
#######################################################
#                                                     #
#                        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   40 (  160),  selected   40 , name T0352TS383_2
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS383_2.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      T       2           -
LGA    T       3      T       3          1.962
LGA    H       4      H       4          1.409
LGA    D       5      D       5          0.775
LGA    R       6      R       6          0.637
LGA    V       7      V       7          0.820
LGA    R       8      R       8          0.596
LGA    L       9      L       9          0.512
LGA    Q      10      Q      10          0.606
LGA    L      11      L      11          1.732
LGA    Q      12      Q      12          2.101
LGA    A      13      A      13          1.130
LGA    L      14      L      14          0.720
LGA    E      15      E      15          1.790
LGA    A      16      A      16          1.859
LGA    L      17      L      17          0.829
LGA    L      18      L      18          0.389
LGA    R      19      R      19          0.602
LGA    E      20      E      20          1.157
LGA    H      21      H      21          1.310
LGA    Q      22      Q      22          0.777
LGA    -       -      H      23           -
LGA    -       -      W      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      E      28           -
LGA    -       -      P      29           -
LGA    -       -      Q      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      Q      33           -
LGA    -       -      F      34           -
LGA    -       -      N      35           -
LGA    -       -      S      36           -
LGA    H      23      T      37          1.978
LGA    R      25      Q      38          1.821
LGA    -       -      P      39           -
LGA    -       -      F      40           -
LGA    N      26      F      41          3.176
LGA    D      27      M      42           #
LGA    E      28      D      43           -
LGA    P      29      -       -           -
LGA    Q      30      -       -           -
LGA    P      31      T      44           #
LGA    H      32      -       -           -
LGA    Q      33      -       -           -
LGA    F      34      M      45           #
LGA    N      35      E      46          2.655
LGA    S      36      P      47          2.348
LGA    T      37      L      48          3.408
LGA    Q      38      E      49          1.998
LGA    P      39      W      50          3.992
LGA    F      40      L      51          3.818
LGA    F      41      -       -           -
LGA    M      42      -       -           -
LGA    D      43      Q      52          2.250
LGA    -       -      W      53           -
LGA    -       -      V      54           -
LGA    -       -      L      55           -
LGA    -       -      I      56           -
LGA    -       -      P      57           -
LGA    -       -      R      58           -
LGA    -       -      M      59           -
LGA    -       -      H      60           -
LGA    -       -      D      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    -       -      N      65           -
LGA    -       -      K      66           -
LGA    -       -      Q      67           -
LGA    -       -      P      68           -
LGA    -       -      L      69           -
LGA    -       -      P      70           -
LGA    -       -      G      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      A      74           -
LGA    -       -      V      75           -
LGA    -       -      A      76           -
LGA    -       -      P      77           -
LGA    -       -      Y      78           -
LGA    -       -      Y      79           -
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      A      82           -
LGA    -       -      L      83           -
LGA    -       -      A      84           -
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    -       -      H      87           -
LGA    -       -      P      88           -
LGA    -       -      Q      89           -
LGA    -       -      R      90           -
LGA    -       -      A      91           -
LGA    -       -      L      92           -
LGA    -       -      I      93           -
LGA    -       -      L      94           -
LGA    -       -      A      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      E      98           -
LGA    -       -      K      99           -
LGA    -       -      L     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      A     105           -
LGA    -       -      D     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      S     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40  109    5.0     30    1.92    66.67     22.558     1.487

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.062390 * X  +  -0.080000 * Y  +   0.994840 * Z  + -101.033211
  Y_new =   0.494007 * X  +   0.868589 * Y  +   0.038867 * Z  + -89.061287
  Z_new =  -0.867216 * X  +   0.489033 * Y  +   0.093712 * Z  + -19.116774 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.381465   -1.760128  [ DEG:    79.1521   -100.8479 ]
  Theta =   1.049585    2.092008  [ DEG:    60.1368    119.8632 ]
  Phi   =   1.445168   -1.696424  [ DEG:    82.8020    -97.1980 ]
 
# 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: T0352TS383_2                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS383_2.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40  109   5.0   30   1.92   66.67  22.558
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS383_2
PFRMAT TS
TARGET T0352
MODEL 2
PARENT 1pyiA
ATOM      1  N   THR     3      -0.878  -4.661  -5.848  1.00  0.00
ATOM      2  CA  THR     3      -1.736  -4.127  -4.807  1.00  0.00
ATOM      3  C   THR     3      -1.931  -2.677  -5.068  1.00  0.00
ATOM      4  O   THR     3      -3.032  -2.160  -4.925  1.00  0.00
ATOM      5  N   HIS     4      -0.842  -2.066  -5.508  1.00  0.00
ATOM      6  CA  HIS     4      -0.923  -0.694  -5.963  1.00  0.00
ATOM      7  C   HIS     4      -1.695  -0.676  -7.267  1.00  0.00
ATOM      8  O   HIS     4      -2.422   0.277  -7.536  1.00  0.00
ATOM      9  N   ASP     5      -1.493  -1.709  -8.100  1.00  0.00
ATOM     10  CA  ASP     5      -2.171  -1.706  -9.379  1.00  0.00
ATOM     11  C   ASP     5      -3.630  -1.495  -9.159  1.00  0.00
ATOM     12  O   ASP     5      -4.222  -0.505  -9.581  1.00  0.00
ATOM     13  N   ARG     6      -4.148  -2.391  -8.366  1.00  0.00
ATOM     14  CA  ARG     6      -5.569  -2.384  -8.180  1.00  0.00
ATOM     15  C   ARG     6      -6.080  -1.208  -7.380  1.00  0.00
ATOM     16  O   ARG     6      -7.145  -0.632  -7.582  1.00  0.00
ATOM     17  N   VAL     7      -5.302  -0.900  -6.413  1.00  0.00
ATOM     18  CA  VAL     7      -5.653   0.217  -5.643  1.00  0.00
ATOM     19  C   VAL     7      -5.695   1.389  -6.588  1.00  0.00
ATOM     20  O   VAL     7      -6.480   2.308  -6.453  1.00  0.00
ATOM     21  N   ARG     8      -4.892   1.353  -7.628  1.00  0.00
ATOM     22  CA  ARG     8      -5.011   2.517  -8.472  1.00  0.00
ATOM     23  C   ARG     8      -6.288   2.457  -9.235  1.00  0.00
ATOM     24  O   ARG     8      -6.885   3.466  -9.572  1.00  0.00
ATOM     25  N   LEU     9      -6.652   1.253  -9.580  1.00  0.00
ATOM     26  CA  LEU     9      -7.843   1.082 -10.357  1.00  0.00
ATOM     27  C   LEU     9      -9.032   1.636  -9.581  1.00  0.00
ATOM     28  O   LEU     9      -9.787   2.504 -10.003  1.00  0.00
ATOM     29  N   GLN    10      -9.100   1.226  -8.344  1.00  0.00
ATOM     30  CA  GLN    10     -10.117   1.694  -7.456  1.00  0.00
ATOM     31  C   GLN    10     -10.268   3.212  -7.381  1.00  0.00
ATOM     32  O   GLN    10     -11.370   3.708  -7.172  1.00  0.00
ATOM     33  N   LEU    11      -9.204   3.990  -7.558  1.00  0.00
ATOM     34  CA  LEU    11      -9.480   5.424  -7.585  1.00  0.00
ATOM     35  C   LEU    11     -10.252   5.580  -8.872  1.00  0.00
ATOM     36  O   LEU    11     -11.145   6.394  -9.033  1.00  0.00
ATOM     37  N   GLN    12      -9.845   4.803  -9.839  1.00  0.00
ATOM     38  CA  GLN    12     -10.385   5.025 -11.148  1.00  0.00
ATOM     39  C   GLN    12     -11.895   4.969 -11.232  1.00  0.00
ATOM     40  O   GLN    12     -12.587   5.853 -11.774  1.00  0.00
ATOM     41  N   ALA    13     -12.358   3.893 -10.632  1.00  0.00
ATOM     42  CA  ALA    13     -13.760   3.689 -10.594  1.00  0.00
ATOM     43  C   ALA    13     -14.353   4.858  -9.883  1.00  0.00
ATOM     44  O   ALA    13     -15.277   5.504 -10.367  1.00  0.00
ATOM     45  N   LEU    14     -13.781   5.059  -8.702  1.00  0.00
ATOM     46  CA  LEU    14     -14.220   6.080  -7.788  1.00  0.00
ATOM     47  C   LEU    14     -14.313   7.436  -8.412  1.00  0.00
ATOM     48  O   LEU    14     -15.123   8.252  -8.002  1.00  0.00
ATOM     49  N   GLU    15     -13.430   7.682  -9.355  1.00  0.00
ATOM     50  CA  GLU    15     -13.416   8.975  -9.975  1.00  0.00
ATOM     51  C   GLU    15     -14.483   9.078 -11.045  1.00  0.00
ATOM     52  O   GLU    15     -15.019  10.162 -11.291  1.00  0.00
ATOM     53  N   ALA    16     -14.802   7.945 -11.690  1.00  0.00
ATOM     54  CA  ALA    16     -15.869   7.997 -12.674  1.00  0.00
ATOM     55  C   ALA    16     -17.067   8.300 -11.825  1.00  0.00
ATOM     56  O   ALA    16     -17.521   9.433 -11.786  1.00  0.00
ATOM     57  N   LEU    17     -17.410   7.345 -10.980  1.00  0.00
ATOM     58  CA  LEU    17     -18.553   7.459 -10.100  1.00  0.00
ATOM     59  C   LEU    17     -18.838   8.842  -9.511  1.00  0.00
ATOM     60  O   LEU    17     -19.806   9.507  -9.854  1.00  0.00
ATOM     61  N   LEU    18     -17.959   9.296  -8.639  1.00  0.00
ATOM     62  CA  LEU    18     -18.080  10.540  -7.895  1.00  0.00
ATOM     63  C   LEU    18     -18.131  11.769  -8.781  1.00  0.00
ATOM     64  O   LEU    18     -18.499  12.866  -8.365  1.00  0.00
ATOM     65  N   ARG    19     -17.724  11.547 -10.021  1.00  0.00
ATOM     66  CA  ARG    19     -17.703  12.590 -11.031  1.00  0.00
ATOM     67  C   ARG    19     -19.100  12.660 -11.626  1.00  0.00
ATOM     68  O   ARG    19     -19.705  13.742 -11.696  1.00  0.00
ATOM     69  N   GLU    20     -19.592  11.450 -11.971  1.00  0.00
ATOM     70  CA  GLU    20     -20.944  11.232 -12.455  1.00  0.00
ATOM     71  C   GLU    20     -21.857  11.991 -11.492  1.00  0.00
ATOM     72  O   GLU    20     -22.525  12.951 -11.860  1.00  0.00
ATOM     73  N   HIS    21     -21.854  11.591 -10.217  1.00  0.00
ATOM     74  CA  HIS    21     -22.732  12.229  -9.263  1.00  0.00
ATOM     75  C   HIS    21     -22.532  13.692  -9.121  1.00  0.00
ATOM     76  O   HIS    21     -23.066  14.276  -8.184  1.00  0.00
ATOM     77  N   GLN    22     -21.653  14.239  -9.928  1.00  0.00
ATOM     78  CA  GLN    22     -21.408  15.648  -9.831  1.00  0.00
ATOM     79  C   GLN    22     -20.300  16.079  -8.890  1.00  0.00
ATOM     80  O   GLN    22     -20.511  17.129  -8.281  1.00  0.00
ATOM     81  N   HIS    23     -11.812  16.117  -7.793  1.00  0.00
ATOM     82  CA  HIS    23     -10.706  16.254  -6.777  1.00  0.00
ATOM     83  C   HIS    23     -10.906  16.536  -5.245  1.00  0.00
ATOM     84  O   HIS    23     -11.051  17.688  -4.783  1.00  0.00
ATOM     85  N   ARG    25     -10.653  15.492  -4.421  1.00  0.00
ATOM     86  CA  ARG    25     -10.828  15.481  -2.953  1.00  0.00
ATOM     87  C   ARG    25      -9.754  15.945  -1.914  1.00  0.00
ATOM     88  O   ARG    25      -8.542  15.715  -1.975  1.00  0.00
ATOM     89  N   ASN    26     -10.213  16.563  -0.833  1.00  0.00
ATOM     90  CA  ASN    26      -9.333  16.903   0.276  1.00  0.00
ATOM     91  C   ASN    26      -8.904  15.575   0.921  1.00  0.00
ATOM     92  O   ASN    26      -9.754  14.699   1.034  1.00  0.00
ATOM     93  N   ASP    27      -7.643  15.412   1.379  1.00  0.00
ATOM     94  CA  ASP    27      -7.105  14.144   1.919  1.00  0.00
ATOM     95  C   ASP    27      -6.592  13.951   3.392  1.00  0.00
ATOM     96  O   ASP    27      -7.370  13.839   4.331  1.00  0.00
ATOM     97  N   GLU    28      -5.274  13.783   3.586  1.00  0.00
ATOM     98  CA  GLU    28      -4.559  13.552   4.831  1.00  0.00
ATOM     99  C   GLU    28      -3.044  13.305   4.620  1.00  0.00
ATOM    100  O   GLU    28      -2.238  14.169   4.895  1.00  0.00
ATOM    101  N   PRO    29      -2.568  12.209   4.018  1.00  0.00
ATOM    102  CA  PRO    29      -1.162  12.159   3.637  1.00  0.00
ATOM    103  C   PRO    29      -1.082  13.136   2.437  1.00  0.00
ATOM    104  O   PRO    29      -2.113  13.601   1.980  1.00  0.00
ATOM    105  N   GLN    30       0.035  13.559   1.850  1.00  0.00
ATOM    106  CA  GLN    30      -0.221  14.490   0.752  1.00  0.00
ATOM    107  C   GLN    30       0.926  14.670  -0.222  1.00  0.00
ATOM    108  O   GLN    30       2.043  14.296   0.118  1.00  0.00
ATOM    109  N   PRO    31       0.618  15.299  -1.374  1.00  0.00
ATOM    110  CA  PRO    31       1.431  15.451  -2.586  1.00  0.00
ATOM    111  C   PRO    31       2.367  16.654  -2.826  1.00  0.00
ATOM    112  O   PRO    31       3.565  16.455  -3.060  1.00  0.00
ATOM    113  N   HIS    32       1.862  17.893  -2.898  1.00  0.00
ATOM    114  CA  HIS    32       2.787  18.995  -3.092  1.00  0.00
ATOM    115  C   HIS    32       3.215  19.721  -1.802  1.00  0.00
ATOM    116  O   HIS    32       2.513  19.740  -0.788  1.00  0.00
ATOM    117  N   GLN    33       4.359  20.414  -1.849  1.00  0.00
ATOM    118  CA  GLN    33       4.818  21.181  -0.699  1.00  0.00
ATOM    119  C   GLN    33       3.830  22.285  -0.375  1.00  0.00
ATOM    120  O   GLN    33       4.117  23.156   0.447  1.00  0.00
ATOM    121  N   PHE    34       2.696  22.263  -1.089  1.00  0.00
ATOM    122  CA  PHE    34       1.629  23.239  -0.997  1.00  0.00
ATOM    123  C   PHE    34       0.327  22.639  -0.493  1.00  0.00
ATOM    124  O   PHE    34      -0.664  23.338  -0.526  1.00  0.00
ATOM    125  N   ASN    35       0.237  21.377  -0.028  1.00  0.00
ATOM    126  CA  ASN    35      -1.052  21.016   0.569  1.00  0.00
ATOM    127  C   ASN    35      -0.888  21.350   2.037  1.00  0.00
ATOM    128  O   ASN    35       0.137  21.932   2.397  1.00  0.00
ATOM    129  N   SER    36      -1.844  20.971   2.894  1.00  0.00
ATOM    130  CA  SER    36      -1.734  21.207   4.348  1.00  0.00
ATOM    131  C   SER    36      -1.097  19.927   4.943  1.00  0.00
ATOM    132  O   SER    36      -1.026  18.919   4.244  1.00  0.00
ATOM    133  N   THR    37      -0.638  19.845   6.193  1.00  0.00
ATOM    134  CA  THR    37       0.018  18.601   6.641  1.00  0.00
ATOM    135  C   THR    37      -0.795  17.544   7.393  1.00  0.00
ATOM    136  O   THR    37      -1.956  17.740   7.730  1.00  0.00
ATOM    137  N   GLN    38      -0.157  16.415   7.761  1.00  0.00
ATOM    138  CA  GLN    38      -0.861  15.373   8.508  1.00  0.00
ATOM    139  C   GLN    38      -0.992  15.737   9.984  1.00  0.00
ATOM    140  O   GLN    38      -0.162  16.575  10.308  1.00  0.00
ATOM    141  N   PRO    39      -1.958  15.177  10.836  1.00  0.00
ATOM    142  CA  PRO    39      -2.036  15.160  12.333  1.00  0.00
ATOM    143  C   PRO    39      -2.779  13.915  12.929  1.00  0.00
ATOM    144  O   PRO    39      -3.993  13.821  12.744  1.00  0.00
ATOM    145  N   PHE    40      -2.065  12.986  13.660  1.00  0.00
ATOM    146  CA  PHE    40      -2.545  11.696  14.221  1.00  0.00
ATOM    147  C   PHE    40      -4.025  11.675  14.509  1.00  0.00
ATOM    148  O   PHE    40      -4.534  12.682  14.975  1.00  0.00
ATOM    149  N   PHE    41      -4.747  10.597  14.176  1.00  0.00
ATOM    150  CA  PHE    41      -6.201  10.603  14.389  1.00  0.00
ATOM    151  C   PHE    41      -7.029  11.499  13.403  1.00  0.00
ATOM    152  O   PHE    41      -7.566  11.048  12.381  1.00  0.00
ATOM    153  N   MET    42      -6.970  12.810  13.670  1.00  0.00
ATOM    154  CA  MET    42      -7.756  13.979  13.292  1.00  0.00
ATOM    155  C   MET    42      -7.983  14.713  11.955  1.00  0.00
ATOM    156  O   MET    42      -8.815  15.609  12.019  1.00  0.00
ATOM    157  N   ASP    43      -7.324  14.562  10.803  1.00  0.00
ATOM    158  CA  ASP    43      -7.662  15.449   9.659  1.00  0.00
ATOM    159  C   ASP    43      -7.521  16.945   9.997  1.00  0.00
ATOM    160  O   ASP    43      -7.384  17.835   9.137  1.00  0.00
TER
END
