
#######################################################
#                                                     #
#                        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  144 (  144),  selected  144 , name T0370TS168_3-D1
# Molecule2: number of CA atoms  144 ( 1104),  selected  144 , name T0370_D1.pdb
# PARAMETERS: T0370TS168_3-D1.T0370_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       8      T       8           -
LGA    A       9      A       9           -
LGA    -       -      K      10           -
LGA    -       -      Q      11           -
LGA    -       -      R      12           -
LGA    -       -      I      13           -
LGA    -       -      Q      14           -
LGA    K      10      D      15           #
LGA    Q      11      T      16           -
LGA    R      12      L      17           -
LGA    I      13      N      18          3.142
LGA    Q      14      -       -           -
LGA    D      15      -       -           -
LGA    T      16      R      19          4.941
LGA    L      17      L      20          3.998
LGA    N      18      E      21          4.726
LGA    R      19      L      22           -
LGA    -       -      D      23           -
LGA    -       -      V      24           -
LGA    -       -      D      25           -
LGA    -       -      A      26           -
LGA    -       -      W      27           -
LGA    -       -      V      28           -
LGA    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      A      31           -
LGA    -       -      G      32           -
LGA    -       -      A      33           -
LGA    -       -      D      34           -
LGA    -       -      G      35           -
LGA    -       -      G      36           -
LGA    -       -      A      37           -
LGA    -       -      P      38           -
LGA    -       -      Y      39           -
LGA    -       -      L      40           -
LGA    -       -      V      41           -
LGA    -       -      P      42           -
LGA    -       -      L      43           -
LGA    -       -      S      44           -
LGA    -       -      Y      45           -
LGA    -       -      L      46           -
LGA    L      20      W      47          2.119
LGA    E      21      D      48          3.111
LGA    L      22      G      49          3.250
LGA    D      23      E      50           #
LGA    V      24      T      51           -
LGA    D      25      F      52           -
LGA    A      26      L      53           -
LGA    W      27      -       -           -
LGA    V      28      -       -           -
LGA    S      29      -       -           -
LGA    T      30      -       -           -
LGA    A      31      -       -           -
LGA    G      32      -       -           -
LGA    A      33      -       -           -
LGA    D      34      -       -           -
LGA    G      35      -       -           -
LGA    G      36      -       -           -
LGA    A      37      -       -           -
LGA    P      38      -       -           -
LGA    Y      39      -       -           -
LGA    L      40      V      54           #
LGA    V      41      A      55           -
LGA    P      42      T      56           -
LGA    L      43      P      57           -
LGA    S      44      A      58           -
LGA    Y      45      A      59           -
LGA    L      46      S      60           -
LGA    W      47      P      61           -
LGA    D      48      T      62           -
LGA    G      49      G      63           -
LGA    E      50      R      64           -
LGA    T      51      N      65           -
LGA    F      52      L      66           -
LGA    L      53      S      67           -
LGA    V      54      E      68           -
LGA    A      55      T      69           -
LGA    -       -      G      70           -
LGA    -       -      R      71           -
LGA    T      56      V      72          3.626
LGA    P      57      R      73          4.495
LGA    A      58      -       -           -
LGA    A      59      -       -           -
LGA    S      60      -       -           -
LGA    P      61      -       -           -
LGA    T      62      -       -           -
LGA    G      63      -       -           -
LGA    R      64      -       -           -
LGA    N      65      -       -           -
LGA    L      66      -       -           -
LGA    S      67      -       -           -
LGA    E      68      -       -           -
LGA    T      69      -       -           -
LGA    G      70      -       -           -
LGA    R      71      -       -           -
LGA    V      72      -       -           -
LGA    R      73      L      74          4.051
LGA    L      74      G      75           -
LGA    G      75      -       -           -
LGA    I      76      -       -           -
LGA    G      77      -       -           -
LGA    P      78      -       -           -
LGA    T      79      -       -           -
LGA    R      80      -       -           -
LGA    D      81      -       -           -
LGA    L      82      -       -           -
LGA    V      83      I      76           #
LGA    L      84      G      77           -
LGA    -       -      P      78           -
LGA    -       -      T      79           -
LGA    -       -      R      80           -
LGA    -       -      D      81           -
LGA    -       -      L      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      V      85           -
LGA    V      85      E      86           #
LGA    -       -      G      87           -
LGA    E      86      T      88          2.855
LGA    G      87      A      89          3.400
LGA    T      88      L      90           #
LGA    A      89      P      91           -
LGA    L      90      L      92           -
LGA    P      91      E      93           -
LGA    -       -      P      94           -
LGA    -       -      A      95           -
LGA    -       -      G      96           -
LGA    L      92      L      97           #
LGA    E      93      P      98          3.490
LGA    P      94      D      99          1.830
LGA    A      95      G     100           #
LGA    G      96      V     101          5.344
LGA    L      97      G     102          1.300
LGA    P      98      D     103          1.588
LGA    D      99      T     104           #
LGA    -       -      F     105           -
LGA    G     100      A     106          2.525
LGA    V     101      E     107          3.230
LGA    G     102      K     108          1.511
LGA    D     103      T     109           #
LGA    T     104      G     110           -
LGA    F     105      F     111           #
LGA    -       -      D     112           -
LGA    -       -      P     113           -
LGA    -       -      R     114           -
LGA    -       -      R     115           -
LGA    -       -      L     116           -
LGA    -       -      T     117           -
LGA    -       -      T     118           -
LGA    -       -      S     119           -
LGA    -       -      Y     120           -
LGA    -       -      L     121           -
LGA    A     106      Y     122          3.931
LGA    E     107      F     123          2.386
LGA    K     108      R     124           #
LGA    T     109      -       -           -
LGA    G     110      -       -           -
LGA    F     111      -       -           -
LGA    D     112      -       -           -
LGA    P     113      -       -           -
LGA    R     114      -       -           -
LGA    R     115      -       -           -
LGA    L     116      -       -           -
LGA    T     117      -       -           -
LGA    T     118      -       -           -
LGA    S     119      -       -           -
LGA    Y     120      I     125          5.984
LGA    L     121      S     126           -
LGA    Y     122      P     127           -
LGA    F     123      R     128           -
LGA    R     124      R     129           -
LGA    I     125      V     130           -
LGA    S     126      Q     131           -
LGA    P     127      -       -           -
LGA    R     128      -       -           -
LGA    R     129      -       -           -
LGA    V     130      -       -           -
LGA    Q     131      -       -           -
LGA    A     132      -       -           -
LGA    W     133      -       -           -
LGA    R     134      -       -           -
LGA    E     135      -       -           -
LGA    A     136      -       -           -
LGA    N     137      A     132           #
LGA    E     138      W     133           #
LGA    L     139      R     134          0.721
LGA    S     140      E     135           #
LGA    G     141      A     136          2.393
LGA    R     142      N     137          2.944
LGA    E     143      E     138          2.202
LGA    L     144      L     139          3.828
LGA    M     145      S     140          3.215
LGA    R     146      G     141          5.551
LGA    D     147      R     142          5.157
LGA    G     148      E     143          1.807
LGA    E     149      L     144           #
LGA    W     150      M     145           -
LGA    L     151      R     146           -
LGA    -       -      D     147           -
LGA    -       -      G     148           -
LGA    -       -      E     149           -
LGA    -       -      W     150           -
LGA    -       -      L     151           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  144  144    5.0     32    3.52     9.38     12.710     0.884

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.198209 * X  +  -0.979823 * Y  +   0.025670 * Z  +   7.727266
  Y_new =  -0.386334 * X  +   0.054028 * Y  +  -0.920775 * Z  +  32.092209
  Z_new =   0.900810 * X  +  -0.192424 * Y  +  -0.389248 * Z  +  15.978275 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.682478    0.459115  [ DEG:  -153.6947     26.3053 ]
  Theta =  -1.121632   -2.019961  [ DEG:   -64.2648   -115.7352 ]
  Phi   =  -2.044831    1.096762  [ DEG:  -117.1602     62.8398 ]
 
# 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: T0370TS168_3-D1                               
REMARK     2: T0370_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0370TS168_3-D1.T0370_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  144  144   5.0   32   3.52    9.38  12.710
REMARK  ---------------------------------------------------------- 
MOLECULE T0370TS168_3-D1
PFRMAT TS
TARGET T0370
MODEL 3
PARENT N/A
ATOM      8  CA  THR     8      19.829  49.373  18.939  1.00 25.00           C
ATOM      9  CA  ALA     9      19.348  45.966  17.256  1.00 25.00           C
ATOM     10  CA  LYS    10      20.440  44.196  20.473  1.00 25.00           C
ATOM     11  CA  GLN    11      17.971  46.307  22.501  1.00 25.00           C
ATOM     12  CA  ARG    12      15.167  45.434  20.043  1.00 25.00           C
ATOM     13  CA  ILE    13      16.038  41.716  20.331  1.00 25.00           C
ATOM     14  CA  GLN    14      15.969  41.971  24.152  1.00 25.00           C
ATOM     15  CA  ASP    15      12.551  43.691  24.000  1.00 25.00           C
ATOM     16  CA  THR    16      11.236  40.928  21.695  1.00 25.00           C
ATOM     17  CA  LEU    17      12.541  38.258  24.111  1.00 25.00           C
ATOM     18  CA  ASN    18      10.831  40.038  27.040  1.00 25.00           C
ATOM     19  CA  ARG    19       7.550  40.179  25.070  1.00 25.00           C
ATOM     20  CA  LEU    20       7.828  36.441  24.288  1.00 25.00           C
ATOM     21  CA  GLU    21       8.442  35.687  27.992  1.00 25.00           C
ATOM     22  CA  LEU    22      10.046  32.248  27.809  1.00 25.00           C
ATOM     23  CA  ASP    23      13.626  31.173  28.695  1.00 25.00           C
ATOM     24  CA  VAL    24      14.879  32.791  25.473  1.00 25.00           C
ATOM     25  CA  ASP    25      12.504  31.954  22.587  1.00 25.00           C
ATOM     26  CA  ALA    26      14.794  29.081  21.504  1.00 25.00           C
ATOM     27  CA  TRP    27      14.867  27.752  25.095  1.00 25.00           C
ATOM     28  CA  VAL    28      11.044  27.921  25.260  1.00 25.00           C
ATOM     29  CA  SER    29      10.792  26.027  21.941  1.00 25.00           C
ATOM     30  CA  THR    30      13.195  23.351  23.257  1.00 25.00           C
ATOM     31  CA  ALA    31      10.351  22.773  25.711  1.00 25.00           C
ATOM     32  CA  GLY    32       9.737  19.143  26.464  1.00 25.00           C
ATOM     33  CA  ALA    33      11.312  17.773  23.329  1.00 25.00           C
ATOM     34  CA  ASP    34       9.360  17.674  20.064  1.00 25.00           C
ATOM     35  CA  GLY    35      11.851  19.400  17.763  1.00 25.00           C
ATOM     36  CA  GLY    36      11.963  20.797  14.278  1.00 25.00           C
ATOM     37  CA  ALA    37      12.343  24.253  12.635  1.00 25.00           C
ATOM     38  CA  PRO    38      11.251  27.858  11.940  1.00 25.00           C
ATOM     39  CA  TYR    39       8.308  29.966  13.245  1.00 25.00           C
ATOM     40  CA  LEU    40       5.408  31.741  14.886  1.00 25.00           C
ATOM     41  CA  VAL    41       4.896  34.988  12.863  1.00 25.00           C
ATOM     42  CA  PRO    42       8.252  34.543  11.058  1.00 25.00           C
ATOM     43  CA  LEU    43      11.839  35.432  11.680  1.00 25.00           C
ATOM     44  CA  SER    44      13.120  37.668  14.537  1.00 25.00           C
ATOM     45  CA  TYR    45      11.341  40.229  12.360  1.00 25.00           C
ATOM     46  CA  LEU    46       8.398  39.536  10.051  1.00 25.00           C
ATOM     47  CA  TRP    47       5.687  40.921   7.866  1.00 25.00           C
ATOM     48  CA  ASP    48       3.104  43.679   8.093  1.00 25.00           C
ATOM     49  CA  GLY    49       5.081  44.755  11.194  1.00 25.00           C
ATOM     50  CA  GLU    50       5.862  42.587  14.243  1.00 25.00           C
ATOM     51  CA  THR    51       7.160  39.015  14.923  1.00 25.00           C
ATOM     52  CA  PHE    52       8.265  35.766  16.584  1.00 25.00           C
ATOM     53  CA  LEU    53       9.140  32.724  18.697  1.00 25.00           C
ATOM     54  CA  VAL    54       8.864  29.046  17.858  1.00 25.00           C
ATOM     55  CA  ALA    55       8.717  25.800  15.853  1.00 25.00           C
ATOM     56  CA  THR    56       6.193  23.241  17.054  1.00 25.00           C
ATOM     57  CA  PRO    57       3.441  21.658  14.929  1.00 25.00           C
ATOM     58  CA  ALA    58       1.646  18.364  14.056  1.00 25.00           C
ATOM     59  CA  ALA    59       1.936  16.572  10.674  1.00 25.00           C
ATOM     60  CA  SER    60       2.043  12.793  11.182  1.00 25.00           C
ATOM     61  CA  PRO    61       1.719  10.034   8.527  1.00 25.00           C
ATOM     62  CA  THR    62       5.331   8.844   8.421  1.00 25.00           C
ATOM     63  CA  GLY    63       6.926  11.087   5.784  1.00 25.00           C
ATOM     64  CA  ARG    64       4.606  13.957   4.985  1.00 25.00           C
ATOM     65  CA  ASN    65       2.379  16.962   4.575  1.00 25.00           C
ATOM     66  CA  LEU    66       5.377  19.082   5.518  1.00 25.00           C
ATOM     67  CA  SER    67       6.934  19.539   2.115  1.00 25.00           C
ATOM     68  CA  GLU    68       4.769  22.713   2.012  1.00 25.00           C
ATOM     69  CA  THR    69       6.664  24.055   5.070  1.00 25.00           C
ATOM     70  CA  GLY    70       9.315  24.668   7.727  1.00 25.00           C
ATOM     71  CA  ARG    71       7.406  23.058  10.634  1.00 25.00           C
ATOM     72  CA  VAL    72       5.493  25.791  12.475  1.00 25.00           C
ATOM     73  CA  ARG    73       3.748  27.360  15.433  1.00 25.00           C
ATOM     74  CA  LEU    74       1.560  29.875  17.367  1.00 25.00           C
ATOM     75  CA  GLY    75       0.165  32.718  15.271  1.00 25.00           C
ATOM     76  CA  ILE    76      -0.291  34.081  11.745  1.00 25.00           C
ATOM     77  CA  GLY    77       1.313  37.064   9.905  1.00 25.00           C
ATOM     78  CA  PRO    78      -2.279  38.087   9.153  1.00 25.00           C
ATOM     79  CA  THR    79      -3.757  39.943  12.104  1.00 25.00           C
ATOM     80  CA  ARG    80      -2.569  38.187  15.245  1.00 25.00           C
ATOM     81  CA  ASP    81       1.181  37.656  15.071  1.00 25.00           C
ATOM     82  CA  LEU    82       3.523  37.491  18.035  1.00 25.00           C
ATOM     83  CA  VAL    83       4.277  33.926  19.161  1.00 25.00           C
ATOM     84  CA  LEU    84       5.093  30.874  21.228  1.00 25.00           C
ATOM     85  CA  VAL    85       4.994  27.116  20.384  1.00 25.00           C
ATOM     86  CA  GLU    86       2.421  25.321  22.511  1.00 25.00           C
ATOM     87  CA  GLY    87      -0.036  28.159  21.694  1.00 25.00           C
ATOM     88  CA  THR    88       1.267  30.387  24.544  1.00 25.00           C
ATOM     89  CA  ALA    89       4.188  32.189  26.106  1.00 25.00           C
ATOM     90  CA  LEU    90       2.566  35.198  27.835  1.00 25.00           C
ATOM     91  CA  PRO    91       0.609  34.128  30.876  1.00 25.00           C
ATOM     92  CA  LEU    92      -3.110  34.778  30.579  1.00 25.00           C
ATOM     93  CA  GLU    93      -3.649  38.561  30.571  1.00 25.00           C
ATOM     94  CA  PRO    94      -7.367  39.385  31.036  1.00 25.00           C
ATOM     95  CA  ALA    95      -8.584  37.709  27.815  1.00 25.00           C
ATOM     96  CA  GLY    96      -8.329  41.044  25.997  1.00 25.00           C
ATOM     97  CA  LEU    97      -4.648  41.643  25.166  1.00 25.00           C
ATOM     98  CA  PRO    98      -3.434  45.240  24.461  1.00 25.00           C
ATOM     99  CA  ASP    99      -5.476  46.080  21.344  1.00 25.00           C
ATOM    100  CA  GLY   100      -3.970  44.844  18.055  1.00 25.00           C
ATOM    101  CA  VAL   101      -0.688  44.018  19.791  1.00 25.00           C
ATOM    102  CA  GLY   102       2.719  44.535  21.400  1.00 25.00           C
ATOM    103  CA  ASP   103       1.408  42.057  23.927  1.00 25.00           C
ATOM    104  CA  THR   104       0.895  38.426  23.099  1.00 25.00           C
ATOM    105  CA  PHE   105      -0.689  36.153  20.423  1.00 25.00           C
ATOM    106  CA  ALA   106      -2.311  32.763  20.260  1.00 25.00           C
ATOM    107  CA  GLU   107      -5.375  31.280  21.949  1.00 25.00           C
ATOM    108  CA  LYS   108      -7.535  29.254  24.360  1.00 25.00           C
ATOM    109  CA  THR   109      -9.358  27.797  21.443  1.00 25.00           C
ATOM    110  CA  GLY   110     -11.807  27.637  18.569  1.00 25.00           C
ATOM    111  CA  PHE   111     -13.954  29.880  16.410  1.00 25.00           C
ATOM    112  CA  ASP   112     -13.250  27.718  13.322  1.00 25.00           C
ATOM    113  CA  PRO   113     -10.784  30.150  11.778  1.00 25.00           C
ATOM    114  CA  ARG   114      -9.491  30.109   8.173  1.00 25.00           C
ATOM    115  CA  ARG   115      -8.146  26.558   8.670  1.00 25.00           C
ATOM    116  CA  LEU   116      -9.624  24.091  11.160  1.00 25.00           C
ATOM    117  CA  THR   117      -9.509  24.245  14.905  1.00 25.00           C
ATOM    118  CA  THR   118      -6.643  24.430  17.324  1.00 25.00           C
ATOM    119  CA  SER   119      -3.428  25.593  18.990  1.00 25.00           C
ATOM    120  CA  TYR   120       0.033  24.395  17.978  1.00 25.00           C
ATOM    121  CA  LEU   121      -0.755  25.646  14.461  1.00 25.00           C
ATOM    122  CA  TYR   122       0.207  28.136  11.831  1.00 25.00           C
ATOM    123  CA  PHE   123       3.022  30.398  10.666  1.00 25.00           C
ATOM    124  CA  ARG   124       6.293  29.774   8.751  1.00 25.00           C
ATOM    125  CA  ILE   125       5.293  31.471   5.445  1.00 25.00           C
ATOM    126  CA  SER   126       5.791  33.266   2.130  1.00 25.00           C
ATOM    127  CA  PRO   127       8.908  34.449   0.307  1.00 25.00           C
ATOM    128  CA  ARG   128      10.058  36.949   2.970  1.00 25.00           C
ATOM    129  CA  ARG   129       9.358  34.377   5.721  1.00 25.00           C
ATOM    130  CA  VAL   130      11.360  31.739   3.797  1.00 25.00           C
ATOM    131  CA  GLN   131      14.273  34.195   3.409  1.00 25.00           C
ATOM    132  CA  ALA   132      14.168  34.949   7.163  1.00 25.00           C
ATOM    133  CA  TRP   133      14.200  31.199   7.942  1.00 25.00           C
ATOM    134  CA  ARG   134      17.202  30.716   5.613  1.00 25.00           C
ATOM    135  CA  GLU   135      19.035  33.602   7.339  1.00 25.00           C
ATOM    136  CA  ALA   136      18.305  32.050  10.763  1.00 25.00           C
ATOM    137  CA  ASN   137      19.633  28.672   9.543  1.00 25.00           C
ATOM    138  CA  GLU   138      22.811  30.365   8.238  1.00 25.00           C
ATOM    139  CA  LEU   139      23.287  32.124  11.606  1.00 25.00           C
ATOM    140  CA  SER   140      22.853  28.789  13.438  1.00 25.00           C
ATOM    141  CA  GLY   141      25.435  27.155  11.129  1.00 25.00           C
ATOM    142  CA  ARG   142      27.881  30.026  11.795  1.00 25.00           C
ATOM    143  CA  GLU   143      27.357  29.630  15.567  1.00 25.00           C
ATOM    144  CA  LEU   144      28.002  25.866  15.287  1.00 25.00           C
ATOM    145  CA  MET   145      24.649  25.243  16.904  1.00 25.00           C
ATOM    146  CA  ARG   146      24.208  22.449  14.373  1.00 25.00           C
ATOM    147  CA  ASP   147      22.528  20.242  16.974  1.00 25.00           C
ATOM    148  CA  GLY   148      20.386  22.717  18.885  1.00 25.00           C
ATOM    149  CA  GLU   149      17.078  23.562  17.229  1.00 25.00           C
ATOM    150  CA  TRP   150      13.350  24.457  17.555  1.00 25.00           C
ATOM    151  CA  LEU   151      13.758  28.104  16.563  1.00 25.00           C
TER
END
