2.838 -17.187  1.00  0.00              
ATOM    132  O   GLU    46      15.788   2.055 -18.112  1.00  0.00              
ATOM    133  N   MET    47      14.722   2.510 -16.176  1.00  0.00              
ATOM    134  CA  MET    47      14.134   1.175 -16.102  1.00  0.00              
ATOM    135  C   MET    47      13.307   0.892 -17.352  1.00  0.00              
ATOM    136  O   MET    47      13.470  -0.145 -18.003  1.00  0.00              
ATOM    137  N   ASN    48      12.418   1.820 -17.689  1.00  0.00              
ATOM    138  CA  ASN    48      11.587   1.649 -18.853  1.00  0.00              
ATOM    139  C   ASN    48      12.426   1.517 -20.116  1.00  0.00              
ATOM    140  O   ASN    48      12.113   0.717 -21.001  1.00  0.00              
ATOM    141  N   LYS    49      13.489   2.308 -20.210  1.00  0.00              
ATOM    142  CA  LYS    49      14.375   2.232 -21.366  1.00  0.00              
ATOM    143  C   LYS    49      15.082   0.871 -21.372  1.00  0.00              
ATOM    144  O   LYS    49      15.254   0.235 -22.414  1.00  0.00              
ATOM    145  N   LEU    50      15.480   0.412 -20.197  1.00  0.00              
ATOM    146  CA  LEU    50      16.157  -0.861 -20.125  1.00  0.00              
ATOM    147  C   LEU    50      15.294  -2.019 -20.611  1.00  0.00              
ATOM    148  O   LEU    50      15.783  -2.914 -21.311  1.00  0.00              
ATOM    149  N   LEU    51      14.024  -2.020 -20.206  1.00  0.00              
ATOM    150  CA  LEU    51      13.110  -3.100 -20.563  1.00  0.00              
ATOM    151  C   LEU    51      12.991  -3.254 -22.068  1.00  0.00              
ATOM    152  O   LEU    51      13.191  -4.348 -22.610  1.00  0.00              
ATOM    153  N   GLU    52      12.693  -2.158 -22.750  1.00  0.00              
ATOM    154  CA  GLU    52      12.556  -2.205 -24.197  1.00  0.00              
ATOM    155  C   GLU    52      13.873  -2.633 -24.835  1.00  0.00              
ATOM    156  O   GLU    52      13.900  -3.523 -25.689  1.00  0.00              
ATOM    157  N   PRO    53      14.967  -2.020 -24.398  1.00  0.00              
ATOM    158  CA  PRO    53      16.284  -2.374 -24.912  1.00  0.00              
ATOM    159  C   PRO    53      16.521  -3.869 -24.721  1.00  0.00              
ATOM    160  O   PRO    53      16.844  -4.571 -25.664  1.00  0.00              
ATOM    161  N   SER    54      16.354  -4.345 -23.492  1.00  0.00              
ATOM    162  CA  SER    54      16.560  -5.754 -23.180  1.00  0.00              
ATOM    163  C   SER    54      15.606  -6.644 -23.949  1.00  0.00              
ATOM    164  O   SER    54      16.022  -7.642 -24.524  1.00  0.00              
ATOM    165  N   GLN    55      14.323  -6.306 -23.952  1.00  0.00              
ATOM    166  CA  GLN    55      13.360  -7.122 -24.684  1.00  0.00              
ATOM    167  C   GLN    55      12.670  -6.320 -25.767  1.00  0.00              
ATOM    168  O   GLN    55      11.658  -5.655 -25.521  1.00  0.00              
ATOM    169  N   VAL    56      13.228  -6.354 -26.986  1.00  0.00              
ATOM    170  CA  VAL    56      12.642  -5.619 -28.103  1.00  0.00              
ATOM    171  C   VAL    56      11.191  -6.031 -28.340  1.00  0.00              
ATOM    172  O   VAL    56      10.371  -5.200 -28.714  1.00  0.00              
ATOM    173  N   HIS    57      10.867  -7.301 -28.102  1.00  0.00              
ATOM    174  CA  HIS    57       9.487  -7.764 -28.276  1.00  0.00              
ATOM    175  C   HIS    57       8.523  -7.071 -27.310  1.00  0.00              
ATOM    176  O   HIS    57       7.324  -7.325 -27.337  1.00  0.00              
ATOM    177  N   LEU    58       9.041  -6.211 -26.442  1.00  0.00              
ATOM    178  CA  LEU    58       8.206  -5.516 -25.464  1.00  0.00              
ATOM    179  C   LEU    58       8.054  -4.036 -25.783  1.00  0.00              
ATOM    180  O   LEU    58       7.279  -3.325 -25.139  1.00  0.00              
ATOM    181  N   LYS    59       8.802  -3.583 -26.783  1.00  0.00              
ATOM    182  CA  LYS    59       8.784  -2.198 -27.214  1.00  0.00              
ATOM    183  C   LYS    59       7.373  -1.606 -27.325  1.00  0.00              
ATOM    184  O   LYS    59       7.160  -0.442 -26.978  1.00  0.00              
ATOM    185  N   PHE    60       6.409  -2.405 -27.784  1.00  0.00              
ATOM    186  CA  PHE    60       5.029  -1.923 -27.947  1.00  0.00              
ATOM    187  C   PHE    60       4.064  -2.340 -26.849  1.00  0.00              
ATOM    188  O   PHE    60       2.910  -1.920 -26.851  1.00  0.00              
ATOM    189  N   GLU    61       4.512  -3.170 -25.922  1.00  0.00              
ATOM    190  CA  GLU    61       3.626  -3.629 -24.868  1.00  0.00              
ATOM    191  C   GLU    61       3.217  -2.561 -23.878  1.00  0.00              
ATOM    192  O   GLU    61       2.271  -2.761 -23.120  1.00  0.00              
ATOM    193  N   LEU    62       3.921  -1.437 -23.872  1.00  0.00              
ATOM    194  CA  LEU    62       3.561  -0.354 -22.970  1.00  0.00              
ATOM    195  C   LEU    62       4.179   1.004 -23.345  1.00  0.00              
ATOM    196  O   LEU    62       5.146   1.067 -24.102  1.00  0.00              
ATOM    197  N   HIS    63       3.598   2.078 -22.817  1.00  0.00              
ATOM    198  CA  HIS    63       4.059   3.438 -23.056  1.00  0.00              
ATOM    199  C   HIS    63       4.214   4.141 -21.711  1.00  0.00              
ATOM    200  O   HIS    63       3.437   3.878 -20.790  1.00  0.00              
END
