
#######################################################
#                                                     #
#                        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  146 (  146),  selected  146 , name T0312TS599_2
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312TS599_2.T0312.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    K       2      K       2           -
LGA    V       3      V       3           -
LGA    F       4      -       -           -
LGA    E       5      -       -           -
LGA    F       6      -       -           -
LGA    E       7      -       -           -
LGA    V       8      -       -           -
LGA    G       9      F       4          5.388
LGA    -       -      E       5           -
LGA    -       -      F       6           -
LGA    K      10      E       7          4.179
LGA    G      11      V       8           #
LGA    F      12      G       9           #
LGA    L      13      K      10           #
LGA    -       -      G      11           -
LGA    L      14      F      12          4.673
LGA    R      15      L      13          4.285
LGA    L      16      L      14          3.371
LGA    D      17      R      15          2.620
LGA    Y      18      L      16          2.486
LGA    G      19      D      17          1.214
LGA    K      20      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      R      24           -
LGA    D      21      Q      25          4.692
LGA    L      22      I      26          4.451
LGA    V      23      E      27          4.142
LGA    R      24      E      28          3.496
LGA    Q      25      F      29          3.487
LGA    I      26      L      30          3.913
LGA    E      27      E      31          4.866
LGA    -       -      E      32           -
LGA    E      28      K      33          2.523
LGA    F      29      G      34          4.272
LGA    L      30      I      35          3.023
LGA    E      31      H      36          5.090
LGA    E      32      -       -           -
LGA    K      33      -       -           -
LGA    G      34      -       -           -
LGA    I      35      -       -           -
LGA    H      36      -       -           -
LGA    A      37      A      37          2.062
LGA    A      38      A      38          1.118
LGA    H      39      H      39          2.411
LGA    I      40      I      40          2.983
LGA    S      41      S      41          2.993
LGA    A      42      A      42          3.865
LGA    I      43      I      43          3.297
LGA    G      44      G      44          3.279
LGA    A      45      A      45          2.728
LGA    V      46      -       -           -
LGA    R      47      V      46           #
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    -       -      A      49           -
LGA    -       -      V      50           -
LGA    -       -      I      51           -
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    -       -      K      63           -
LGA    -       -      K      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    -       -      P      69           -
LGA    -       -      L      70           -
LGA    S      48      E      71          1.121
LGA    A      49      I      72          2.117
LGA    -       -      L      73           -
LGA    V      50      S      74          4.544
LGA    I      51      L      75          3.608
LGA    G      52      S      76          3.071
LGA    Y      53      G      77          3.762
LGA    Y      54      N      78          1.816
LGA    D      55      V      79          1.358
LGA    Q      56      S      80          1.705
LGA    E      57      M      81          3.382
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    K      58      P      86           #
LGA    K      59      F      87          4.000
LGA    E      60      C      88           #
LGA    Y      61      -       -           -
LGA    V      62      -       -           -
LGA    K      63      -       -           -
LGA    K      64      -       -           -
LGA    E      65      -       -           -
LGA    L      66      -       -           -
LGA    M      67      -       -           -
LGA    E      68      -       -           -
LGA    P      69      -       -           -
LGA    L      70      -       -           -
LGA    E      71      -       -           -
LGA    I      72      -       -           -
LGA    L      73      -       -           -
LGA    S      74      H      89           #
LGA    L      75      I      90          2.785
LGA    S      76      H      91          1.460
LGA    G      77      V      92          0.997
LGA    N      78      L      93          1.875
LGA    V      79      L      94          0.473
LGA    S      80      G      95          2.633
LGA    M      81      K      96          1.404
LGA    K      82      D      97          0.595
LGA    D      83      G      98          0.726
LGA    S      84      E      99          5.165
LGA    K      85      V     100          3.405
LGA    P      86      Y     101          3.158
LGA    F      87      G     102          3.383
LGA    C      88      G     103          2.492
LGA    H      89      -       -           -
LGA    I      90      H     104          3.122
LGA    H      91      -       -           -
LGA    V      92      -       -           -
LGA    L      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      -       -           -
LGA    K      96      -       -           -
LGA    D      97      -       -           -
LGA    G      98      -       -           -
LGA    E      99      -       -           -
LGA    V     100      -       -           -
LGA    Y     101      -       -           -
LGA    G     102      -       -           -
LGA    G     103      -       -           -
LGA    H     104      -       -           -
LGA    L     105      -       -           -
LGA    F     106      -       -           -
LGA    S     107      -       -           -
LGA    A     108      -       -           -
LGA    E     109      -       -           -
LGA    V     110      L     105          3.683
LGA    F     111      F     106          3.729
LGA    A     112      -       -           -
LGA    C     113      S     107          3.120
LGA    E     114      A     108          3.623
LGA    V     115      -       -           -
LGA    F     116      -       -           -
LGA    V     117      E     109          1.889
LGA    L     118      V     110          3.534
LGA    P     119      F     111          0.936
LGA    L     120      A     112          3.489
LGA    S     121      C     113           -
LGA    G     122      E     114           -
LGA    E     123      V     115           -
LGA    A     124      F     116           -
LGA    P     125      V     117           -
LGA    E     126      L     118           -
LGA    R     127      P     119           -
LGA    A     128      L     120           -
LGA    F     129      S     121           -
LGA    D     130      G     122           -
LGA    E     131      E     123           -
LGA    Q     132      A     124           -
LGA    T     133      P     125           -
LGA    G     134      E     126           -
LGA    L     135      R     127           -
LGA    F     136      A     128           -
LGA    L     137      F     129           -
LGA    W     138      D     130           -
LGA    L     139      E     131           -
LGA    E     140      Q     132           -
LGA    H     141      T     133           -
LGA    H     142      G     134           -
LGA    H     143      L     135           -
LGA    H     144      F     136           -
LGA    H     145      L     137           -
LGA    H     146      W     138           -
LGA    -       -      L     139           -
LGA    -       -      E     140           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  146  140    5.0     62    3.23    19.35     24.848     1.863

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.728226 * X  +   0.621756 * Y  +   0.288280 * Z  +  56.721111
  Y_new =  -0.237138 * X  +   0.623258 * Y  +  -0.745195 * Z  +   4.097360
  Z_new =  -0.643003 * X  +   0.474308 * Y  +   0.601315 * Z  +  16.091206 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.667865   -2.473727  [ DEG:    38.2659   -141.7341 ]
  Theta =   0.698412    2.443180  [ DEG:    40.0161    139.9839 ]
  Phi   =  -0.314808    2.826784  [ DEG:   -18.0372    161.9628 ]
 
# 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: T0312TS599_2                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS599_2.T0312.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  146  140   5.0   62   3.23   19.35  24.848
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS599_2
PFRMAT TS                                                                       
TARGET T0312                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      54.786  21.594  22.025  1.00  0.00              
ATOM      2  CA  LYS     2      58.613  20.033  22.787  1.00  0.00              
ATOM      3  CA  VAL     3      59.609  19.004  26.160  1.00  0.00              
ATOM      4  CA  PHE     4      63.065  18.580  26.955  1.00  0.00              
ATOM      5  CA  GLU     5      63.916  16.918  30.222  1.00  0.00              
ATOM      6  CA  PHE     6      67.575  16.201  30.271  1.00  0.00              
ATOM      7  CA  GLU     7      69.110  14.916  33.534  1.00  0.00              
ATOM      8  CA  VAL     8      70.871  11.729  32.403  1.00  0.00              
ATOM      9  CA  GLY     9      68.215   9.000  32.154  1.00  0.00              
ATOM     10  CA  LYS    10      65.245  11.372  32.354  1.00  0.00              
ATOM     11  CA  GLY    11      62.829  11.260  29.477  1.00  0.00              
ATOM     12  CA  PHE    12      62.619  13.981  26.882  1.00  0.00              
ATOM     13  CA  LEU    13      59.711  14.280  24.568  1.00  0.00              
ATOM     14  CA  LEU    14      60.201  15.527  21.012  1.00  0.00              
ATOM     15  CA  ARG    15      57.271  16.408  18.833  1.00  0.00              
ATOM     16  CA  LEU    16      57.681  16.195  15.147  1.00  0.00              
ATOM     17  CA  ASP    17      55.240  17.958  12.765  1.00  0.00              
ATOM     18  CA  TYR    18      54.798  16.594   9.307  1.00  0.00              
ATOM     19  CA  GLY    19      57.933  16.738   7.041  1.00  0.00              
ATOM     20  CA  LYS    20      60.202  17.303   9.980  1.00  0.00              
ATOM     21  CA  ASP    21      63.190  15.675  11.584  1.00  0.00              
ATOM     22  CA  LEU    22      62.160  15.513  15.295  1.00  0.00              
ATOM     23  CA  VAL    23      63.483  12.046  15.931  1.00  0.00              
ATOM     24  CA  ARG    24      66.854  12.734  14.423  1.00  0.00              
ATOM     25  CA  GLN    25      67.349  15.902  16.426  1.00  0.00              
ATOM     26  CA  ILE    26      66.346  14.284  19.630  1.00  0.00              
ATOM     27  CA  GLU    27      68.664  11.378  19.152  1.00  0.00              
ATOM     28  CA  GLU    28      71.519  13.654  18.394  1.00  0.00              
ATOM     29  CA  PHE    29      70.916  15.827  21.413  1.00  0.00              
ATOM     30  CA  LEU    30      70.607  12.869  23.721  1.00  0.00              
ATOM     31  CA  GLU    31      73.828  11.365  22.431  1.00  0.00              
ATOM     32  CA  GLU    32      75.785  14.668  22.683  1.00  0.00              
ATOM     33  CA  LYS    33      74.839  15.237  26.260  1.00  0.00              
ATOM     34  CA  GLY    34      75.243  11.590  27.384  1.00  0.00              
ATOM     35  CA  ILE    35      71.505  11.432  28.082  1.00  0.00              
ATOM     36  CA  HIS    36      69.453   8.346  27.958  1.00  0.00              
ATOM     37  CA  ALA    37      65.917   8.520  26.754  1.00  0.00              
ATOM     38  CA  ALA    38      64.208  10.394  23.932  1.00  0.00              
ATOM     39  CA  HIS    39      60.534   9.930  23.026  1.00  0.00              
ATOM     40  CA  ILE    40      59.427  10.898  19.640  1.00  0.00              
ATOM     41  CA  SER    41      55.862  11.912  18.943  1.00  0.00              
ATOM     42  CA  ALA    42      54.760  12.285  15.419  1.00  0.00              
ATOM     43  CA  ILE    43      51.636  14.236  14.585  1.00  0.00              
ATOM     44  CA  GLY    44      50.173  14.043  11.073  1.00  0.00              
ATOM     45  CA  ALA    45      46.998  15.801  10.208  1.00  0.00              
ATOM     46  CA  VAL    46      45.152  14.377   7.214  1.00  0.00              
ATOM     47  CA  ARG    47      42.335  12.484   9.024  1.00  0.00              
ATOM     48  CA  SER    48      44.082  12.103  12.313  1.00  0.00              
ATOM     49  CA  ALA    49      47.289  10.143  12.458  1.00  0.00              
ATOM     50  CA  VAL    50      49.301  10.051  15.739  1.00  0.00              
ATOM     51  CA  ILE    51      52.442   8.073  15.922  1.00  0.00              
ATOM     52  CA  GLY    52      54.374   7.717  19.198  1.00  0.00              
ATOM     53  CA  TYR    53      57.912   6.366  19.040  1.00  0.00              
ATOM     54  CA  TYR    54      60.043   5.315  21.952  1.00  0.00              
ATOM     55  CA  ASP    55      63.839   5.272  21.424  1.00  0.00              
ATOM     56  CA  GLN    56      65.871   2.481  22.970  1.00  0.00              
ATOM     57  CA  GLU    57      67.118   0.710  19.812  1.00  0.00              
ATOM     58  CA  LYS    58      63.957   1.380  17.895  1.00  0.00              
ATOM     59  CA  LYS    59      64.354   2.076  14.267  1.00  0.00              
ATOM     60  CA  GLU    60      61.380   0.448  12.688  1.00  0.00              
ATOM     61  CA  TYR    61      60.332  -3.037  12.261  1.00  0.00              
ATOM     62  CA  VAL    62      62.438  -6.000  11.399  1.00  0.00              
ATOM     63  CA  LYS    63      61.435  -8.666  13.838  1.00  0.00              
ATOM     64  CA  LYS    64      64.245 -10.436  15.632  1.00  0.00              
ATOM     65  CA  GLU    65      63.655 -12.963  18.366  1.00  0.00              
ATOM     66  CA  LEU    66      66.054 -12.748  21.350  1.00  0.00              
ATOM     67  CA  MET    67      65.526 -14.399  24.669  1.00  0.00              
ATOM     68  CA  GLU    68      67.030 -12.732  27.671  1.00  0.00              
ATOM     69  CA  PRO    69      67.594  -9.506  29.524  1.00  0.00              
ATOM     70  CA  LEU    70      64.154  -7.857  29.170  1.00  0.00              
ATOM     71  CA  GLU    71      63.658  -4.242  28.231  1.00  0.00              
ATOM     72  CA  ILE    72      60.275  -3.163  27.282  1.00  0.00              
ATOM     73  CA  LEU    73      59.778  -0.649  24.720  1.00  0.00              
ATOM     74  CA  SER    74      56.265   0.571  24.129  1.00  0.00              
ATOM     75  CA  LEU    75      55.158   1.958  20.834  1.00  0.00              
ATOM     76  CA  SER    76      51.897   3.815  20.657  1.00  0.00              
ATOM     77  CA  GLY    77      49.990   4.127  17.431  1.00  0.00              
ATOM     78  CA  ASN    78      46.963   6.384  17.277  1.00  0.00              
ATOM     79  CA  VAL    79      44.723   6.312  14.414  1.00  0.00              
ATOM     80  CA  SER    80      41.640   8.470  14.467  1.00  0.00              
ATOM     81  CA  MET    81      38.451   7.643  12.513  1.00  0.00              
ATOM     82  CA  LYS    82      35.290   8.835  14.144  1.00  0.00              
ATOM     83  CA  ASP    83      33.485   5.623  14.851  1.00  0.00              
ATOM     84  CA  SER    84      35.295   4.537  17.950  1.00  0.00              
ATOM     85  CA  LYS    85      38.849   5.707  17.580  1.00  0.00              
ATOM     86  CA  PRO    86      41.409   3.164  16.890  1.00  0.00              
ATOM     87  CA  PHE    87      44.348   3.078  19.332  1.00  0.00              
ATOM     88  CA  CYS    88      47.203   0.710  18.685  1.00  0.00              
ATOM     89  CA  HIS    89      49.693  -0.293  21.286  1.00  0.00              
ATOM     90  CA  ILE    90      52.788  -2.093  20.152  1.00  0.00              
ATOM     91  CA  HIS    91      54.968  -3.862  22.539  1.00  0.00              
ATOM     92  CA  VAL    92      58.612  -4.280  21.660  1.00  0.00              
ATOM     93  CA  LEU    93      60.890  -6.399  23.810  1.00  0.00              
ATOM     94  CA  LEU    94      64.579  -5.577  23.868  1.00  0.00              
ATOM     95  CA  GLY    95      67.085  -8.175  25.308  1.00  0.00              
ATOM     96  CA  LYS    96      70.362  -7.056  26.939  1.00  0.00              
ATOM     97  CA  ASP    97      72.347  -8.443  23.969  1.00  0.00              
ATOM     98  CA  GLY    98      70.453  -6.224  21.486  1.00  0.00              
ATOM     99  CA  GLU    99      68.221  -8.896  20.126  1.00  0.00              
ATOM    100  CA  VAL   100      64.918  -7.452  19.264  1.00  0.00              
ATOM    101  CA  TYR   101      61.814  -9.303  19.903  1.00  0.00              
ATOM    102  CA  GLY   102      58.706  -8.210  18.089  1.00  0.00              
ATOM    103  CA  GLY   103      55.437  -9.845  18.932  1.00  0.00              
ATOM    104  CA  HIS   104      52.205  -9.247  17.142  1.00  0.00              
ATOM    105  CA  LEU   105      51.461  -5.669  18.245  1.00  0.00              
ATOM    106  CA  PHE   106      54.994  -4.448  17.276  1.00  0.00              
ATOM    107  CA  SER   107      55.593  -6.167  13.915  1.00  0.00              
ATOM    108  CA  ALA   108      52.110  -5.291  12.659  1.00  0.00              
ATOM    109  CA  GLU   109      52.394  -1.624  13.683  1.00  0.00              
ATOM    110  CA  VAL   110      55.659  -0.315  12.178  1.00  0.00              
ATOM    111  CA  PHE   111      55.057  -1.820   8.745  1.00  0.00              
ATOM    112  CA  ALA   112      51.455  -0.574   8.644  1.00  0.00              
ATOM    113  CA  CYS   113      52.235   3.047   9.626  1.00  0.00              
ATOM    114  CA  GLU   114      54.986   3.241   6.997  1.00  0.00              
ATOM    115  CA  VAL   115      52.770   1.733   4.221  1.00  0.00              
ATOM    116  CA  PHE   116      49.880   4.187   4.984  1.00  0.00              
ATOM    117  CA  VAL   117      51.483   7.521   5.723  1.00  0.00              
ATOM    118  CA  LEU   118      49.499  10.527   6.865  1.00  0.00              
ATOM    119  CA  PRO   119      50.770  14.043   6.204  1.00  0.00              
ATOM    120  CA  LEU   120      48.386  16.924   6.002  1.00  0.00              
ATOM    121  CA  SER   121      49.186  19.477   3.394  1.00  0.00              
ATOM    122  CA  GLY   122      47.114  18.253   0.517  1.00  0.00              
ATOM    123  CA  GLU   123      48.296  14.596   0.428  1.00  0.00              
ATOM    124  CA  ALA   124      45.691  11.851   0.198  1.00  0.00              
ATOM    125  CA  PRO   125      47.142   8.961   2.186  1.00  0.00              
ATOM    126  CA  GLU   126      46.889   6.173  -0.396  1.00  0.00              
ATOM    127  CA  ARG   127      48.295   8.570  -3.037  1.00  0.00              
ATOM    128  CA  ALA   128      51.284   9.756  -1.023  1.00  0.00              
ATOM    129  CA  PHE   129      52.280   6.218   0.046  1.00  0.00              
ATOM    130  CA  ASP   130      52.037   4.270  -3.154  1.00  0.00              
ATOM    131  CA  GLU   131      48.737   2.371  -2.831  1.00  0.00              
ATOM    132  CA  GLN   132      50.132  -0.663  -4.569  1.00  0.00              
ATOM    133  CA  THR   133      52.974  -0.985  -2.023  1.00  0.00              
ATOM    134  CA  GLY   134      50.823  -0.064   1.002  1.00  0.00              
ATOM    135  CA  LEU   135      50.110  -3.318   2.482  1.00  0.00              
ATOM    136  CA  PHE   136      50.571  -3.873   6.111  1.00  0.00              
ATOM    137  CA  LEU   137      50.559  -7.569   6.745  1.00  0.00              
ATOM    138  CA  TRP   138      52.634  -9.305   9.406  1.00  0.00              
ATOM    139  CA  LEU   139      52.588 -13.137   9.453  1.00  0.00              
ATOM    140  CA  GLU   140      51.482 -13.594  13.068  1.00  0.00              
ATOM    141  CA  HIS   141      48.788 -10.909  12.597  1.00  0.00              
ATOM    142  CA  HIS   142      47.239 -12.243   9.437  1.00  0.00              
ATOM    143  CA  HIS   143      47.407 -15.848  10.478  1.00  0.00              
ATOM    144  CA  HIS   144      46.485 -15.592  13.932  1.00  0.00              
ATOM    145  CA  HIS   145      45.039 -17.868  10.705  1.00  0.00              
ATOM    146  CA  HIS   146      48.367 -16.930   8.324  1.00  0.00              
TER                                                                             
END
