
#######################################################
#                                                     #
#                        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  160 (  160),  selected  160 , name T0374TS393_2
# Molecule2: number of CA atoms  160 ( 2486),  selected  160 , name T0374.pdb
# PARAMETERS: T0374TS393_2.T0374.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          5.565
LGA    Q       2      Q       2          2.594
LGA    L       3      L       3          1.636
LGA    S       4      S       4          2.225
LGA    H       5      H       5          2.059
LGA    R       6      R       6          1.590
LGA    P       7      P       7          1.945
LGA    A       8      A       8          2.936
LGA    E       9      E       9          4.916
LGA    T      10      T      10           #
LGA    G      11      G      11          1.176
LGA    D      12      D      12          1.096
LGA    L      13      L      13          1.482
LGA    E      14      E      14          1.187
LGA    T      15      T      15          2.260
LGA    V      16      V      16          2.762
LGA    A      17      A      17          1.702
LGA    G      18      G      18          2.394
LGA    F      19      F      19          2.720
LGA    P      20      P      20          1.200
LGA    Q      21      Q      21          2.617
LGA    D      22      -       -           -
LGA    R      23      D      22          3.991
LGA    D      24      R      23          4.204
LGA    E      25      D      24          3.340
LGA    L      26      E      25          4.461
LGA    F      27      -       -           -
LGA    Y      28      L      26           #
LGA    C      29      F      27          0.518
LGA    Y      30      Y      28           #
LGA    P      31      C      29           -
LGA    K      32      Y      30           -
LGA    A      33      P      31           -
LGA    -       -      K      32           -
LGA    -       -      A      33           -
LGA    -       -      I      34           -
LGA    I      34      W      35          2.914
LGA    -       -      P      36           -
LGA    W      35      F      37           #
LGA    P      36      S      38           -
LGA    -       -      V      39           -
LGA    F      37      A      40           #
LGA    S      38      Q      41          3.107
LGA    V      39      L      42          3.640
LGA    A      40      A      43          4.026
LGA    Q      41      A      44          1.938
LGA    L      42      A      45          2.576
LGA    A      43      I      46          4.419
LGA    A      44      A      47          3.158
LGA    A      45      E      48          3.978
LGA    I      46      -       -           -
LGA    A      47      -       -           -
LGA    E      48      -       -           -
LGA    R      49      R      49           #
LGA    R      50      R      50          1.618
LGA    G      51      G      51          0.947
LGA    S      52      S      52          1.595
LGA    T      53      T      53          2.129
LGA    V      54      V      54          1.661
LGA    A      55      A      55          2.149
LGA    V      56      V      56          1.418
LGA    H      57      H      57          2.137
LGA    D      58      D      58          1.593
LGA    G      59      G      59          1.854
LGA    Q      60      Q      60          1.753
LGA    V      61      V      61          2.497
LGA    L      62      L      62          1.153
LGA    G      63      G      63          1.666
LGA    F      64      F      64          1.712
LGA    A      65      A      65          1.361
LGA    N      66      N      66          2.840
LGA    F      67      F      67          1.932
LGA    Y      68      Y      68          2.788
LGA    Q      69      Q      69          2.635
LGA    W      70      W      70          4.181
LGA    -       -      Q      71           -
LGA    Q      71      H      72           #
LGA    H      72      G      73           -
LGA    G      73      -       -           -
LGA    D      74      D      74          3.475
LGA    F      75      F      75          2.588
LGA    C      76      C      76          0.883
LGA    A      77      A      77          0.967
LGA    L      78      L      78          1.087
LGA    G      79      G      79          1.697
LGA    N      80      N      80          3.172
LGA    M      81      M      81          2.679
LGA    M      82      M      82          1.844
LGA    V      83      V      83          2.270
LGA    A      84      A      84          2.405
LGA    P      85      P      85          1.643
LGA    A      86      A      86          1.904
LGA    A      87      A      87          1.365
LGA    R      88      R      88          2.280
LGA    G      89      G      89          1.591
LGA    L      90      L      90          1.410
LGA    G      91      G      91          1.440
LGA    V      92      V      92          0.914
LGA    A      93      A      93          0.657
LGA    R      94      R      94          1.294
LGA    Y      95      Y      95          1.057
LGA    L      96      L      96          0.308
LGA    I      97      I      97          1.033
LGA    G      98      G      98          1.401
LGA    V      99      V      99          0.795
LGA    M     100      M     100          0.314
LGA    E     101      E     101          1.019
LGA    N     102      N     102          1.031
LGA    L     103      L     103          0.543
LGA    A     104      A     104          0.388
LGA    R     105      R     105          0.683
LGA    E     106      E     106          0.725
LGA    Q     107      Q     107          0.566
LGA    Y     108      Y     108          0.862
LGA    K     109      K     109          4.212
LGA    A     110      A     110          1.638
LGA    R     111      R     111          1.921
LGA    L     112      L     112          1.770
LGA    M     113      M     113          1.695
LGA    K     114      K     114          2.522
LGA    I     115      I     115          2.203
LGA    S     116      S     116          4.137
LGA    C     117      C     117          2.937
LGA    F     118      F     118          2.593
LGA    N     119      N     119          2.579
LGA    A     120      A     120          3.377
LGA    N     121      N     121          1.555
LGA    A     122      A     122          1.248
LGA    A     123      A     123          0.642
LGA    G     124      G     124          0.690
LGA    L     125      L     125          1.158
LGA    L     126      L     126          1.683
LGA    L     127      L     127          1.569
LGA    Y     128      Y     128          0.821
LGA    T     129      T     129          1.455
LGA    Q     130      Q     130          2.163
LGA    L     131      L     131          1.735
LGA    G     132      G     132          1.279
LGA    Y     133      Y     133          0.372
LGA    Q     134      Q     134          0.700
LGA    P     135      P     135          1.481
LGA    R     136      R     136          2.706
LGA    A     137      A     137          2.351
LGA    I     138      I     138          1.334
LGA    A     139      A     139          0.512
LGA    E     140      E     140          1.951
LGA    R     141      R     141          1.667
LGA    H     142      H     142          2.164
LGA    D     143      D     143           #
LGA    P     144      P     144          4.981
LGA    D     145      D     145          2.565
LGA    G     146      G     146          2.607
LGA    R     147      R     147          2.679
LGA    R     148      R     148          3.243
LGA    V     149      V     149          3.580
LGA    A     150      A     150           #
LGA    L     151      L     151           #
LGA    I     152      I     152          4.402
LGA    Q     153      Q     153          2.228
LGA    M     154      M     154          1.962
LGA    D     155      D     155          2.037
LGA    K     156      K     156          3.670
LGA    P     157      P     157          3.563
LGA    L     158      L     158          3.200
LGA    E     159      E     159          3.276
LGA    P     160      P     160          4.233

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  160  160    5.0    139    2.39    91.37     60.384     5.589

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.369682 * X  +   0.916833 * Y  +   0.150839 * Z  +  16.463367
  Y_new =  -0.871672 * X  +   0.398425 * Y  +  -0.285386 * Z  +  11.890294
  Z_new =  -0.321750 * X  +  -0.025980 * Y  +   0.946468 * Z  +   9.003348 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.027443    3.114150  [ DEG:    -1.5723    178.4276 ]
  Theta =   0.327577    2.814016  [ DEG:    18.7688    161.2312 ]
  Phi   =  -1.169683    1.971910  [ DEG:   -67.0179    112.9821 ]
 
# 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: T0374TS393_2                                  
REMARK     2: T0374.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0374TS393_2.T0374.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  160  160   5.0  139   2.39   91.37  60.384
REMARK  ---------------------------------------------------------- 
MOLECULE T0374TS393_2
PFRMAT TS
TARGET T0374
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      23.775  32.694   2.227  1.00 25.00           C
ATOM      2  CA  GLN     2      23.838  29.866   4.763  1.00 25.00           C
ATOM      3  CA  LEU     3      21.883  27.493   7.062  1.00 25.00           C
ATOM      4  CA  SER     4      18.549  26.868   8.902  1.00 25.00           C
ATOM      5  CA  HIS     5      15.788  24.479  10.102  1.00 25.00           C
ATOM      6  CA  ARG     6      12.087  25.353   9.619  1.00 25.00           C
ATOM      7  CA  PRO     7       8.328  24.958   9.474  1.00 25.00           C
ATOM      8  CA  ALA     8       6.448  24.180   6.253  1.00 25.00           C
ATOM      9  CA  GLU     9       5.775  27.716   4.951  1.00 25.00           C
ATOM     10  CA  THR    10       3.632  27.760   1.815  1.00 25.00           C
ATOM     11  CA  GLY    11       4.377  24.923  -0.664  1.00 25.00           C
ATOM     12  CA  ASP    12       7.008  22.449   0.574  1.00 25.00           C
ATOM     13  CA  LEU    13       5.709  18.884   0.052  1.00 25.00           C
ATOM     14  CA  GLU    14       7.748  18.586  -3.176  1.00 25.00           C
ATOM     15  CA  THR    15      10.876  19.822  -1.344  1.00 25.00           C
ATOM     16  CA  VAL    16      10.288  17.256   1.438  1.00 25.00           C
ATOM     17  CA  ALA    17       9.902  14.479  -1.170  1.00 25.00           C
ATOM     18  CA  GLY    18      13.160  15.575  -2.857  1.00 25.00           C
ATOM     19  CA  PHE    19      15.650  14.712  -0.116  1.00 25.00           C
ATOM     20  CA  PRO    20      16.148  11.618  -2.190  1.00 25.00           C
ATOM     21  CA  GLN    21      16.369  11.470  -5.947  1.00 25.00           C
ATOM     22  CA  ASP    22      20.033  12.237  -6.633  1.00 25.00           C
ATOM     23  CA  ARG    23      21.738   8.859  -6.233  1.00 25.00           C
ATOM     24  CA  ASP    24      19.354   6.755  -4.235  1.00 25.00           C
ATOM     25  CA  GLU    25      22.280   4.285  -4.203  1.00 25.00           C
ATOM     26  CA  LEU    26      23.736   6.010  -1.110  1.00 25.00           C
ATOM     27  CA  PHE    27      20.332   5.813   0.633  1.00 25.00           C
ATOM     28  CA  TYR    28      19.487   2.068   0.407  1.00 25.00           C
ATOM     29  CA  CYS    29      15.865   3.312   0.346  1.00 25.00           C
ATOM     30  CA  TYR    30      15.584   2.960  -3.475  1.00 25.00           C
ATOM     31  CA  PRO    31      15.695   2.248  -7.181  1.00 25.00           C
ATOM     32  CA  LYS    32      12.347   0.428  -6.563  1.00 25.00           C
ATOM     33  CA  ALA    33      10.191   1.891  -9.377  1.00 25.00           C
ATOM     34  CA  ILE    34       8.172   3.652  -6.757  1.00 25.00           C
ATOM     35  CA  TRP    35       8.808   2.435  -3.164  1.00 25.00           C
ATOM     36  CA  PRO    36       5.132   3.195  -2.564  1.00 25.00           C
ATOM     37  CA  PHE    37       5.805   6.643  -1.101  1.00 25.00           C
ATOM     38  CA  SER    38       2.476   6.989   0.582  1.00 25.00           C
ATOM     39  CA  VAL    39       3.153  10.690   0.169  1.00 25.00           C
ATOM     40  CA  ALA    40      -0.354  11.734   1.302  1.00 25.00           C
ATOM     41  CA  GLN    41       0.102   9.798   4.575  1.00 25.00           C
ATOM     42  CA  LEU    42       3.481  11.508   5.145  1.00 25.00           C
ATOM     43  CA  ALA    43       1.884  14.931   4.514  1.00 25.00           C
ATOM     44  CA  ALA    44      -0.910  14.113   7.003  1.00 25.00           C
ATOM     45  CA  ALA    45       1.689  13.056   9.610  1.00 25.00           C
ATOM     46  CA  ILE    46       3.611  16.322   9.056  1.00 25.00           C
ATOM     47  CA  ALA    47       0.376  18.326   9.481  1.00 25.00           C
ATOM     48  CA  GLU    48      -0.392  16.445  12.728  1.00 25.00           C
ATOM     49  CA  ARG    49       1.125  14.099  15.349  1.00 25.00           C
ATOM     50  CA  ARG    50       4.939  14.154  15.105  1.00 25.00           C
ATOM     51  CA  GLY    51       7.599  16.818  14.249  1.00 25.00           C
ATOM     52  CA  SER    52       9.859  17.767  11.329  1.00 25.00           C
ATOM     53  CA  THR    53      13.095  19.254   9.988  1.00 25.00           C
ATOM     54  CA  VAL    54      12.029  20.549   6.598  1.00 25.00           C
ATOM     55  CA  ALA    55      15.216  22.345   5.506  1.00 25.00           C
ATOM     56  CA  VAL    56      15.521  25.887   4.195  1.00 25.00           C
ATOM     57  CA  HIS    57      18.917  26.701   2.645  1.00 25.00           C
ATOM     58  CA  ASP    58      18.751  30.184   1.009  1.00 25.00           C
ATOM     59  CA  GLY    59      15.582  29.656  -1.094  1.00 25.00           C
ATOM     60  CA  GLN    60      16.580  26.050  -1.830  1.00 25.00           C
ATOM     61  CA  VAL    61      15.179  22.651  -0.716  1.00 25.00           C
ATOM     62  CA  LEU    62      18.030  21.048   1.226  1.00 25.00           C
ATOM     63  CA  GLY    63      18.668  18.847   4.272  1.00 25.00           C
ATOM     64  CA  PHE    64      15.864  17.008   6.006  1.00 25.00           C
ATOM     65  CA  ALA    65      14.991  14.658   8.813  1.00 25.00           C
ATOM     66  CA  ASN    66      11.707  12.770   8.917  1.00 25.00           C
ATOM     67  CA  PHE    67      11.215  12.842  12.655  1.00 25.00           C
ATOM     68  CA  TYR    68       9.513  10.430  15.117  1.00 25.00           C
ATOM     69  CA  GLN    69       8.601   9.285  18.665  1.00 25.00           C
ATOM     70  CA  TRP    70       9.410   5.583  19.000  1.00 25.00           C
ATOM     71  CA  GLN    71       6.783   4.994  21.727  1.00 25.00           C
ATOM     72  CA  HIS    72       7.276   1.981  24.006  1.00 25.00           C
ATOM     73  CA  GLY    73      10.663   2.084  25.672  1.00 25.00           C
ATOM     74  CA  ASP    74      11.557   5.821  25.396  1.00 25.00           C
ATOM     75  CA  PHE    75      13.707   6.799  22.423  1.00 25.00           C
ATOM     76  CA  CYS    76      12.971  10.279  21.063  1.00 25.00           C
ATOM     77  CA  ALA    77      13.625   8.773  17.576  1.00 25.00           C
ATOM     78  CA  LEU    78      15.260  10.745  14.755  1.00 25.00           C
ATOM     79  CA  GLY    79      14.679   9.388  11.268  1.00 25.00           C
ATOM     80  CA  ASN    80      16.670   9.969   8.096  1.00 25.00           C
ATOM     81  CA  MET    81      19.460  12.404   7.280  1.00 25.00           C
ATOM     82  CA  MET    82      18.327  12.686   3.684  1.00 25.00           C
ATOM     83  CA  VAL    83      20.949  14.930   2.062  1.00 25.00           C
ATOM     84  CA  ALA    84      21.055  16.444  -1.396  1.00 25.00           C
ATOM     85  CA  PRO    85      23.808  16.254  -4.084  1.00 25.00           C
ATOM     86  CA  ALA    86      22.458  19.722  -4.987  1.00 25.00           C
ATOM     87  CA  ALA    87      23.757  21.120  -1.666  1.00 25.00           C
ATOM     88  CA  ARG    88      26.567  19.743   0.473  1.00 25.00           C
ATOM     89  CA  GLY    89      29.294  19.371   3.154  1.00 25.00           C
ATOM     90  CA  LEU    90      28.118  22.897   4.133  1.00 25.00           C
ATOM     91  CA  GLY    91      27.125  22.338   7.728  1.00 25.00           C
ATOM     92  CA  VAL    92      23.624  20.977   6.977  1.00 25.00           C
ATOM     93  CA  ALA    93      22.233  17.466   7.617  1.00 25.00           C
ATOM     94  CA  ARG    94      24.213  17.252  10.888  1.00 25.00           C
ATOM     95  CA  TYR    95      22.854  20.668  11.962  1.00 25.00           C
ATOM     96  CA  LEU    96      19.286  19.528  11.167  1.00 25.00           C
ATOM     97  CA  ILE    97      19.822  16.338  13.220  1.00 25.00           C
ATOM     98  CA  GLY    98      21.143  18.418  16.151  1.00 25.00           C
ATOM     99  CA  VAL    99      18.088  20.716  15.931  1.00 25.00           C
ATOM    100  CA  MET   100      15.767  17.669  15.925  1.00 25.00           C
ATOM    101  CA  GLU   101      17.569  16.261  18.998  1.00 25.00           C
ATOM    102  CA  ASN   102      17.203  19.629  20.786  1.00 25.00           C
ATOM    103  CA  LEU   103      13.468  19.698  19.942  1.00 25.00           C
ATOM    104  CA  ALA   104      13.070  16.139  21.297  1.00 25.00           C
ATOM    105  CA  ARG   105      14.882  17.135  24.520  1.00 25.00           C
ATOM    106  CA  GLU   106      12.590  20.181  24.896  1.00 25.00           C
ATOM    107  CA  GLN   107       9.340  18.833  23.538  1.00 25.00           C
ATOM    108  CA  TYR   108       9.009  15.457  25.219  1.00 25.00           C
ATOM    109  CA  LYS   109       9.081  12.281  27.341  1.00 25.00           C
ATOM    110  CA  ALA   110      12.587  11.946  25.822  1.00 25.00           C
ATOM    111  CA  ARG   111      16.127  10.547  26.243  1.00 25.00           C
ATOM    112  CA  LEU   112      17.753   9.881  22.865  1.00 25.00           C
ATOM    113  CA  MET   113      18.020  10.919  19.198  1.00 25.00           C
ATOM    114  CA  LYS   114      19.282   8.366  16.591  1.00 25.00           C
ATOM    115  CA  ILE   115      19.992   7.529  12.932  1.00 25.00           C
ATOM    116  CA  SER   116      20.607   6.275   9.374  1.00 25.00           C
ATOM    117  CA  CYS   117      21.497   3.357   7.102  1.00 25.00           C
ATOM    118  CA  PHE   118      24.607   1.640   8.458  1.00 25.00           C
ATOM    119  CA  ASN   119      28.061   0.191   7.996  1.00 25.00           C
ATOM    120  CA  ALA   120      29.281   1.828   4.838  1.00 25.00           C
ATOM    121  CA  ASN   121      27.477   5.151   4.103  1.00 25.00           C
ATOM    122  CA  ALA   122      30.497   6.751   5.675  1.00 25.00           C
ATOM    123  CA  ALA   123      28.586  10.070   5.658  1.00 25.00           C
ATOM    124  CA  GLY   124      26.126   8.694   8.250  1.00 25.00           C
ATOM    125  CA  LEU   125      29.044   7.548  10.449  1.00 25.00           C
ATOM    126  CA  LEU   126      30.644  11.016  10.176  1.00 25.00           C
ATOM    127  CA  LEU   127      27.323  12.653  11.154  1.00 25.00           C
ATOM    128  CA  TYR   128      27.030  10.310  14.170  1.00 25.00           C
ATOM    129  CA  THR   129      30.606  11.183  15.226  1.00 25.00           C
ATOM    130  CA  GLN   130      29.810  14.917  14.926  1.00 25.00           C
ATOM    131  CA  LEU   131      28.622  14.465  18.506  1.00 25.00           C
ATOM    132  CA  GLY   132      29.379  11.164  20.270  1.00 25.00           C
ATOM    133  CA  TYR   133      26.508   9.071  19.115  1.00 25.00           C
ATOM    134  CA  GLN   134      27.387   5.569  20.231  1.00 25.00           C
ATOM    135  CA  PRO   135      27.426   3.435  17.109  1.00 25.00           C
ATOM    136  CA  ARG   136      25.347   0.259  17.652  1.00 25.00           C
ATOM    137  CA  ALA   137      21.979  -1.375  17.046  1.00 25.00           C
ATOM    138  CA  ILE   138      22.713  -3.196  13.789  1.00 25.00           C
ATOM    139  CA  ALA   139      19.740  -5.338  12.996  1.00 25.00           C
ATOM    140  CA  GLU   140      17.658  -6.932  10.307  1.00 25.00           C
ATOM    141  CA  ARG   141      16.588  -6.849   6.660  1.00 25.00           C
ATOM    142  CA  HIS   142      14.816  -7.163   3.313  1.00 25.00           C
ATOM    143  CA  ASP   143      11.936  -9.343   2.088  1.00 25.00           C
ATOM    144  CA  PRO   144      11.753  -7.263  -1.023  1.00 25.00           C
ATOM    145  CA  ASP   145      15.300  -6.698  -2.247  1.00 25.00           C
ATOM    146  CA  GLY   146      18.827  -7.788  -1.182  1.00 25.00           C
ATOM    147  CA  ARG   147      21.907  -6.722   0.862  1.00 25.00           C
ATOM    148  CA  ARG   148      21.246  -5.205   4.285  1.00 25.00           C
ATOM    149  CA  VAL   149      20.811  -2.176   6.538  1.00 25.00           C
ATOM    150  CA  ALA   150      18.337  -0.318   8.699  1.00 25.00           C
ATOM    151  CA  LEU   151      16.469   1.130  11.669  1.00 25.00           C
ATOM    152  CA  ILE   152      19.903   2.491  12.571  1.00 25.00           C
ATOM    153  CA  GLN   153      20.769   3.488  16.124  1.00 25.00           C
ATOM    154  CA  MET   154      22.376   5.244  19.079  1.00 25.00           C
ATOM    155  CA  ASP   155      22.600   7.342  22.296  1.00 25.00           C
ATOM    156  CA  LYS   156      22.619   8.826  25.797  1.00 25.00           C
ATOM    157  CA  PRO   157      24.305  10.715  28.652  1.00 25.00           C
ATOM    158  CA  LEU   158      21.683  13.443  28.656  1.00 25.00           C
ATOM    159  CA  GLU   159      22.980  16.116  31.075  1.00 25.00           C
ATOM    160  CA  PRO   160      20.047  16.995  33.287  1.00 25.00           C
TER
END
