
#######################################################
#                                                     #
#                        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  119 (  119),  selected  119 , name T0382TS168_2-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS168_2-D1.T0382_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L       4      L       4           -
LGA    D       5      D       5           -
LGA    L       6      L       6           -
LGA    H       7      H       7           -
LGA    Q       8      Q       8           -
LGA    M       9      -       -           -
LGA    T      10      -       -           -
LGA    T      11      -       -           -
LGA    Q      12      -       -           -
LGA    D      13      -       -           -
LGA    L      14      -       -           -
LGA    V      15      M       9          3.412
LGA    A      16      -       -           -
LGA    L      17      -       -           -
LGA    F      18      -       -           -
LGA    A      19      -       -           -
LGA    K      20      -       -           -
LGA    V      21      -       -           -
LGA    T      22      -       -           -
LGA    V      23      -       -           -
LGA    E      24      -       -           -
LGA    Q      25      -       -           -
LGA    D      26      -       -           -
LGA    D      27      -       -           -
LGA    A      28      -       -           -
LGA    L      29      -       -           -
LGA    L      30      -       -           -
LGA    G      31      -       -           -
LGA    N      32      -       -           -
LGA    Q      33      T      10          3.641
LGA    I      34      T      11          2.093
LGA    S      35      -       -           -
LGA    R      36      Q      12          1.188
LGA    F      37      D      13          1.408
LGA    N      38      L      14          1.697
LGA    R      39      V      15          1.286
LGA    L      40      A      16          1.152
LGA    F      41      L      17          1.916
LGA    G      42      F      18          1.982
LGA    V      43      A      19          1.282
LGA    M      44      K      20          1.670
LGA    A      45      V      21          2.873
LGA    E      46      T      22          2.744
LGA    I      47      V      23          1.331
LGA    A      48      E      24          2.074
LGA    D      49      Q      25          2.942
LGA    E      50      D      26          2.593
LGA    L      51      D      27          2.228
LGA    K      52      A      28          3.511
LGA    A      53      L      29          3.428
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    R      54      F      37          0.549
LGA    D      55      N      38          1.476
LGA    G      56      R      39          3.301
LGA    -       -      L      40           -
LGA    -       -      F      41           -
LGA    -       -      G      42           -
LGA    D      57      V      43          1.320
LGA    Q      58      M      44          1.399
LGA    R      59      A      45          0.875
LGA    T      60      E      46          1.371
LGA    A      61      I      47          2.179
LGA    L      62      A      48          2.380
LGA    L      63      D      49          2.377
LGA    S      64      E      50          3.110
LGA    L      65      L      51          3.614
LGA    F      66      K      52          3.800
LGA    E      67      A      53          4.217
LGA    Y      68      -       -           -
LGA    P      69      -       -           -
LGA    N      70      -       -           -
LGA    M      71      -       -           -
LGA    Q      72      -       -           -
LGA    V      73      -       -           -
LGA    R      74      R      54          4.500
LGA    L      75      D      55          2.808
LGA    Q      76      G      56          1.842
LGA    A      77      D      57          4.808
LGA    A      78      Q      58          0.558
LGA    K      79      R      59          3.247
LGA    L      80      T      60          1.658
LGA    T      81      A      61          2.346
LGA    L      82      L      62          4.345
LGA    A      83      -       -           -
LGA    V      84      L      63          2.009
LGA    A      85      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    P      86      A      78          1.072
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    V      87      R      90          6.078
LGA    K      88      E      91           -
LGA    A      89      -       -           -
LGA    R      90      Q      92          3.743
LGA    E      91      L      93          5.032
LGA    Q      92      E      94           -
LGA    -       -      A      95           -
LGA    L      93      I      96          2.512
LGA    E      94      V      97          3.143
LGA    A      95      S      98          5.580
LGA    I      96      S      99          3.895
LGA    V      97      K     100          0.796
LGA    S      98      W     101           #
LGA    S      99      -       -           -
LGA    K     100      F     102           #
LGA    W     101      P     103           #
LGA    F     102      Q     104           #
LGA    -       -      A     105           -
LGA    P     103      G     106          2.832
LGA    Q     104      D     107           #
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    A     105      M     110           #
LGA    G     106      C     111           #
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    D     107      L     114           #
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    A     108      P     122           #
LGA    G     109      -       -           -
LGA    M     110      -       -           -
LGA    C     111      -       -           -
LGA    L     112      -       -           -
LGA    D     113      -       -           -
LGA    L     114      -       -           -
LGA    L     115      -       -           -
LGA    D     116      -       -           -
LGA    D     117      -       -           -
LGA    G     118      -       -           -
LGA    T     119      -       -           -
LGA    F     120      -       -           -
LGA    K     121      -       -           -
LGA    P     122      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  119  119    5.0     55    2.87     5.45     31.841     1.852

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.141179 * X  +   0.496237 * Y  +   0.856632 * Z  + -15.750764
  Y_new =  -0.290094 * X  +  -0.806578 * Y  +   0.515051 * Z  +  41.510426
  Z_new =   0.946527 * X  +  -0.321218 * Y  +   0.030084 * Z  +  -2.971577 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.477414    1.664179  [ DEG:   -84.6496     95.3504 ]
  Theta =  -1.242296   -1.899296  [ DEG:   -71.1783   -108.8217 ]
  Phi   =  -1.117873    2.023720  [ DEG:   -64.0494    115.9506 ]
 
# 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: T0382TS168_2-D1                               
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS168_2-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  119  119   5.0   55   2.87    5.45  31.841
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS168_2-D1
PFRMAT TS
TARGET T0382
MODEL 2
PARENT N/A
ATOM      4  CA  LEU     4     -15.798  19.913  -2.428  1.00 25.00           C
ATOM      5  CA  ASP     5     -14.786  23.608  -2.416  1.00 25.00           C
ATOM      6  CA  LEU     6     -18.029  24.642  -4.174  1.00 25.00           C
ATOM      7  CA  HIS     7     -17.085  28.334  -3.796  1.00 25.00           C
ATOM      8  CA  GLN     8     -13.616  27.623  -5.255  1.00 25.00           C
ATOM      9  CA  MET     9     -15.211  25.782  -8.211  1.00 25.00           C
ATOM     10  CA  THR    10     -17.571  28.737  -8.809  1.00 25.00           C
ATOM     11  CA  THR    11     -14.603  31.156  -8.730  1.00 25.00           C
ATOM     12  CA  GLN    12     -12.719  28.965 -11.243  1.00 25.00           C
ATOM     13  CA  ASP    13     -15.788  28.912 -13.534  1.00 25.00           C
ATOM     14  CA  LEU    14     -16.051  32.726 -13.310  1.00 25.00           C
ATOM     15  CA  VAL    15     -12.337  33.059 -14.181  1.00 25.00           C
ATOM     16  CA  ALA    16     -12.809  30.734 -17.188  1.00 25.00           C
ATOM     17  CA  LEU    17     -15.805  32.813 -18.357  1.00 25.00           C
ATOM     18  CA  PHE    18     -13.739  36.021 -18.029  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.906  34.432 -20.059  1.00 25.00           C
ATOM     20  CA  LYS    20     -13.401  33.381 -22.766  1.00 25.00           C
ATOM     21  CA  VAL    21     -14.813  36.940 -22.880  1.00 25.00           C
ATOM     22  CA  THR    22     -15.780  38.188 -26.361  1.00 25.00           C
ATOM     23  CA  VAL    23     -18.199  39.949 -28.802  1.00 25.00           C
ATOM     24  CA  GLU    24     -18.860  43.172 -26.843  1.00 25.00           C
ATOM     25  CA  GLN    25     -21.813  41.510 -25.058  1.00 25.00           C
ATOM     26  CA  ASP    26     -19.616  38.501 -24.172  1.00 25.00           C
ATOM     27  CA  ASP    27     -16.916  40.846 -22.800  1.00 25.00           C
ATOM     28  CA  ALA    28     -19.541  42.677 -20.698  1.00 25.00           C
ATOM     29  CA  LEU    29     -20.819  39.335 -19.335  1.00 25.00           C
ATOM     30  CA  LEU    30     -17.239  38.301 -18.446  1.00 25.00           C
ATOM     31  CA  GLY    31     -16.695  41.641 -16.653  1.00 25.00           C
ATOM     32  CA  ASN    32     -19.952  41.151 -14.700  1.00 25.00           C
ATOM     33  CA  GLN    33     -18.856  37.619 -13.706  1.00 25.00           C
ATOM     34  CA  ILE    34     -15.468  38.972 -12.539  1.00 25.00           C
ATOM     35  CA  SER    35     -17.230  41.672 -10.473  1.00 25.00           C
ATOM     36  CA  ARG    36     -19.496  39.019  -8.893  1.00 25.00           C
ATOM     37  CA  PHE    37     -16.435  36.878  -8.043  1.00 25.00           C
ATOM     38  CA  ASN    38     -14.724  39.912  -6.453  1.00 25.00           C
ATOM     39  CA  ARG    39     -17.868  40.637  -4.391  1.00 25.00           C
ATOM     40  CA  LEU    40     -17.977  36.989  -3.232  1.00 25.00           C
ATOM     41  CA  PHE    41     -14.285  37.169  -2.233  1.00 25.00           C
ATOM     42  CA  GLY    42     -14.947  40.392  -0.273  1.00 25.00           C
ATOM     43  CA  VAL    43     -17.900  38.730   1.512  1.00 25.00           C
ATOM     44  CA  MET    44     -15.702  35.722   2.397  1.00 25.00           C
ATOM     45  CA  ALA    45     -13.002  38.066   3.770  1.00 25.00           C
ATOM     46  CA  GLU    46     -15.626  39.898   5.872  1.00 25.00           C
ATOM     47  CA  ILE    47     -16.904  36.554   7.234  1.00 25.00           C
ATOM     48  CA  ALA    48     -13.325  35.521   8.124  1.00 25.00           C
ATOM     49  CA  ASP    49     -12.780  38.861   9.917  1.00 25.00           C
ATOM     50  CA  GLU    50     -16.038  38.372  11.870  1.00 25.00           C
ATOM     51  CA  LEU    51     -14.941  34.839  12.864  1.00 25.00           C
ATOM     52  CA  LYS    52     -11.553  36.192  14.030  1.00 25.00           C
ATOM     53  CA  ALA    53      -8.885  35.907  11.323  1.00 25.00           C
ATOM     54  CA  ARG    54      -6.299  36.993   8.752  1.00 25.00           C
ATOM     55  CA  ASP    55      -4.021  39.092   6.579  1.00 25.00           C
ATOM     56  CA  GLY    56      -3.633  39.045   2.781  1.00 25.00           C
ATOM     57  CA  ASP    57      -6.563  38.101   0.572  1.00 25.00           C
ATOM     58  CA  GLN    58      -9.103  40.242  -1.316  1.00 25.00           C
ATOM     59  CA  ARG    59      -6.613  43.140  -1.576  1.00 25.00           C
ATOM     60  CA  THR    60      -4.637  41.233  -4.247  1.00 25.00           C
ATOM     61  CA  ALA    61      -7.864  40.581  -6.204  1.00 25.00           C
ATOM     62  CA  LEU    62      -8.770  44.296  -5.999  1.00 25.00           C
ATOM     63  CA  LEU    63      -5.279  45.241  -7.258  1.00 25.00           C
ATOM     64  CA  SER    64      -5.635  42.779 -10.171  1.00 25.00           C
ATOM     65  CA  LEU    65      -9.053  44.272 -11.045  1.00 25.00           C
ATOM     66  CA  PHE    66      -7.559  47.797 -10.974  1.00 25.00           C
ATOM     67  CA  GLU    67      -4.711  46.662 -13.269  1.00 25.00           C
ATOM     68  CA  TYR    68      -3.109  50.130 -13.763  1.00 25.00           C
ATOM     69  CA  PRO    69      -6.443  51.016 -15.447  1.00 25.00           C
ATOM     70  CA  ASN    70      -8.944  49.899 -18.100  1.00 25.00           C
ATOM     71  CA  MET    71     -12.374  49.267 -19.716  1.00 25.00           C
ATOM     72  CA  GLN    72     -13.310  52.626 -18.129  1.00 25.00           C
ATOM     73  CA  VAL    73     -16.892  51.390 -17.568  1.00 25.00           C
ATOM     74  CA  ARG    74     -15.558  48.188 -15.942  1.00 25.00           C
ATOM     75  CA  LEU    75     -13.287  50.264 -13.662  1.00 25.00           C
ATOM     76  CA  GLN    76     -16.256  52.471 -12.673  1.00 25.00           C
ATOM     77  CA  ALA    77     -18.343  49.358 -11.890  1.00 25.00           C
ATOM     78  CA  ALA    78     -15.497  47.958  -9.744  1.00 25.00           C
ATOM     79  CA  LYS    79     -15.245  51.286  -7.865  1.00 25.00           C
ATOM     80  CA  LEU    80     -19.025  51.257  -7.257  1.00 25.00           C
ATOM     81  CA  THR    81     -18.811  47.667  -5.941  1.00 25.00           C
ATOM     82  CA  LEU    82     -15.951  48.671  -3.600  1.00 25.00           C
ATOM     83  CA  ALA    83     -18.007  51.639  -2.322  1.00 25.00           C
ATOM     84  CA  VAL    84     -20.999  49.333  -1.700  1.00 25.00           C
ATOM     85  CA  ALA    85     -18.752  46.892   0.213  1.00 25.00           C
ATOM     86  CA  PRO    86     -17.387  49.775   2.334  1.00 25.00           C
ATOM     87  CA  VAL    87     -20.954  50.941   3.090  1.00 25.00           C
ATOM     88  CA  LYS    88     -21.929  47.382   4.114  1.00 25.00           C
ATOM     89  CA  ALA    89     -18.868  47.179   6.408  1.00 25.00           C
ATOM     90  CA  ARG    90     -19.805  50.537   7.995  1.00 25.00           C
ATOM     91  CA  GLU    91     -23.386  49.300   8.556  1.00 25.00           C
ATOM     92  CA  GLN    92     -22.054  46.100  10.181  1.00 25.00           C
ATOM     93  CA  LEU    93     -19.782  48.174  12.462  1.00 25.00           C
ATOM     94  CA  GLU    94     -22.751  50.383  13.451  1.00 25.00           C
ATOM     95  CA  ALA    95     -24.838  47.269  14.233  1.00 25.00           C
ATOM     96  CA  ILE    96     -21.992  45.869  16.380  1.00 25.00           C
ATOM     97  CA  VAL    97     -21.740  49.198  18.258  1.00 25.00           C
ATOM     98  CA  SER    98     -25.522  49.168  18.866  1.00 25.00           C
ATOM     99  CA  SER    99     -25.306  45.578  20.183  1.00 25.00           C
ATOM    100  CA  LYS   100     -22.144  45.732  22.290  1.00 25.00           C
ATOM    101  CA  TRP   101     -18.528  46.683  21.547  1.00 25.00           C
ATOM    102  CA  PHE   102     -16.469  48.801  19.195  1.00 25.00           C
ATOM    103  CA  PRO   103     -13.474  51.066  19.446  1.00 25.00           C
ATOM    104  CA  GLN   104     -10.384  52.987  18.388  1.00 25.00           C
ATOM    105  CA  ALA   105      -7.532  53.692  16.024  1.00 25.00           C
ATOM    106  CA  GLY   106      -5.267  54.862  13.146  1.00 25.00           C
ATOM    107  CA  ASP   107      -4.565  54.701   9.376  1.00 25.00           C
ATOM    108  CA  ALA   108      -6.344  53.440   6.259  1.00 25.00           C
ATOM    109  CA  GLY   109      -7.789  51.236   3.477  1.00 25.00           C
ATOM    110  CA  MET   110      -7.800  48.580   0.718  1.00 25.00           C
ATOM    111  CA  CYS   111      -9.158  45.987   3.186  1.00 25.00           C
ATOM    112  CA  LEU   112     -11.910  48.421   4.268  1.00 25.00           C
ATOM    113  CA  ASP   113     -12.831  49.046   0.604  1.00 25.00           C
ATOM    114  CA  LEU   114     -12.994  45.273  -0.025  1.00 25.00           C
ATOM    115  CA  LEU   115     -15.251  44.835   3.038  1.00 25.00           C
ATOM    116  CA  ASP   116     -18.649  43.214   3.627  1.00 25.00           C
ATOM    117  CA  ASP   117     -22.333  42.387   3.644  1.00 25.00           C
ATOM    118  CA  GLY   118     -25.881  41.231   2.682  1.00 25.00           C
ATOM    119  CA  THR   119     -29.550  40.806   3.567  1.00 25.00           C
ATOM    120  CA  PHE   120     -33.266  39.972   3.610  1.00 25.00           C
ATOM    121  CA  LYS   121     -36.586  39.421   1.732  1.00 25.00           C
ATOM    122  CA  PRO   122     -36.822  35.841   0.445  1.00 25.00           C
TER
END
