
#######################################################
#                                                     #
#                        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 T0354TS599_1
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS599_1.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    M       1      E       2          3.060
LGA    E       2      I       3          4.061
LGA    I       3      Q       4           #
LGA    Q       4      E       5           #
LGA    E       5      I       6          4.688
LGA    I       6      S       7          1.040
LGA    S       7      -       -           -
LGA    K       8      K       8          2.707
LGA    L       9      L       9          2.596
LGA    A      10      A      10          3.400
LGA    I      11      I      11          3.425
LGA    E      12      E      12          2.172
LGA    A      13      A      13          2.420
LGA    L      14      L      14          3.233
LGA    E      15      E      15          3.010
LGA    D      16      D      16          2.937
LGA    I      17      I      17          2.884
LGA    K      18      K      18          3.275
LGA    G      19      G      19          3.778
LGA    K      20      -       -           -
LGA    D      21      K      20          0.963
LGA    I      22      D      21          3.614
LGA    I      23      I      22          2.015
LGA    E      24      I      23          1.140
LGA    L      25      E      24          3.493
LGA    D      26      L      25          1.350
LGA    T      27      D      26          3.287
LGA    S      28      -       -           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    T      31      T      27          5.312
LGA    S      32      S      28          2.234
LGA    L      33      K      29           #
LGA    F      34      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    Q      35      L      33          4.457
LGA    R      36      F      34          3.305
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    M      37      M      37          1.603
LGA    I      38      I      38          3.074
LGA    V      39      V      39          1.775
LGA    A      40      A      40          2.328
LGA    T      41      T      41          1.697
LGA    G      42      G      42          3.086
LGA    D      43      D      43          3.019
LGA    S      44      S      44          2.630
LGA    N      45      N      45          2.141
LGA    R      46      R      46          1.183
LGA    Q      47      Q      47          1.623
LGA    V      48      V      48          1.833
LGA    K      49      K      49          1.014
LGA    A      50      A      50          1.126
LGA    L      51      L      51          1.728
LGA    A      52      A      52          1.030
LGA    N      53      N      53          0.931
LGA    S      54      S      54          1.558
LGA    V      55      V      55          1.280
LGA    Q      56      Q      56          1.040
LGA    V      57      V      57          1.468
LGA    K      58      K      58          2.200
LGA    L      59      L      59          2.382
LGA    K      60      K      60          2.207
LGA    E      61      E      61          2.583
LGA    A      62      A      62          3.475
LGA    G      63      G      63          3.485
LGA    -       -      V      64           -
LGA    V      64      D      65          1.011
LGA    D      65      I      66          3.454
LGA    I      66      V      67          5.214
LGA    V      67      G      68          1.652
LGA    G      68      S      69          1.936
LGA    S      69      E      70          1.578
LGA    E      70      G      71          1.847
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    G      71      S      74          5.461
LGA    H      72      G      75           -
LGA    E      73      -       -           -
LGA    S      74      -       -           -
LGA    G      75      -       -           -
LGA    E      76      E      76          3.432
LGA    W      77      W      77          2.719
LGA    V      78      V      78          1.678
LGA    L      79      L      79          2.119
LGA    V      80      V      80          1.546
LGA    D      81      D      81          2.431
LGA    A      82      A      82          1.793
LGA    G      83      G      83          1.975
LGA    D      84      D      84          1.740
LGA    V      85      V      85          4.498
LGA    V      86      V      86          1.486
LGA    V      87      V      87          3.433
LGA    H      88      H      88          1.247
LGA    V      89      V      89          3.222
LGA    M      90      M      90          0.539
LGA    L      91      L      91          1.774
LGA    P      92      P      92          1.566
LGA    A      93      A      93          1.515
LGA    V      94      V      94          2.042
LGA    R      95      R      95          2.336
LGA    D      96      D      96          2.098
LGA    Y      97      Y      97          2.896
LGA    Y      98      Y      98          3.340
LGA    D      99      -       -           -
LGA    I     100      D      99          2.328
LGA    E     101      I     100          4.832
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      E     101          4.320
LGA    H     129      A     102          3.368
LGA    H     130      L     103          0.621
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           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  130  122    5.0     90    2.71    72.22     47.410     3.199

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.172318 * X  +   0.628585 * Y  +   0.758411 * Z  +  38.351368
  Y_new =  -0.926482 * X  +  -0.364932 * Y  +   0.091958 * Z  +  26.785831
  Z_new =   0.334572 * X  +  -0.686808 * Y  +   0.645257 * Z  +  23.681330 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.816581    2.325012  [ DEG:   -46.7866    133.2134 ]
  Theta =  -0.341151   -2.800442  [ DEG:   -19.5465   -160.4535 ]
  Phi   =  -1.754687    1.386906  [ DEG:  -100.5361     79.4639 ]
 
# 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: T0354TS599_1                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS599_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   90   2.71   72.22  47.410
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS599_1
PFRMAT TS                                                                       
TARGET T0354                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      51.998  20.095  17.670  1.00  0.00              
ATOM      2  CA  GLU     2      48.638  17.981  18.868  1.00  0.00              
ATOM      3  CA  ILE     3      46.114  20.682  19.531  1.00  0.00              
ATOM      4  CA  GLN     4      47.010  17.708  22.370  1.00  0.00              
ATOM      5  CA  GLU     5      49.903  19.875  23.368  1.00  0.00              
ATOM      6  CA  ILE     6      47.702  22.960  23.646  1.00  0.00              
ATOM      7  CA  SER     7      45.188  21.016  25.804  1.00  0.00              
ATOM      8  CA  LYS     8      47.963  19.787  28.092  1.00  0.00              
ATOM      9  CA  LEU     9      49.361  23.331  28.401  1.00  0.00              
ATOM     10  CA  ALA    10      45.972  24.835  29.248  1.00  0.00              
ATOM     11  CA  ILE    11      45.306  22.201  31.849  1.00  0.00              
ATOM     12  CA  GLU    12      48.676  22.753  33.422  1.00  0.00              
ATOM     13  CA  ALA    13      48.318  26.542  33.568  1.00  0.00              
ATOM     14  CA  LEU    14      44.881  26.303  35.096  1.00  0.00              
ATOM     15  CA  GLU    15      46.076  23.816  37.733  1.00  0.00              
ATOM     16  CA  ASP    16      49.029  26.002  38.644  1.00  0.00              
ATOM     17  CA  ILE    17      46.810  29.068  39.056  1.00  0.00              
ATOM     18  CA  LYS    18      44.094  27.315  41.071  1.00  0.00              
ATOM     19  CA  GLY    19      41.336  27.481  38.397  1.00  0.00              
ATOM     20  CA  LYS    20      39.220  24.537  39.350  1.00  0.00              
ATOM     21  CA  ASP    21      37.474  23.383  36.328  1.00  0.00              
ATOM     22  CA  ILE    22      39.164  23.216  32.901  1.00  0.00              
ATOM     23  CA  ILE    23      37.479  21.341  30.109  1.00  0.00              
ATOM     24  CA  GLU    24      39.326  20.424  26.981  1.00  0.00              
ATOM     25  CA  LEU    25      37.340  19.461  23.880  1.00  0.00              
ATOM     26  CA  ASP    26      38.780  16.916  21.376  1.00  0.00              
ATOM     27  CA  THR    27      37.386  17.302  17.962  1.00  0.00              
ATOM     28  CA  SER    28      37.141  13.725  16.843  1.00  0.00              
ATOM     29  CA  LYS    29      39.176  13.857  13.680  1.00  0.00              
ATOM     30  CA  LEU    30      42.239  15.472  15.136  1.00  0.00              
ATOM     31  CA  THR    31      43.257  17.630  12.187  1.00  0.00              
ATOM     32  CA  SER    32      40.050  19.683  12.116  1.00  0.00              
ATOM     33  CA  LEU    33      40.294  20.061  15.875  1.00  0.00              
ATOM     34  CA  PHE    34      43.857  21.356  15.642  1.00  0.00              
ATOM     35  CA  GLN    35      42.803  24.169  13.336  1.00  0.00              
ATOM     36  CA  ARG    36      40.375  25.250  16.086  1.00  0.00              
ATOM     37  CA  MET    37      40.976  24.505  19.708  1.00  0.00              
ATOM     38  CA  ILE    38      38.181  24.794  22.272  1.00  0.00              
ATOM     39  CA  VAL    39      38.858  25.306  25.829  1.00  0.00              
ATOM     40  CA  ALA    40      36.158  25.298  28.278  1.00  0.00              
ATOM     41  CA  THR    41      36.687  27.053  31.430  1.00  0.00              
ATOM     42  CA  GLY    42      34.273  27.016  34.271  1.00  0.00              
ATOM     43  CA  ASP    43      36.039  28.502  37.208  1.00  0.00              
ATOM     44  CA  SER    44      35.076  32.009  38.115  1.00  0.00              
ATOM     45  CA  ASN    45      35.205  34.877  35.701  1.00  0.00              
ATOM     46  CA  ARG    46      38.363  36.508  37.176  1.00  0.00              
ATOM     47  CA  GLN    47      40.148  33.192  37.037  1.00  0.00              
ATOM     48  CA  VAL    48      39.250  32.724  33.345  1.00  0.00              
ATOM     49  CA  LYS    49      40.528  36.258  32.552  1.00  0.00              
ATOM     50  CA  ALA    50      43.731  35.528  34.369  1.00  0.00              
ATOM     51  CA  LEU    51      44.086  32.283  32.368  1.00  0.00              
ATOM     52  CA  ALA    52      43.430  34.014  29.108  1.00  0.00              
ATOM     53  CA  ASN    53      46.050  36.598  29.894  1.00  0.00              
ATOM     54  CA  SER    54      48.583  33.859  30.799  1.00  0.00              
ATOM     55  CA  VAL    55      47.890  32.017  27.545  1.00  0.00              
ATOM     56  CA  GLN    56      48.346  35.256  25.633  1.00  0.00              
ATOM     57  CA  VAL    57      51.773  35.762  27.214  1.00  0.00              
ATOM     58  CA  LYS    58      52.735  32.199  26.357  1.00  0.00              
ATOM     59  CA  LEU    59      51.665  32.712  22.750  1.00  0.00              
ATOM     60  CA  LYS    60      53.647  35.955  22.479  1.00  0.00              
ATOM     61  CA  GLU    61      56.745  34.247  23.859  1.00  0.00              
ATOM     62  CA  ALA    62      56.384  31.531  21.178  1.00  0.00              
ATOM     63  CA  GLY    63      56.005  34.069  18.430  1.00  0.00              
ATOM     64  CA  VAL    64      52.220  33.766  17.922  1.00  0.00              
ATOM     65  CA  ASP    65      50.380  37.019  17.289  1.00  0.00              
ATOM     66  CA  ILE    66      48.003  37.713  20.194  1.00  0.00              
ATOM     67  CA  VAL    67      44.773  38.671  18.775  1.00  0.00              
ATOM     68  CA  GLY    68      42.379  39.066  21.629  1.00  0.00              
ATOM     69  CA  SER    69      38.662  39.148  21.059  1.00  0.00              
ATOM     70  CA  GLU    70      36.374  39.829  23.970  1.00  0.00              
ATOM     71  CA  GLY    71      32.905  38.860  24.438  1.00  0.00              
ATOM     72  CA  HIS    72      30.099  39.837  22.127  1.00  0.00              
ATOM     73  CA  GLU    73      28.691  36.470  21.070  1.00  0.00              
ATOM     74  CA  SER    74      25.802  36.210  23.452  1.00  0.00              
ATOM     75  CA  GLY    75      26.791  33.791  26.144  1.00  0.00              
ATOM     76  CA  GLU    76      30.434  34.398  26.666  1.00  0.00              
ATOM     77  CA  TRP    77      32.953  33.355  23.983  1.00  0.00              
ATOM     78  CA  VAL    78      36.481  34.538  24.096  1.00  0.00              
ATOM     79  CA  LEU    79      38.662  34.294  20.978  1.00  0.00              
ATOM     80  CA  VAL    80      42.334  33.988  21.227  1.00  0.00              
ATOM     81  CA  ASP    81      44.449  33.929  18.184  1.00  0.00              
ATOM     82  CA  ALA    82      47.538  31.973  18.353  1.00  0.00              
ATOM     83  CA  GLY    83      48.344  30.540  15.010  1.00  0.00              
ATOM     84  CA  ASP    84      45.732  27.762  14.958  1.00  0.00              
ATOM     85  CA  VAL    85      42.813  29.435  16.641  1.00  0.00              
ATOM     86  CA  VAL    86      41.932  28.986  20.199  1.00  0.00              
ATOM     87  CA  VAL    87      38.572  29.471  21.503  1.00  0.00              
ATOM     88  CA  HIS    88      37.812  29.887  24.956  1.00  0.00              
ATOM     89  CA  VAL    89      34.579  29.267  26.431  1.00  0.00              
ATOM     90  CA  MET    90      33.451  30.695  29.724  1.00  0.00              
ATOM     91  CA  LEU    91      30.732  29.192  31.823  1.00  0.00              
ATOM     92  CA  PRO    92      28.945  26.104  33.019  1.00  0.00              
ATOM     93  CA  ALA    93      25.430  27.527  32.853  1.00  0.00              
ATOM     94  CA  VAL    94      25.956  28.931  29.424  1.00  0.00              
ATOM     95  CA  ARG    95      27.191  25.793  27.774  1.00  0.00              
ATOM     96  CA  ASP    96      24.358  23.645  29.028  1.00  0.00              
ATOM     97  CA  TYR    97      21.632  26.107  28.061  1.00  0.00              
ATOM     98  CA  TYR    98      22.795  26.909  24.578  1.00  0.00              
ATOM     99  CA  ASP    99      23.818  23.455  23.269  1.00  0.00              
ATOM    100  CA  ILE   100      27.231  23.207  21.643  1.00  0.00              
ATOM    101  CA  GLU   101      26.425  23.450  17.934  1.00  0.00              
ATOM    102  CA  ALA   102      24.404  26.607  18.620  1.00  0.00              
ATOM    103  CA  LEU   103      27.211  28.224  20.635  1.00  0.00              
ATOM    104  CA  TRP   104      29.755  27.611  17.885  1.00  0.00              
ATOM    105  CA  GLY   105      27.409  29.130  15.298  1.00  0.00              
ATOM    106  CA  GLY   106      26.743  32.256  17.365  1.00  0.00              
ATOM    107  CA  GLN   107      30.485  33.009  17.863  1.00  0.00              
ATOM    108  CA  LYS   108      31.548  32.914  14.261  1.00  0.00              
ATOM    109  CA  PRO   109      33.392  29.693  13.877  1.00  0.00              
ATOM    110  CA  SER   110      36.448  29.988  11.683  1.00  0.00              
ATOM    111  CA  PHE   111      36.807  27.392   9.056  1.00  0.00              
ATOM    112  CA  ALA   112      40.011  25.426   8.993  1.00  0.00              
ATOM    113  CA  VAL   113      39.357  22.134   7.181  1.00  0.00              
ATOM    114  CA  GLY   114      35.695  21.602   8.119  1.00  0.00              
ATOM    115  CA  ALA   115      34.944  18.224   6.647  1.00  0.00              
ATOM    116  CA  ALA   116      32.637  16.381   8.913  1.00  0.00              
ATOM    117  CA  LYS   117      29.000  17.342   9.219  1.00  0.00              
ATOM    118  CA  PRO   118      28.587  17.742  13.019  1.00  0.00              
ATOM    119  CA  TRP   119      25.495  15.738  13.774  1.00  0.00              
ATOM    120  CA  SER   120      26.587  13.354  16.460  1.00  0.00              
ATOM    121  CA  ALA   121      24.199  13.774  19.327  1.00  0.00              
ATOM    122  CA  VAL   122      26.192  15.268  22.185  1.00  0.00              
ATOM    123  CA  LEU   123      24.070  16.538  25.043  1.00  0.00              
ATOM    124  CA  GLU   124      26.032  14.721  27.805  1.00  0.00              
ATOM    125  CA  HIS   125      29.464  15.337  26.421  1.00  0.00              
ATOM    126  CA  HIS   126      31.816  16.116  29.300  1.00  0.00              
ATOM    127  CA  HIS   127      34.083  18.018  26.852  1.00  0.00              
ATOM    128  CA  HIS   128      33.628  17.428  22.706  1.00  0.00              
ATOM    129  CA  HIS   129      31.571  20.842  21.335  1.00  0.00              
ATOM    130  CA  HIS   130      29.876  20.525  17.816  1.00  0.00              
TER                                                                             
END
