
#######################################################
#                                                     #
#                        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 T0382TS168_3
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS168_3.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      -       -           -
LGA    D       5      -       -           -
LGA    L       6      -       -           -
LGA    H       7      -       -           -
LGA    Q       8      -       -           -
LGA    M       9      -       -           -
LGA    T      10      -       -           -
LGA    T      11      -       -           -
LGA    Q      12      -       -           -
LGA    D      13      -       -           -
LGA    L      14      -       -           -
LGA    V      15      L       6           #
LGA    A      16      H       7           -
LGA    L      17      Q       8           #
LGA    F      18      M       9          2.521
LGA    A      19      T      10          4.935
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      T      11          3.422
LGA    N      32      Q      12          3.108
LGA    Q      33      D      13          2.424
LGA    I      34      L      14          2.231
LGA    S      35      V      15          2.119
LGA    R      36      A      16          1.738
LGA    F      37      L      17          1.283
LGA    N      38      F      18          1.572
LGA    R      39      A      19          1.616
LGA    L      40      K      20          1.061
LGA    F      41      V      21          0.980
LGA    G      42      T      22          1.769
LGA    V      43      V      23          1.637
LGA    M      44      E      24          0.992
LGA    A      45      Q      25          1.226
LGA    E      46      D      26          1.631
LGA    I      47      D      27          1.442
LGA    A      48      A      28          1.146
LGA    D      49      L      29          1.735
LGA    E      50      L      30          1.979
LGA    L      51      G      31          1.259
LGA    K      52      N      32          1.691
LGA    A      53      Q      33          2.444
LGA    R      54      I      34          2.656
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    D      55      F      37          3.454
LGA    G      56      N      38          1.363
LGA    D      57      R      39          3.373
LGA    Q      58      L      40          3.962
LGA    R      59      F      41          3.230
LGA    T      60      G      42          1.661
LGA    A      61      V      43          2.567
LGA    L      62      M      44          4.020
LGA    L      63      A      45          3.367
LGA    S      64      E      46          2.954
LGA    L      65      I      47          4.358
LGA    -       -      A      48           -
LGA    F      66      D      49          1.648
LGA    E      67      E      50          6.411
LGA    Y      68      L      51           -
LGA    P      69      -       -           -
LGA    N      70      K      52          5.025
LGA    M      71      A      53          2.179
LGA    Q      72      -       -           -
LGA    V      73      R      54          2.854
LGA    R      74      D      55           -
LGA    L      75      G      56           -
LGA    Q      76      D      57          4.092
LGA    A      77      Q      58          3.823
LGA    A      78      R      59          3.915
LGA    K      79      T      60          5.067
LGA    L      80      A      61          3.549
LGA    T      81      L      62          3.813
LGA    L      82      L      63           #
LGA    -       -      S      64           -
LGA    A      83      L      65          3.268
LGA    V      84      F      66          5.224
LGA    -       -      E      67           -
LGA    A      85      Y      68          5.702
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    P      86      R      74          0.873
LGA    V      87      L      75           -
LGA    K      88      Q      76           -
LGA    A      89      A      77           -
LGA    -       -      A      78           -
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    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    R      90      I      96           #
LGA    E      91      V      97           -
LGA    Q      92      S      98           -
LGA    L      93      S      99           #
LGA    E      94      -       -           -
LGA    A      95      -       -           -
LGA    I      96      -       -           -
LGA    V      97      -       -           -
LGA    S      98      -       -           -
LGA    S      99      -       -           -
LGA    K     100      -       -           -
LGA    W     101      -       -           -
LGA    F     102      -       -           -
LGA    P     103      -       -           -
LGA    Q     104      K     100           #
LGA    A     105      W     101           #
LGA    G     106      F     102           #
LGA    D     107      P     103          3.304
LGA    A     108      Q     104          0.679
LGA    G     109      A     105           -
LGA    M     110      G     106           -
LGA    C     111      D     107           -
LGA    L     112      A     108           #
LGA    D     113      G     109           -
LGA    L     114      M     110           -
LGA    L     115      -       -           -
LGA    D     116      C     111           #
LGA    D     117      L     112          4.025
LGA    G     118      D     113           #
LGA    -       -      L     114           -
LGA    T     119      L     115          3.598
LGA    F     120      D     116           #
LGA    K     121      D     117          3.374
LGA    -       -      G     118           -
LGA    P     122      T     119          0.782
LGA    K     123      F     120          3.949
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     59    3.07     5.08     32.352     1.863

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.808191 * X  +  -0.206862 * Y  +   0.551395 * Z  + -14.952560
  Y_new =   0.513594 * X  +  -0.705730 * Y  +   0.488023 * Z  +  40.008343
  Z_new =   0.288182 * X  +   0.677609 * Y  +   0.676607 * Z  +   1.262358 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.786137   -2.355455  [ DEG:    45.0424   -134.9576 ]
  Theta =  -0.292328   -2.849265  [ DEG:   -16.7492   -163.2508 ]
  Phi   =   2.575488   -0.566105  [ DEG:   147.5646    -32.4354 ]
 
# 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_3                                  
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS168_3.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   59   3.07    5.08  32.352
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS168_3
PFRMAT TS
TARGET T0382
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -2.092  17.736   1.706  1.00 25.00           C
ATOM      2  CA  SER     2      -3.740  15.435  -0.797  1.00 25.00           C
ATOM      3  CA  LYS     3      -7.383  16.191  -1.593  1.00 25.00           C
ATOM      4  CA  LEU     4     -10.640  17.900  -2.348  1.00 25.00           C
ATOM      5  CA  ASP     5     -10.630  21.337  -0.619  1.00 25.00           C
ATOM      6  CA  LEU     6     -14.262  22.284  -1.381  1.00 25.00           C
ATOM      7  CA  HIS     7     -13.509  25.943  -0.539  1.00 25.00           C
ATOM      8  CA  GLN     8     -10.452  25.871  -2.843  1.00 25.00           C
ATOM      9  CA  MET     9     -12.580  24.383  -5.660  1.00 25.00           C
ATOM     10  CA  THR    10     -15.211  27.118  -5.151  1.00 25.00           C
ATOM     11  CA  THR    11     -12.483  29.802  -5.286  1.00 25.00           C
ATOM     12  CA  GLN    12     -11.112  28.280  -8.522  1.00 25.00           C
ATOM     13  CA  ASP    13     -14.629  28.270 -10.036  1.00 25.00           C
ATOM     14  CA  LEU    14     -15.092  31.942  -9.049  1.00 25.00           C
ATOM     15  CA  VAL    15     -11.727  32.822 -10.651  1.00 25.00           C
ATOM     16  CA  ALA    16     -12.745  30.991 -13.856  1.00 25.00           C
ATOM     17  CA  LEU    17     -16.070  32.892 -13.915  1.00 25.00           C
ATOM     18  CA  PHE    18     -14.209  36.208 -13.463  1.00 25.00           C
ATOM     19  CA  ALA    19     -11.844  35.302 -16.336  1.00 25.00           C
ATOM     20  CA  LYS    20     -14.839  34.446 -18.564  1.00 25.00           C
ATOM     21  CA  VAL    21     -16.478  37.796 -17.691  1.00 25.00           C
ATOM     22  CA  THR    22     -18.546  39.094 -20.642  1.00 25.00           C
ATOM     23  CA  VAL    23     -21.730  40.113 -22.545  1.00 25.00           C
ATOM     24  CA  GLU    24     -23.624  42.173 -19.930  1.00 25.00           C
ATOM     25  CA  GLN    25     -25.075  38.967 -18.420  1.00 25.00           C
ATOM     26  CA  ASP    26     -21.573  37.424 -18.269  1.00 25.00           C
ATOM     27  CA  ASP    27     -20.235  40.568 -16.542  1.00 25.00           C
ATOM     28  CA  ALA    28     -23.098  40.422 -14.003  1.00 25.00           C
ATOM     29  CA  LEU    29     -22.338  36.731 -13.322  1.00 25.00           C
ATOM     30  CA  LEU    30     -18.636  37.562 -12.808  1.00 25.00           C
ATOM     31  CA  GLY    31     -19.577  40.368 -10.377  1.00 25.00           C
ATOM     32  CA  ASN    32     -21.850  37.965  -8.446  1.00 25.00           C
ATOM     33  CA  GLN    33     -19.015  35.397  -8.258  1.00 25.00           C
ATOM     34  CA  ILE    34     -16.624  38.095  -6.965  1.00 25.00           C
ATOM     35  CA  SER    35     -19.186  39.129  -4.312  1.00 25.00           C
ATOM     36  CA  ARG    36     -19.583  35.474  -3.237  1.00 25.00           C
ATOM     37  CA  PHE    37     -15.780  35.113  -2.973  1.00 25.00           C
ATOM     38  CA  ASN    38     -15.599  38.295  -0.850  1.00 25.00           C
ATOM     39  CA  ARG    39     -18.362  36.955   1.438  1.00 25.00           C
ATOM     40  CA  LEU    40     -16.479  33.641   1.811  1.00 25.00           C
ATOM     41  CA  PHE    41     -13.267  35.536   2.682  1.00 25.00           C
ATOM     42  CA  GLY    42     -15.162  37.595   5.298  1.00 25.00           C
ATOM     43  CA  VAL    43     -16.612  34.388   6.808  1.00 25.00           C
ATOM     44  CA  MET    44     -13.110  32.845   6.958  1.00 25.00           C
ATOM     45  CA  ALA    45     -11.772  35.991   8.685  1.00 25.00           C
ATOM     46  CA  GLU    46     -14.636  35.844  11.225  1.00 25.00           C
ATOM     47  CA  ILE    47     -13.875  32.152  11.905  1.00 25.00           C
ATOM     48  CA  ALA    48     -10.172  32.984  12.419  1.00 25.00           C
ATOM     49  CA  ASP    49     -11.114  35.789  14.850  1.00 25.00           C
ATOM     50  CA  GLU    50     -13.387  33.387  16.781  1.00 25.00           C
ATOM     51  CA  LEU    51     -10.552  30.818  16.970  1.00 25.00           C
ATOM     52  CA  LYS    52      -8.161  33.516  18.262  1.00 25.00           C
ATOM     53  CA  ALA    53      -6.242  34.608  15.200  1.00 25.00           C
ATOM     54  CA  ARG    54      -5.738  36.410  11.824  1.00 25.00           C
ATOM     55  CA  ASP    55      -4.678  39.651  10.068  1.00 25.00           C
ATOM     56  CA  GLY    56      -3.481  39.252   6.539  1.00 25.00           C
ATOM     57  CA  ASP    57      -5.968  37.924   3.920  1.00 25.00           C
ATOM     58  CA  GLN    58      -8.754  39.059   1.595  1.00 25.00           C
ATOM     59  CA  ARG    59      -7.097  42.489   1.997  1.00 25.00           C
ATOM     60  CA  THR    60      -3.987  41.230   0.150  1.00 25.00           C
ATOM     61  CA  ALA    61      -6.185  39.878  -2.679  1.00 25.00           C
ATOM     62  CA  LEU    62      -7.992  43.246  -2.919  1.00 25.00           C
ATOM     63  CA  LEU    63      -4.627  45.067  -3.075  1.00 25.00           C
ATOM     64  CA  SER    64      -3.448  42.706  -5.850  1.00 25.00           C
ATOM     65  CA  LEU    65      -6.683  43.343  -7.799  1.00 25.00           C
ATOM     66  CA  PHE    66      -6.199  47.123  -7.416  1.00 25.00           C
ATOM     67  CA  GLU    67      -2.592  46.812  -8.669  1.00 25.00           C
ATOM     68  CA  TYR    68      -1.836  49.168  -5.779  1.00 25.00           C
ATOM     69  CA  PRO    69      -3.463  51.968  -7.663  1.00 25.00           C
ATOM     70  CA  ASN    70      -6.922  52.372  -9.145  1.00 25.00           C
ATOM     71  CA  MET    71      -8.183  50.453 -12.212  1.00 25.00           C
ATOM     72  CA  GLN    72     -11.660  51.991 -11.755  1.00 25.00           C
ATOM     73  CA  VAL    73     -13.280  48.583 -12.407  1.00 25.00           C
ATOM     74  CA  ARG    74     -10.952  46.957  -9.837  1.00 25.00           C
ATOM     75  CA  LEU    75     -11.854  49.658  -7.276  1.00 25.00           C
ATOM     76  CA  GLN    76     -15.581  49.074  -7.935  1.00 25.00           C
ATOM     77  CA  ALA    77     -15.098  45.304  -7.465  1.00 25.00           C
ATOM     78  CA  ALA    78     -13.251  45.925  -4.169  1.00 25.00           C
ATOM     79  CA  LYS    79     -16.088  48.208  -2.981  1.00 25.00           C
ATOM     80  CA  LEU    80     -18.662  45.522  -3.889  1.00 25.00           C
ATOM     81  CA  THR    81     -16.644  42.900  -1.961  1.00 25.00           C
ATOM     82  CA  LEU    82     -16.483  45.225   1.079  1.00 25.00           C
ATOM     83  CA  ALA    83     -20.269  45.767   0.896  1.00 25.00           C
ATOM     84  CA  VAL    84     -20.828  41.982   0.722  1.00 25.00           C
ATOM     85  CA  ALA    85     -18.560  41.482   3.767  1.00 25.00           C
ATOM     86  CA  PRO    86     -20.502  44.169   5.685  1.00 25.00           C
ATOM     87  CA  VAL    87     -23.808  42.464   4.775  1.00 25.00           C
ATOM     88  CA  LYS    88     -22.430  39.097   5.973  1.00 25.00           C
ATOM     89  CA  ALA    89     -21.315  40.700   9.268  1.00 25.00           C
ATOM     90  CA  ARG    90     -24.792  42.238   9.726  1.00 25.00           C
ATOM     91  CA  GLU    91     -26.412  38.829   9.074  1.00 25.00           C
ATOM     92  CA  GLN    92     -24.084  37.203  11.644  1.00 25.00           C
ATOM     93  CA  LEU    93     -24.986  39.904  14.205  1.00 25.00           C
ATOM     94  CA  GLU    94     -28.713  39.320  13.546  1.00 25.00           C
ATOM     95  CA  ALA    95     -28.230  35.550  14.015  1.00 25.00           C
ATOM     96  CA  ILE    96     -26.383  36.171  17.312  1.00 25.00           C
ATOM     97  CA  VAL    97     -29.219  38.454  18.499  1.00 25.00           C
ATOM     98  CA  SER    98     -31.794  35.768  17.592  1.00 25.00           C
ATOM     99  CA  SER    99     -29.775  33.146  19.521  1.00 25.00           C
ATOM    100  CA  LYS   100     -27.797  34.802  22.340  1.00 25.00           C
ATOM    101  CA  TRP   101     -24.680  37.047  22.728  1.00 25.00           C
ATOM    102  CA  PHE   102     -22.704  39.749  20.903  1.00 25.00           C
ATOM    103  CA  PRO   103     -22.364  41.672  24.169  1.00 25.00           C
ATOM    104  CA  GLN   104     -20.031  44.637  23.904  1.00 25.00           C
ATOM    105  CA  ALA   105     -18.016  47.752  23.000  1.00 25.00           C
ATOM    106  CA  GLY   106     -15.506  49.469  20.738  1.00 25.00           C
ATOM    107  CA  ASP   107     -15.241  48.423  17.073  1.00 25.00           C
ATOM    108  CA  ALA   108     -15.143  46.011  14.071  1.00 25.00           C
ATOM    109  CA  GLY   109     -13.891  43.935  11.094  1.00 25.00           C
ATOM    110  CA  MET   110     -12.322  42.871   7.767  1.00 25.00           C
ATOM    111  CA  CYS   111     -15.439  44.062   5.888  1.00 25.00           C
ATOM    112  CA  LEU   112     -15.286  47.424   7.715  1.00 25.00           C
ATOM    113  CA  ASP   113     -11.582  47.777   6.807  1.00 25.00           C
ATOM    114  CA  LEU   114     -12.383  47.005   3.142  1.00 25.00           C
ATOM    115  CA  LEU   115     -15.169  49.632   3.170  1.00 25.00           C
ATOM    116  CA  ASP   116     -16.131  52.850   4.977  1.00 25.00           C
ATOM    117  CA  ASP   117     -16.014  56.152   6.939  1.00 25.00           C
ATOM    118  CA  GLY   118     -16.179  59.617   8.499  1.00 25.00           C
ATOM    119  CA  THR   119     -15.397  61.908   5.556  1.00 25.00           C
ATOM    120  CA  PHE   120     -11.904  63.183   4.906  1.00 25.00           C
ATOM    121  CA  LYS   121      -8.950  64.708   6.667  1.00 25.00           C
ATOM    122  CA  PRO   122      -5.428  63.893   5.528  1.00 25.00           C
ATOM    123  CA  LYS   123      -4.690  61.196   8.108  1.00 25.00           C
TER
END
