
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0382TS393_4
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS393_4.T0382.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      K       3           -
LGA    S       2      L       4           -
LGA    K       3      D       5           -
LGA    L       4      L       6           -
LGA    D       5      H       7           -
LGA    L       6      Q       8           -
LGA    H       7      M       9           -
LGA    Q       8      T      10           -
LGA    M       9      T      11           -
LGA    T      10      Q      12           -
LGA    T      11      D      13           -
LGA    Q      12      L      14           -
LGA    D      13      V      15           -
LGA    L      14      A      16           -
LGA    V      15      L      17           -
LGA    A      16      F      18           -
LGA    L      17      A      19           -
LGA    F      18      K      20           -
LGA    A      19      V      21           -
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      -       -           -
LGA    I      34      -       -           -
LGA    S      35      -       -           -
LGA    R      36      -       -           -
LGA    F      37      -       -           -
LGA    N      38      -       -           -
LGA    R      39      -       -           -
LGA    L      40      -       -           -
LGA    F      41      -       -           -
LGA    G      42      -       -           -
LGA    V      43      -       -           -
LGA    M      44      T      22           #
LGA    A      45      V      23           -
LGA    E      46      E      24           -
LGA    I      47      Q      25          4.763
LGA    A      48      -       -           -
LGA    D      49      -       -           -
LGA    E      50      D      26           #
LGA    L      51      D      27          3.055
LGA    K      52      A      28          4.897
LGA    A      53      L      29          4.012
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    R      54      R      36          3.938
LGA    D      55      F      37          4.238
LGA    -       -      N      38           -
LGA    G      56      R      39          3.760
LGA    D      57      L      40          3.695
LGA    Q      58      F      41          2.264
LGA    R      59      G      42          3.148
LGA    T      60      V      43          2.495
LGA    A      61      M      44          1.495
LGA    L      62      A      45          1.957
LGA    L      63      E      46          1.853
LGA    S      64      I      47          2.199
LGA    L      65      A      48          2.470
LGA    F      66      D      49          1.822
LGA    E      67      E      50          2.013
LGA    Y      68      L      51          4.913
LGA    P      69      K      52           -
LGA    N      70      A      53           #
LGA    M      71      R      54          4.695
LGA    Q      72      D      55          1.873
LGA    V      73      -       -           -
LGA    R      74      -       -           -
LGA    L      75      G      56          3.758
LGA    Q      76      D      57          3.261
LGA    A      77      Q      58          1.632
LGA    A      78      R      59          2.881
LGA    K      79      T      60          3.705
LGA    L      80      A      61          3.124
LGA    T      81      L      62          3.270
LGA    L      82      -       -           -
LGA    A      83      -       -           -
LGA    V      84      L      63          3.830
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    P      86      Q      76           #
LGA    V      87      A      77          4.762
LGA    K      88      A      78          4.266
LGA    A      89      K      79          4.742
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    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    R      90      L      93          1.852
LGA    E      91      E      94           #
LGA    Q      92      A      95           -
LGA    L      93      I      96          4.433
LGA    E      94      V      97          1.822
LGA    A      95      S      98           #
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    I      96      A     105          2.815
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    V      97      G     109           #
LGA    S      98      -       -           -
LGA    S      99      -       -           -
LGA    K     100      -       -           -
LGA    W     101      -       -           -
LGA    F     102      -       -           -
LGA    P     103      M     110           #
LGA    Q     104      C     111           -
LGA    A     105      L     112           -
LGA    G     106      -       -           -
LGA    D     107      -       -           -
LGA    A     108      D     113          2.885
LGA    G     109      L     114          1.654
LGA    M     110      -       -           -
LGA    C     111      -       -           -
LGA    L     112      L     115          3.363
LGA    D     113      D     116           #
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    L     114      P     122           #
LGA    L     115      K     123           -
LGA    D     116      -       -           -
LGA    D     117      -       -           -
LGA    G     118      -       -           -
LGA    T     119      -       -           -
LGA    F     120      -       -           -
LGA    K     121      -       -           -
LGA    P     122      -       -           -
LGA    K     123      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  121    5.0     39    3.35     7.69     18.682     1.132

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.852795 * X  +   0.303415 * Y  +   0.425065 * Z  + -10.775499
  Y_new =  -0.419145 * X  +   0.087892 * Y  +  -0.903655 * Z  +  52.433163
  Z_new =  -0.311542 * X  +  -0.948796 * Y  +   0.052221 * Z  +   2.917772 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.515812    1.625780  [ DEG:   -86.8496     93.1504 ]
  Theta =   0.316815    2.824777  [ DEG:    18.1522    161.8478 ]
  Phi   =  -2.684772    0.456821  [ DEG:  -153.8261     26.1739 ]
 
# 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: T0382TS393_4                                  
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS393_4.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  121   5.0   39   3.35    7.69  18.682
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS393_4
PFRMAT TS
TARGET T0382
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       7.582  60.551  12.774  1.00 25.00           C
ATOM      2  CA  SER     2      10.519  58.377  11.689  1.00 25.00           C
ATOM      3  CA  LYS     3      11.107  57.610   8.017  1.00 25.00           C
ATOM      4  CA  LEU     4       9.370  54.231   7.570  1.00 25.00           C
ATOM      5  CA  ASP     5       7.003  54.093   4.676  1.00 25.00           C
ATOM      6  CA  LEU     6       6.025  57.771   4.245  1.00 25.00           C
ATOM      7  CA  HIS     7       7.526  57.783   0.722  1.00 25.00           C
ATOM      8  CA  GLN     8       5.578  54.603  -0.147  1.00 25.00           C
ATOM      9  CA  MET     9       2.348  56.195   1.156  1.00 25.00           C
ATOM     10  CA  THR    10       3.013  59.324  -0.951  1.00 25.00           C
ATOM     11  CA  THR    11       3.608  57.144  -4.043  1.00 25.00           C
ATOM     12  CA  GLN    12       0.331  55.274  -3.385  1.00 25.00           C
ATOM     13  CA  ASP    13      -1.531  58.603  -3.043  1.00 25.00           C
ATOM     14  CA  LEU    14      -0.012  59.818  -6.343  1.00 25.00           C
ATOM     15  CA  VAL    15      -1.083  56.567  -8.061  1.00 25.00           C
ATOM     16  CA  ALA    16      -4.633  56.982  -6.688  1.00 25.00           C
ATOM     17  CA  LEU    17      -4.735  60.589  -7.969  1.00 25.00           C
ATOM     18  CA  PHE    18      -3.554  59.422 -11.420  1.00 25.00           C
ATOM     19  CA  ALA    19      -6.268  56.720 -11.463  1.00 25.00           C
ATOM     20  CA  LYS    20      -8.911  59.326 -10.519  1.00 25.00           C
ATOM     21  CA  VAL    21      -7.684  61.624 -13.326  1.00 25.00           C
ATOM     22  CA  THR    22      -6.536  64.864 -11.819  1.00 25.00           C
ATOM     23  CA  VAL    23      -5.876  67.878  -9.622  1.00 25.00           C
ATOM     24  CA  GLU    24      -7.007  68.777  -6.076  1.00 25.00           C
ATOM     25  CA  GLN    25     -10.284  66.867  -6.610  1.00 25.00           C
ATOM     26  CA  ASP    26      -8.333  63.824  -7.872  1.00 25.00           C
ATOM     27  CA  ASP    27      -6.051  63.982  -4.800  1.00 25.00           C
ATOM     28  CA  ALA    28      -9.113  64.163  -2.505  1.00 25.00           C
ATOM     29  CA  LEU    29     -10.647  61.133  -4.275  1.00 25.00           C
ATOM     30  CA  LEU    30      -7.371  59.195  -3.855  1.00 25.00           C
ATOM     31  CA  GLY    31      -7.291  60.090  -0.132  1.00 25.00           C
ATOM     32  CA  ASN    32     -10.913  58.908   0.255  1.00 25.00           C
ATOM     33  CA  GLN    33     -10.052  55.616  -1.502  1.00 25.00           C
ATOM     34  CA  ILE    34      -7.047  55.133   0.821  1.00 25.00           C
ATOM     35  CA  SER    35      -9.268  55.784   3.871  1.00 25.00           C
ATOM     36  CA  ARG    36     -11.820  53.232   2.588  1.00 25.00           C
ATOM     37  CA  PHE    37      -9.030  50.659   2.083  1.00 25.00           C
ATOM     38  CA  ASN    38      -7.764  51.296   5.641  1.00 25.00           C
ATOM     39  CA  ARG    39     -11.312  50.839   7.010  1.00 25.00           C
ATOM     40  CA  LEU    40     -11.662  47.553   5.076  1.00 25.00           C
ATOM     41  CA  PHE    41      -8.311  46.342   6.479  1.00 25.00           C
ATOM     42  CA  GLY    42      -9.442  47.241  10.025  1.00 25.00           C
ATOM     43  CA  VAL    43     -12.718  45.330   9.491  1.00 25.00           C
ATOM     44  CA  MET    44     -10.766  42.287   8.230  1.00 25.00           C
ATOM     45  CA  ALA    45      -8.485  42.445  11.302  1.00 25.00           C
ATOM     46  CA  GLU    46     -11.547  42.626  13.595  1.00 25.00           C
ATOM     47  CA  ILE    47     -13.082  39.596  11.826  1.00 25.00           C
ATOM     48  CA  ALA    48      -9.805  37.660  12.247  1.00 25.00           C
ATOM     49  CA  ASP    49      -9.725  38.553  15.970  1.00 25.00           C
ATOM     50  CA  GLU    50     -13.347  37.371  16.356  1.00 25.00           C
ATOM     51  CA  LEU    51     -12.486  34.079  14.599  1.00 25.00           C
ATOM     52  CA  LYS    52      -9.480  33.596  16.922  1.00 25.00           C
ATOM     53  CA  ALA    53      -8.047  33.524  13.401  1.00 25.00           C
ATOM     54  CA  ARG    54      -8.216  33.654   9.593  1.00 25.00           C
ATOM     55  CA  ASP    55      -8.471  34.964   6.049  1.00 25.00           C
ATOM     56  CA  GLY    56      -6.575  36.666   3.224  1.00 25.00           C
ATOM     57  CA  ASP    57      -9.545  38.983   3.182  1.00 25.00           C
ATOM     58  CA  GLN    58      -7.514  42.169   3.435  1.00 25.00           C
ATOM     59  CA  ARG    59      -4.552  43.452   1.374  1.00 25.00           C
ATOM     60  CA  THR    60      -4.818  40.416  -0.946  1.00 25.00           C
ATOM     61  CA  ALA    61      -8.571  41.044  -1.377  1.00 25.00           C
ATOM     62  CA  LEU    62      -7.885  44.719  -2.208  1.00 25.00           C
ATOM     63  CA  LEU    63      -5.254  43.672  -4.785  1.00 25.00           C
ATOM     64  CA  SER    64      -7.737  41.218  -6.359  1.00 25.00           C
ATOM     65  CA  LEU    65     -10.389  43.975  -6.533  1.00 25.00           C
ATOM     66  CA  PHE    66      -7.869  46.329  -8.198  1.00 25.00           C
ATOM     67  CA  GLU    67      -6.976  43.611 -10.744  1.00 25.00           C
ATOM     68  CA  TYR    68      -9.908  41.237 -10.873  1.00 25.00           C
ATOM     69  CA  PRO    69     -10.130  42.180 -14.588  1.00 25.00           C
ATOM     70  CA  ASN    70      -9.981  44.873 -17.347  1.00 25.00           C
ATOM     71  CA  MET    71     -11.461  48.076 -18.870  1.00 25.00           C
ATOM     72  CA  GLN    72     -14.340  50.416 -17.917  1.00 25.00           C
ATOM     73  CA  VAL    73     -16.378  47.431 -16.651  1.00 25.00           C
ATOM     74  CA  ARG    74     -13.388  46.239 -14.575  1.00 25.00           C
ATOM     75  CA  LEU    75     -12.985  49.748 -13.094  1.00 25.00           C
ATOM     76  CA  GLN    76     -16.712  49.832 -12.216  1.00 25.00           C
ATOM     77  CA  ALA    77     -16.418  46.405 -10.533  1.00 25.00           C
ATOM     78  CA  ALA    78     -13.391  47.621  -8.528  1.00 25.00           C
ATOM     79  CA  LYS    79     -15.334  50.736  -7.439  1.00 25.00           C
ATOM     80  CA  LEU    80     -18.284  48.548  -6.355  1.00 25.00           C
ATOM     81  CA  THR    81     -15.913  46.303  -4.352  1.00 25.00           C
ATOM     82  CA  LEU    82     -14.384  49.382  -2.664  1.00 25.00           C
ATOM     83  CA  ALA    83     -17.882  50.668  -1.784  1.00 25.00           C
ATOM     84  CA  VAL    84     -18.794  47.253  -0.310  1.00 25.00           C
ATOM     85  CA  ALA    85     -15.576  47.264   1.767  1.00 25.00           C
ATOM     86  CA  PRO    86     -16.379  50.785   3.040  1.00 25.00           C
ATOM     87  CA  VAL    87     -19.915  49.662   3.989  1.00 25.00           C
ATOM     88  CA  LYS    88     -18.481  46.640   5.855  1.00 25.00           C
ATOM     89  CA  ALA    89     -16.040  48.923   7.725  1.00 25.00           C
ATOM     90  CA  ARG    90     -18.919  51.263   8.678  1.00 25.00           C
ATOM     91  CA  GLU    91     -20.958  48.278   9.945  1.00 25.00           C
ATOM     92  CA  GLN    92     -17.968  47.085  12.021  1.00 25.00           C
ATOM     93  CA  LEU    93     -17.565  50.595  13.501  1.00 25.00           C
ATOM     94  CA  GLU    94     -21.292  50.678  14.380  1.00 25.00           C
ATOM     95  CA  ALA    95     -20.997  47.251  16.062  1.00 25.00           C
ATOM     96  CA  ILE    96     -17.970  48.467  18.067  1.00 25.00           C
ATOM     97  CA  VAL    97     -19.914  51.583  19.157  1.00 25.00           C
ATOM     98  CA  SER    98     -22.863  49.394  20.241  1.00 25.00           C
ATOM     99  CA  SER    99     -20.492  47.149  22.244  1.00 25.00           C
ATOM    100  CA  LYS   100     -19.748  50.388  24.152  1.00 25.00           C
ATOM    101  CA  TRP   101     -16.898  52.860  23.872  1.00 25.00           C
ATOM    102  CA  PHE   102     -14.820  53.568  20.757  1.00 25.00           C
ATOM    103  CA  PRO   103     -13.766  56.706  22.678  1.00 25.00           C
ATOM    104  CA  GLN   104     -11.798  59.900  23.275  1.00 25.00           C
ATOM    105  CA  ALA   105      -9.715  60.742  20.160  1.00 25.00           C
ATOM    106  CA  GLY   106     -10.668  64.425  19.839  1.00 25.00           C
ATOM    107  CA  ASP   107     -10.063  64.453  16.087  1.00 25.00           C
ATOM    108  CA  ALA   108     -10.381  61.768  13.478  1.00 25.00           C
ATOM    109  CA  GLY   109     -11.450  59.954  10.355  1.00 25.00           C
ATOM    110  CA  MET   110     -11.220  57.115   7.794  1.00 25.00           C
ATOM    111  CA  CYS   111     -14.983  56.483   8.120  1.00 25.00           C
ATOM    112  CA  LEU   112     -15.680  60.212   7.600  1.00 25.00           C
ATOM    113  CA  ASP   113     -13.448  60.220   4.488  1.00 25.00           C
ATOM    114  CA  LEU   114     -15.300  57.159   3.122  1.00 25.00           C
ATOM    115  CA  LEU   115     -18.661  58.885   3.741  1.00 25.00           C
ATOM    116  CA  ASP   116     -21.336  61.563   4.143  1.00 25.00           C
ATOM    117  CA  ASP   117     -24.146  64.121   3.947  1.00 25.00           C
ATOM    118  CA  GLY   118     -27.181  66.318   3.688  1.00 25.00           C
ATOM    119  CA  THR   119     -26.048  69.153   6.026  1.00 25.00           C
ATOM    120  CA  PHE   120     -27.848  67.033   8.659  1.00 25.00           C
ATOM    121  CA  LYS   121     -27.367  70.211  10.775  1.00 25.00           C
ATOM    122  CA  PRO   122     -26.276  73.414   9.100  1.00 25.00           C
ATOM    123  CA  LYS   123     -22.816  73.059   7.523  1.00 25.00           C
TER
END
