
#######################################################
#                                                     #
#                        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  130 (  130),  selected  130 , name T0354TS168_1
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS168_1.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    E       2      -       -           -
LGA    I       3      -       -           -
LGA    Q       4      -       -           -
LGA    E       5      E       2          2.517
LGA    I       6      -       -           -
LGA    S       7      I       3          3.582
LGA    K       8      Q       4          1.104
LGA    L       9      E       5          1.822
LGA    A      10      I       6          2.700
LGA    I      11      S       7          2.793
LGA    E      12      K       8          2.554
LGA    A      13      L       9          1.879
LGA    -       -      A      10           -
LGA    L      14      I      11          2.507
LGA    E      15      E      12           #
LGA    D      16      A      13           -
LGA    I      17      -       -           -
LGA    K      18      L      14           #
LGA    G      19      E      15          1.240
LGA    K      20      D      16           #
LGA    D      21      -       -           -
LGA    I      22      -       -           -
LGA    I      23      -       -           -
LGA    E      24      -       -           -
LGA    L      25      I      17          2.638
LGA    D      26      K      18          3.132
LGA    T      27      -       -           -
LGA    S      28      -       -           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    T      31      G      19          3.423
LGA    S      32      K      20          3.247
LGA    L      33      D      21          1.963
LGA    F      34      I      22          3.034
LGA    Q      35      I      23          3.386
LGA    -       -      E      24           -
LGA    -       -      L      25           -
LGA    -       -      D      26           -
LGA    -       -      T      27           -
LGA    -       -      S      28           -
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    R      36      M      37          2.836
LGA    M      37      I      38          3.507
LGA    I      38      V      39          3.795
LGA    V      39      A      40           #
LGA    A      40      T      41           #
LGA    T      41      G      42          4.991
LGA    G      42      D      43          5.773
LGA    D      43      S      44          2.977
LGA    S      44      -       -           -
LGA    N      45      N      45          1.372
LGA    R      46      R      46          1.962
LGA    Q      47      Q      47          1.695
LGA    V      48      V      48          0.340
LGA    K      49      K      49          1.328
LGA    A      50      A      50          1.779
LGA    L      51      L      51          1.446
LGA    A      52      A      52          0.882
LGA    N      53      N      53          0.974
LGA    S      54      S      54          1.917
LGA    V      55      V      55          2.137
LGA    Q      56      Q      56          1.016
LGA    V      57      V      57          1.786
LGA    K      58      K      58          3.712
LGA    L      59      L      59          3.485
LGA    K      60      K      60          0.891
LGA    -       -      E      61           -
LGA    E      61      A      62          2.321
LGA    A      62      G      63          1.807
LGA    -       -      V      64           -
LGA    G      63      D      65          1.203
LGA    V      64      I      66          1.796
LGA    D      65      V      67          5.115
LGA    I      66      G      68          3.589
LGA    V      67      S      69          3.755
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    -       -      S      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      W      77           -
LGA    G      68      V      78          4.071
LGA    S      69      L      79          2.904
LGA    E      70      V      80           -
LGA    -       -      D      81           -
LGA    -       -      A      82           -
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    -       -      H      88           -
LGA    -       -      V      89           -
LGA    -       -      M      90           -
LGA    -       -      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    G      71      V      94           #
LGA    H      72      R      95           #
LGA    -       -      D      96           -
LGA    -       -      Y      97           -
LGA    E      73      Y      98          3.761
LGA    S      74      D      99          3.858
LGA    -       -      I     100           -
LGA    G      75      E     101          1.684
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    E      76      G     106          3.838
LGA    W      77      Q     107          3.307
LGA    V      78      K     108          3.158
LGA    L      79      P     109          2.164
LGA    V      80      S     110          3.588
LGA    D      81      F     111          3.012
LGA    A      82      A     112           -
LGA    G      83      V     113           -
LGA    D      84      G     114           -
LGA    V      85      A     115           -
LGA    V      86      A     116           -
LGA    V      87      K     117           -
LGA    H      88      -       -           -
LGA    V      89      -       -           -
LGA    M      90      P     118           #
LGA    L      91      W     119          4.282
LGA    -       -      S     120           -
LGA    P      92      A     121           #
LGA    A      93      V     122           -
LGA    V      94      -       -           -
LGA    R      95      -       -           -
LGA    D      96      -       -           -
LGA    Y      97      -       -           -
LGA    Y      98      -       -           -
LGA    D      99      -       -           -
LGA    I     100      -       -           -
LGA    E     101      -       -           -
LGA    A     102      -       -           -
LGA    L     103      -       -           -
LGA    W     104      -       -           -
LGA    G     105      -       -           -
LGA    G     106      -       -           -
LGA    Q     107      -       -           -
LGA    K     108      -       -           -
LGA    P     109      -       -           -
LGA    S     110      -       -           -
LGA    F     111      -       -           -
LGA    A     112      -       -           -
LGA    V     113      -       -           -
LGA    G     114      -       -           -
LGA    A     115      -       -           -
LGA    A     116      -       -           -
LGA    K     117      -       -           -
LGA    P     118      -       -           -
LGA    W     119      -       -           -
LGA    S     120      -       -           -
LGA    A     121      -       -           -
LGA    V     122      -       -           -
LGA    L     123      -       -           -
LGA    E     124      -       -           -
LGA    H     125      -       -           -
LGA    H     126      -       -           -
LGA    H     127      -       -           -
LGA    H     128      -       -           -
LGA    H     129      -       -           -
LGA    H     130      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  130  122    5.0     58    2.88    29.31     29.876     1.943

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.444439 * X  +  -0.746705 * Y  +  -0.494880 * Z  +  38.969666
  Y_new =  -0.231752 * X  +  -0.629473 * Y  +   0.741657 * Z  +  33.235882
  Z_new =  -0.865312 * X  +  -0.214932 * Y  +  -0.452813 * Z  +  30.493355 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.698421    0.443171  [ DEG:  -154.6082     25.3918 ]
  Theta =   1.045773    2.095820  [ DEG:    59.9184    120.0816 ]
  Phi   =  -0.480658    2.660935  [ DEG:   -27.5397    152.4603 ]
 
# 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: T0354TS168_1                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS168_1.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  130  122   5.0   58   2.88   29.31  29.876
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS168_1
PFRMAT TS
TARGET T0354
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      53.699  22.701   9.461  1.00 25.00           C
ATOM      2  CA  GLU     2      50.351  24.428   9.494  1.00 25.00           C
ATOM      3  CA  ILE     3      48.724  24.536  12.898  1.00 25.00           C
ATOM      4  CA  GLN     4      49.276  20.882  13.902  1.00 25.00           C
ATOM      5  CA  GLU     5      52.529  21.838  15.682  1.00 25.00           C
ATOM      6  CA  ILE     6      50.715  24.652  17.541  1.00 25.00           C
ATOM      7  CA  SER     7      47.959  22.211  18.598  1.00 25.00           C
ATOM      8  CA  LYS     8      50.599  19.737  19.853  1.00 25.00           C
ATOM      9  CA  LEU     9      52.305  22.529  21.843  1.00 25.00           C
ATOM     10  CA  ALA    10      48.940  23.525  23.378  1.00 25.00           C
ATOM     11  CA  ILE    11      48.271  19.878  24.337  1.00 25.00           C
ATOM     12  CA  GLU    12      51.736  19.642  25.951  1.00 25.00           C
ATOM     13  CA  ALA    13      51.070  22.863  27.913  1.00 25.00           C
ATOM     14  CA  LEU    14      47.704  21.473  29.099  1.00 25.00           C
ATOM     15  CA  GLU    15      49.407  18.227  30.207  1.00 25.00           C
ATOM     16  CA  ASP    16      52.049  20.235  32.117  1.00 25.00           C
ATOM     17  CA  ILE    17      52.043  23.675  33.822  1.00 25.00           C
ATOM     18  CA  LYS    18      49.442  24.819  36.432  1.00 25.00           C
ATOM     19  CA  GLY    19      46.462  24.782  34.005  1.00 25.00           C
ATOM     20  CA  LYS    20      47.974  26.580  30.977  1.00 25.00           C
ATOM     21  CA  ASP    21      46.733  26.234  27.419  1.00 25.00           C
ATOM     22  CA  ILE    22      43.554  25.779  25.370  1.00 25.00           C
ATOM     23  CA  ILE    23      41.576  26.556  28.555  1.00 25.00           C
ATOM     24  CA  GLU    24      41.549  26.454  32.352  1.00 25.00           C
ATOM     25  CA  LEU    25      43.027  28.104  35.490  1.00 25.00           C
ATOM     26  CA  ASP    26      41.234  29.066  38.720  1.00 25.00           C
ATOM     27  CA  THR    27      39.045  31.228  40.950  1.00 25.00           C
ATOM     28  CA  SER    28      36.800  30.610  43.899  1.00 25.00           C
ATOM     29  CA  LYS    29      37.882  27.003  43.923  1.00 25.00           C
ATOM     30  CA  LEU    30      39.297  24.730  41.219  1.00 25.00           C
ATOM     31  CA  THR    31      40.853  23.724  37.895  1.00 25.00           C
ATOM     32  CA  SER    32      40.283  21.677  34.798  1.00 25.00           C
ATOM     33  CA  LEU    33      38.067  20.926  31.746  1.00 25.00           C
ATOM     34  CA  PHE    34      38.977  19.653  28.250  1.00 25.00           C
ATOM     35  CA  GLN    35      41.461  21.034  25.657  1.00 25.00           C
ATOM     36  CA  ARG    36      39.573  22.867  22.950  1.00 25.00           C
ATOM     37  CA  MET    37      37.567  24.309  25.916  1.00 25.00           C
ATOM     38  CA  ILE    38      37.255  28.091  26.482  1.00 25.00           C
ATOM     39  CA  VAL    39      36.033  30.848  28.706  1.00 25.00           C
ATOM     40  CA  ALA    40      32.216  30.436  28.955  1.00 25.00           C
ATOM     41  CA  THR    41      31.356  30.558  32.657  1.00 25.00           C
ATOM     42  CA  GLY    42      28.893  32.138  35.087  1.00 25.00           C
ATOM     43  CA  ASP    43      31.235  32.301  38.005  1.00 25.00           C
ATOM     44  CA  SER    44      31.358  36.078  38.242  1.00 25.00           C
ATOM     45  CA  ASN    45      34.562  36.253  36.150  1.00 25.00           C
ATOM     46  CA  ARG    46      37.919  35.643  37.893  1.00 25.00           C
ATOM     47  CA  GLN    47      38.146  32.171  36.295  1.00 25.00           C
ATOM     48  CA  VAL    48      37.400  33.678  32.854  1.00 25.00           C
ATOM     49  CA  LYS    49      40.120  36.321  33.394  1.00 25.00           C
ATOM     50  CA  ALA    50      42.610  33.588  34.394  1.00 25.00           C
ATOM     51  CA  LEU    51      41.714  31.588  31.253  1.00 25.00           C
ATOM     52  CA  ALA    52      42.223  34.708  29.091  1.00 25.00           C
ATOM     53  CA  ASN    53      45.631  35.317  30.730  1.00 25.00           C
ATOM     54  CA  SER    54      46.626  31.679  30.070  1.00 25.00           C
ATOM     55  CA  VAL    55      45.561  32.026  26.408  1.00 25.00           C
ATOM     56  CA  GLN    56      47.623  35.237  26.087  1.00 25.00           C
ATOM     57  CA  VAL    57      50.660  33.468  27.608  1.00 25.00           C
ATOM     58  CA  LYS    58      50.231  30.564  25.148  1.00 25.00           C
ATOM     59  CA  LEU    59      50.032  33.035  22.228  1.00 25.00           C
ATOM     60  CA  LYS    60      53.218  34.773  23.449  1.00 25.00           C
ATOM     61  CA  GLU    61      54.999  31.391  23.691  1.00 25.00           C
ATOM     62  CA  ALA    62      55.817  32.154  20.037  1.00 25.00           C
ATOM     63  CA  GLY    63      53.081  34.146  18.179  1.00 25.00           C
ATOM     64  CA  VAL    64      49.344  34.336  17.447  1.00 25.00           C
ATOM     65  CA  ASP    65      49.168  37.676  19.262  1.00 25.00           C
ATOM     66  CA  ILE    66      45.995  36.767  21.111  1.00 25.00           C
ATOM     67  CA  VAL    67      43.334  35.043  23.239  1.00 25.00           C
ATOM     68  CA  GLY    68      39.581  34.609  22.942  1.00 25.00           C
ATOM     69  CA  SER    69      36.098  34.764  21.380  1.00 25.00           C
ATOM     70  CA  GLU    70      32.689  33.908  19.804  1.00 25.00           C
ATOM     71  CA  GLY    71      32.021  31.488  22.708  1.00 25.00           C
ATOM     72  CA  HIS    72      31.354  27.957  21.433  1.00 25.00           C
ATOM     73  CA  GLU    73      28.083  26.081  20.690  1.00 25.00           C
ATOM     74  CA  SER    74      29.268  22.471  20.879  1.00 25.00           C
ATOM     75  CA  GLY    75      32.904  22.131  21.968  1.00 25.00           C
ATOM     76  CA  GLU    76      32.002  19.783  24.784  1.00 25.00           C
ATOM     77  CA  TRP    77      32.959  16.922  27.034  1.00 25.00           C
ATOM     78  CA  VAL    78      31.541  18.672  30.083  1.00 25.00           C
ATOM     79  CA  LEU    79      29.614  19.099  33.296  1.00 25.00           C
ATOM     80  CA  VAL    80      27.967  20.744  36.355  1.00 25.00           C
ATOM     81  CA  ASP    81      27.999  24.290  34.886  1.00 25.00           C
ATOM     82  CA  ALA    82      30.414  25.748  37.438  1.00 25.00           C
ATOM     83  CA  GLY    83      32.274  25.709  40.787  1.00 25.00           C
ATOM     84  CA  ASP    84      35.237  26.928  38.724  1.00 25.00           C
ATOM     85  CA  VAL    85      35.754  23.756  36.742  1.00 25.00           C
ATOM     86  CA  VAL    86      34.668  24.721  33.173  1.00 25.00           C
ATOM     87  CA  VAL    87      32.948  23.656  29.959  1.00 25.00           C
ATOM     88  CA  HIS    88      31.512  24.627  26.568  1.00 25.00           C
ATOM     89  CA  VAL    89      28.620  26.698  28.055  1.00 25.00           C
ATOM     90  CA  MET    90      27.239  30.082  26.975  1.00 25.00           C
ATOM     91  CA  LEU    91      25.568  33.328  27.983  1.00 25.00           C
ATOM     92  CA  PRO    92      28.608  35.511  28.581  1.00 25.00           C
ATOM     93  CA  ALA    93      30.716  35.609  25.386  1.00 25.00           C
ATOM     94  CA  VAL    94      30.946  39.424  25.626  1.00 25.00           C
ATOM     95  CA  ARG    95      32.040  39.152  29.286  1.00 25.00           C
ATOM     96  CA  ASP    96      34.711  36.583  28.323  1.00 25.00           C
ATOM     97  CA  TYR    97      35.972  38.898  25.544  1.00 25.00           C
ATOM     98  CA  TYR    98      36.145  41.816  28.020  1.00 25.00           C
ATOM     99  CA  ASP    99      38.106  39.639  30.487  1.00 25.00           C
ATOM    100  CA  ILE   100      40.534  38.628  27.702  1.00 25.00           C
ATOM    101  CA  GLU   101      41.012  42.308  26.752  1.00 25.00           C
ATOM    102  CA  ALA   102      41.700  43.191  30.414  1.00 25.00           C
ATOM    103  CA  LEU   103      44.265  40.357  30.640  1.00 25.00           C
ATOM    104  CA  TRP   104      45.968  41.609  27.447  1.00 25.00           C
ATOM    105  CA  GLY   105      48.185  44.061  29.303  1.00 25.00           C
ATOM    106  CA  GLY   106      49.656  42.197  32.246  1.00 25.00           C
ATOM    107  CA  GLN   107      51.463  42.719  35.563  1.00 25.00           C
ATOM    108  CA  LYS   108      50.602  42.544  39.236  1.00 25.00           C
ATOM    109  CA  PRO   109      49.540  44.573  42.333  1.00 25.00           C
ATOM    110  CA  SER   110      46.132  46.063  43.067  1.00 25.00           C
ATOM    111  CA  PHE   111      43.185  43.786  44.010  1.00 25.00           C
ATOM    112  CA  ALA   112      40.237  43.286  46.426  1.00 25.00           C
ATOM    113  CA  VAL   113      37.009  44.944  47.455  1.00 25.00           C
ATOM    114  CA  GLY   114      35.796  47.333  50.194  1.00 25.00           C
ATOM    115  CA  ALA   115      33.711  50.341  51.107  1.00 25.00           C
ATOM    116  CA  ALA   116      31.252  52.385  49.081  1.00 25.00           C
ATOM    117  CA  LYS   117      27.942  53.184  50.814  1.00 25.00           C
ATOM    118  CA  PRO   118      25.167  51.170  49.094  1.00 25.00           C
ATOM    119  CA  TRP   119      24.890  51.583  45.297  1.00 25.00           C
ATOM    120  CA  SER   120      22.104  50.751  42.839  1.00 25.00           C
ATOM    121  CA  ALA   121      21.886  54.546  42.459  1.00 25.00           C
ATOM    122  CA  VAL   122      20.761  53.771  38.848  1.00 25.00           C
ATOM    123  CA  LEU   123      24.281  54.342  37.480  1.00 25.00           C
ATOM    124  CA  GLU   124      23.993  58.151  37.748  1.00 25.00           C
ATOM    125  CA  HIS   125      21.601  58.205  34.758  1.00 25.00           C
ATOM    126  CA  HIS   126      21.428  54.651  33.361  1.00 25.00           C
ATOM    127  CA  HIS   127      23.144  56.113  30.296  1.00 25.00           C
ATOM    128  CA  HIS   128      24.009  56.450  26.608  1.00 25.00           C
ATOM    129  CA  HIS   129      27.358  57.057  24.977  1.00 25.00           C
ATOM    130  CA  HIS   130      28.793  53.581  25.649  1.00 25.00           C
TER
END
