
#######################################################
#                                                     #
#                        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  108 (  108),  selected  108 , name T0291TS393_5-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS393_5-D1.T0291_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       1      -       -           -
LGA    Y       2      T       1          2.616
LGA    V       3      Y       2          4.367
LGA    D       4      V       3          4.623
LGA    P       5      D       4          4.970
LGA    H       6      P       5          2.866
LGA    T       7      H       6          5.302
LGA    Y       8      -       -           -
LGA    E       9      -       -           -
LGA    D      10      -       -           -
LGA    P      11      -       -           -
LGA    T      12      -       -           -
LGA    Q      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      V      15          1.169
LGA    H      16      H      16          0.753
LGA    E      17      E      17          1.416
LGA    F      18      F      18          0.758
LGA    A      19      A      19          1.000
LGA    K      20      K      20          3.739
LGA    E      21      E      21          3.306
LGA    L      22      L      22          4.430
LGA    D      23      D      23          3.442
LGA    A      24      A      24          4.615
LGA    T      25      T      25           #
LGA    N      26      N      26           #
LGA    I      27      I      27           #
LGA    S      28      -       -           -
LGA    I      29      -       -           -
LGA    D      30      -       -           -
LGA    K      31      S      28           #
LGA    -       -      I      29           -
LGA    V      32      D      30          3.301
LGA    V      33      K      31          3.615
LGA    -       -      V      32           -
LGA    G      34      V      33          1.846
LGA    A      35      G      34          2.381
LGA    G      36      A      35          2.350
LGA    E      37      G      36          1.756
LGA    F      38      E      37          2.645
LGA    -       -      F      38           -
LGA    -       -      G      39           -
LGA    G      39      E      40          2.500
LGA    E      40      V      41          0.543
LGA    V      41      C      42          1.648
LGA    C      42      S      43          4.902
LGA    S      43      G      44          3.556
LGA    G      44      -       -           -
LGA    R      45      -       -           -
LGA    L      46      -       -           -
LGA    K      47      -       -           -
LGA    L      48      -       -           -
LGA    P      49      -       -           -
LGA    S      50      -       -           -
LGA    K      51      -       -           -
LGA    K      52      -       -           -
LGA    E      53      -       -           -
LGA    I      54      R      45          4.390
LGA    S      55      L      46          4.247
LGA    V      56      K      47           #
LGA    -       -      L      48           -
LGA    -       -      P      49           -
LGA    -       -      S      50           -
LGA    -       -      K      51           -
LGA    -       -      K      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      S      55           -
LGA    -       -      V      56           -
LGA    A      57      A      57          3.041
LGA    I      58      I      58          0.808
LGA    K      59      K      59          1.332
LGA    T      60      T      60          1.070
LGA    L      61      L      61          1.635
LGA    K      62      K      62          2.105
LGA    V      63      V      63          1.563
LGA    G      64      G      64          1.782
LGA    Y      65      Y      65          0.820
LGA    T      66      T      66          2.440
LGA    E      67      E      67          0.943
LGA    K      68      K      68          1.623
LGA    Q      69      Q      69          1.274
LGA    R      70      R      70          0.319
LGA    R      71      R      71          1.020
LGA    D      72      D      72          1.221
LGA    F      73      F      73          0.743
LGA    L      74      L      74          1.637
LGA    G      75      G      75          1.603
LGA    E      76      E      76          1.521
LGA    A      77      A      77          1.132
LGA    S      78      S      78          2.142
LGA    I      79      I      79          2.839
LGA    M      80      M      80          1.822
LGA    G      81      G      81          2.142
LGA    Q      82      Q      82          3.888
LGA    F      83      F      83          2.878
LGA    D      84      D      84          2.405
LGA    H      85      H      85          2.039
LGA    P      86      P      86          1.976
LGA    N      87      N      87          2.313
LGA    I      88      I      88          2.558
LGA    I      89      I      89          1.450
LGA    R      90      R      90          1.098
LGA    L      91      L      91          1.992
LGA    E      92      E      92          0.856
LGA    G      93      G      93          0.558
LGA    V      94      V      94          1.620
LGA    V      95      V      95          2.196
LGA    T      96      T      96          1.191
LGA    K      97      K      97          2.005
LGA    S      98      S      98          2.335
LGA    K      99      K      99          0.741
LGA    P     100      P     100          1.000
LGA    V     101      V     101          1.160
LGA    M     102      M     102          1.632
LGA    I     103      I     103          0.460
LGA    V     104      V     104          0.696
LGA    T     105      T     105          0.937
LGA    E     106      E     106          1.332
LGA    Y     107      Y     107          1.197
LGA    M     108      M     108          3.784

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     82    2.45    75.61     58.508     3.211

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.742253 * X  +   0.406378 * Y  +   0.532839 * Z  +  -1.649377
  Y_new =  -0.597816 * X  +  -0.042286 * Y  +  -0.800517 * Z  +   8.955132
  Z_new =  -0.302781 * X  +  -0.912726 * Y  +   0.274326 * Z  +  54.122852 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.278829    1.862764  [ DEG:   -73.2715    106.7285 ]
  Theta =   0.307609    2.833983  [ DEG:    17.6247    162.3753 ]
  Phi   =  -2.463563    0.678029  [ DEG:  -141.1518     38.8482 ]
 
# 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: T0291TS393_5-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS393_5-D1.T0291_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  100   5.0   82   2.45   75.61  58.508
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS393_5-D1
PFRMAT TS
TARGET T0291
MODEL 5
PARENT N/A
ATOM      1  CA  THR     1      -1.847  33.945  45.939  1.00 25.00           C
ATOM      2  CA  TYR     2      -4.038  31.120  47.198  1.00 25.00           C
ATOM      3  CA  VAL     3      -7.392  29.584  48.051  1.00 25.00           C
ATOM      4  CA  ASP     4     -10.597  28.872  49.971  1.00 25.00           C
ATOM      5  CA  PRO     5     -12.386  28.234  53.226  1.00 25.00           C
ATOM      6  CA  HIS     6     -11.001  31.001  55.410  1.00 25.00           C
ATOM      7  CA  THR     7     -14.042  32.369  57.178  1.00 25.00           C
ATOM      8  CA  TYR     8     -15.024  34.698  54.288  1.00 25.00           C
ATOM      9  CA  GLU     9     -18.680  35.803  54.846  1.00 25.00           C
ATOM     10  CA  ASP    10     -20.420  32.378  54.954  1.00 25.00           C
ATOM     11  CA  PRO    11     -17.930  29.484  55.300  1.00 25.00           C
ATOM     12  CA  THR    12     -20.565  27.395  53.467  1.00 25.00           C
ATOM     13  CA  GLN    13     -20.432  29.796  50.486  1.00 25.00           C
ATOM     14  CA  ALA    14     -16.611  29.542  50.421  1.00 25.00           C
ATOM     15  CA  VAL    15     -16.839  25.720  50.492  1.00 25.00           C
ATOM     16  CA  HIS    16     -19.348  25.792  47.600  1.00 25.00           C
ATOM     17  CA  GLU    17     -17.017  28.080  45.601  1.00 25.00           C
ATOM     18  CA  PHE    18     -14.085  25.704  46.254  1.00 25.00           C
ATOM     19  CA  ALA    19     -16.203  22.731  45.094  1.00 25.00           C
ATOM     20  CA  LYS    20     -17.168  24.630  41.911  1.00 25.00           C
ATOM     21  CA  GLU    21     -19.842  22.008  41.382  1.00 25.00           C
ATOM     22  CA  LEU    22     -23.439  20.751  41.383  1.00 25.00           C
ATOM     23  CA  ASP    23     -26.439  18.428  40.877  1.00 25.00           C
ATOM     24  CA  ALA    24     -23.770  15.726  40.787  1.00 25.00           C
ATOM     25  CA  THR    25     -23.994  15.971  36.972  1.00 25.00           C
ATOM     26  CA  ASN    26     -20.487  14.466  36.645  1.00 25.00           C
ATOM     27  CA  ILE    27     -17.748  11.777  36.520  1.00 25.00           C
ATOM     28  CA  SER    28     -16.480   8.229  35.905  1.00 25.00           C
ATOM     29  CA  ILE    29     -14.801   5.049  37.134  1.00 25.00           C
ATOM     30  CA  ASP    30     -14.361   2.148  39.480  1.00 25.00           C
ATOM     31  CA  LYS    31     -15.939   0.639  42.550  1.00 25.00           C
ATOM     32  CA  VAL    32     -16.622  -1.532  45.600  1.00 25.00           C
ATOM     33  CA  VAL    33     -14.693  -1.000  48.837  1.00 25.00           C
ATOM     34  CA  GLY    34     -14.130  -1.311  52.538  1.00 25.00           C
ATOM     35  CA  ALA    35     -14.411   0.705  55.801  1.00 25.00           C
ATOM     36  CA  GLY    36     -14.700   3.107  58.770  1.00 25.00           C
ATOM     37  CA  GLU    37     -14.784   6.265  60.967  1.00 25.00           C
ATOM     38  CA  PHE    38     -17.407   8.911  60.357  1.00 25.00           C
ATOM     39  CA  GLY    39     -18.130   7.296  56.928  1.00 25.00           C
ATOM     40  CA  GLU    40     -16.838   4.825  54.293  1.00 25.00           C
ATOM     41  CA  VAL    41     -15.677   3.929  50.845  1.00 25.00           C
ATOM     42  CA  CYS    42     -19.454   3.853  50.120  1.00 25.00           C
ATOM     43  CA  SER    43     -19.625   3.159  46.385  1.00 25.00           C
ATOM     44  CA  GLY    44     -21.541   5.880  44.540  1.00 25.00           C
ATOM     45  CA  ARG    45     -23.204   6.961  41.361  1.00 25.00           C
ATOM     46  CA  LEU    46     -22.132   9.987  39.357  1.00 25.00           C
ATOM     47  CA  LYS    47     -22.466   9.929  35.540  1.00 25.00           C
ATOM     48  CA  LEU    48     -24.194  12.599  33.423  1.00 25.00           C
ATOM     49  CA  PRO    49     -22.133  13.039  30.187  1.00 25.00           C
ATOM     50  CA  SER    50     -24.257  10.311  28.579  1.00 25.00           C
ATOM     51  CA  LYS    51     -23.585   7.109  30.523  1.00 25.00           C
ATOM     52  CA  LYS    52     -19.958   6.035  30.498  1.00 25.00           C
ATOM     53  CA  GLU    53     -20.945   4.417  33.813  1.00 25.00           C
ATOM     54  CA  ILE    54     -19.600   2.921  37.024  1.00 25.00           C
ATOM     55  CA  SER    55     -18.687   4.657  40.304  1.00 25.00           C
ATOM     56  CA  VAL    56     -16.875   7.562  42.067  1.00 25.00           C
ATOM     57  CA  ALA    57     -16.240   6.800  45.776  1.00 25.00           C
ATOM     58  CA  ILE    58     -17.468   8.595  48.909  1.00 25.00           C
ATOM     59  CA  LYS    59     -16.447   9.911  52.372  1.00 25.00           C
ATOM     60  CA  THR    60     -20.171  10.266  53.062  1.00 25.00           C
ATOM     61  CA  LEU    61     -21.410  10.527  56.656  1.00 25.00           C
ATOM     62  CA  LYS    62     -23.787   8.022  58.183  1.00 25.00           C
ATOM     63  CA  VAL    63     -27.231   8.691  59.545  1.00 25.00           C
ATOM     64  CA  GLY    64     -27.658  11.143  62.404  1.00 25.00           C
ATOM     65  CA  TYR    65     -26.359  14.677  62.195  1.00 25.00           C
ATOM     66  CA  THR    66     -27.584  17.681  64.255  1.00 25.00           C
ATOM     67  CA  GLU    67     -24.936  20.007  62.735  1.00 25.00           C
ATOM     68  CA  LYS    68     -21.563  19.225  64.373  1.00 25.00           C
ATOM     69  CA  GLN    69     -21.066  16.265  61.993  1.00 25.00           C
ATOM     70  CA  ARG    70     -21.884  18.506  58.996  1.00 25.00           C
ATOM     71  CA  ARG    71     -19.370  21.118  60.231  1.00 25.00           C
ATOM     72  CA  ASP    72     -16.698  18.401  60.613  1.00 25.00           C
ATOM     73  CA  PHE    73     -17.414  17.163  57.061  1.00 25.00           C
ATOM     74  CA  LEU    74     -17.111  20.741  55.727  1.00 25.00           C
ATOM     75  CA  GLY    75     -13.774  21.167  57.557  1.00 25.00           C
ATOM     76  CA  GLU    76     -12.509  17.873  56.070  1.00 25.00           C
ATOM     77  CA  ALA    77     -13.558  19.021  52.570  1.00 25.00           C
ATOM     78  CA  SER    78     -11.732  22.347  53.088  1.00 25.00           C
ATOM     79  CA  ILE    79      -8.590  20.474  54.222  1.00 25.00           C
ATOM     80  CA  MET    80      -8.781  18.229  51.125  1.00 25.00           C
ATOM     81  CA  GLY    81      -9.130  21.312  48.881  1.00 25.00           C
ATOM     82  CA  GLN    82      -6.091  22.918  50.572  1.00 25.00           C
ATOM     83  CA  PHE    83      -4.165  20.439  48.423  1.00 25.00           C
ATOM     84  CA  ASP    84      -3.281  20.159  44.704  1.00 25.00           C
ATOM     85  CA  HIS    85      -0.230  17.932  44.199  1.00 25.00           C
ATOM     86  CA  PRO    86       1.287  14.961  42.431  1.00 25.00           C
ATOM     87  CA  ASN    87       1.604  12.043  44.927  1.00 25.00           C
ATOM     88  CA  ILE    88      -1.844  13.437  45.696  1.00 25.00           C
ATOM     89  CA  ILE    89      -5.133  12.195  47.160  1.00 25.00           C
ATOM     90  CA  ARG    90      -7.285  14.204  44.672  1.00 25.00           C
ATOM     91  CA  LEU    91      -9.966  16.888  44.305  1.00 25.00           C
ATOM     92  CA  GLU    92     -13.156  15.752  42.611  1.00 25.00           C
ATOM     93  CA  GLY    93     -16.132  17.264  44.406  1.00 25.00           C
ATOM     94  CA  VAL    94     -19.581  17.953  45.823  1.00 25.00           C
ATOM     95  CA  VAL    95     -23.304  18.228  46.425  1.00 25.00           C
ATOM     96  CA  THR    96     -23.796  18.990  50.129  1.00 25.00           C
ATOM     97  CA  LYS    97     -27.557  19.153  49.831  1.00 25.00           C
ATOM     98  CA  SER    98     -30.229  16.582  50.878  1.00 25.00           C
ATOM     99  CA  LYS    99     -29.170  13.020  51.621  1.00 25.00           C
ATOM    100  CA  PRO   100     -26.036  11.965  53.577  1.00 25.00           C
ATOM    101  CA  VAL   101     -23.547  14.867  53.177  1.00 25.00           C
ATOM    102  CA  MET   102     -21.381  14.551  50.105  1.00 25.00           C
ATOM    103  CA  ILE   103     -17.634  14.077  49.461  1.00 25.00           C
ATOM    104  CA  VAL   104     -15.586  12.747  46.587  1.00 25.00           C
ATOM    105  CA  THR   105     -12.283  11.157  45.636  1.00 25.00           C
ATOM    106  CA  GLU   106     -10.193   9.278  43.050  1.00 25.00           C
ATOM    107  CA  TYR   107     -10.661   5.953  44.904  1.00 25.00           C
ATOM    108  CA  MET   108      -8.133   4.222  42.606  1.00 25.00           C
TER
END
