
#######################################################
#                                                     #
#                        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  126 (  126),  selected  126 , name T0372TS599_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS599_1-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    M       1      I       2          3.846
LGA    I       2      P       3           -
LGA    P       3      F       4           -
LGA    F       4      K       5           -
LGA    K       5      -       -           -
LGA    D       6      -       -           -
LGA    I       7      -       -           -
LGA    T       8      -       -           -
LGA    L       9      D       6           #
LGA    -       -      I       7           -
LGA    A      10      T       8          2.904
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    D      11      D      11          1.302
LGA    R      12      R      12          1.237
LGA    D      13      D      13          1.568
LGA    T      14      T      14          1.484
LGA    I      15      I      15          1.194
LGA    T      16      T      16          0.808
LGA    A      17      A      17          0.252
LGA    F      18      F      18          1.517
LGA    T      19      T      19          1.009
LGA    M      20      M      20          3.189
LGA    K      21      K      21          4.656
LGA    S      22      -       -           -
LGA    D      23      S      22          1.831
LGA    R      24      D      23          3.037
LGA    R      25      R      24          2.778
LGA    N      26      R      25          2.471
LGA    C      27      N      26          2.855
LGA    D      28      C      27          1.631
LGA    -       -      D      28           -
LGA    L      29      L      29          3.665
LGA    S      30      S      30          1.821
LGA    F      31      F      31          1.648
LGA    S      32      S      32          4.254
LGA    N      33      N      33          4.043
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    L      34      V      53           #
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    C      35      M      65           #
LGA    S      36      -       -           -
LGA    W      37      -       -           -
LGA    R      38      -       -           -
LGA    F      39      -       -           -
LGA    L      40      -       -           -
LGA    Y      41      -       -           -
LGA    D      42      -       -           -
LGA    T      43      -       -           -
LGA    Q      44      -       -           -
LGA    F      45      -       -           -
LGA    A      46      -       -           -
LGA    V      47      -       -           -
LGA    I      48      -       -           -
LGA    D      49      -       -           -
LGA    D      50      -       -           -
LGA    F      51      -       -           -
LGA    L      52      -       -           -
LGA    V      53      -       -           -
LGA    F      54      M      66           #
LGA    K      55      P      67           -
LGA    F      56      V      68           -
LGA    W      57      G      69           -
LGA    A      58      -       -           -
LGA    G      59      -       -           -
LGA    E      60      -       -           -
LGA    Q      61      -       -           -
LGA    L      62      N      70           #
LGA    A      63      G      71           -
LGA    -       -      D      72           -
LGA    Y      64      L      73          2.848
LGA    M      65      K      74          2.732
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    M      66      L      77          1.783
LGA    P      67      R      78          2.791
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    V      68      E      82          1.605
LGA    G      69      D      83          3.595
LGA    -       -      A      84           -
LGA    N      70      D      85          3.960
LGA    G      71      K      86          2.089
LGA    D      72      E      87          2.400
LGA    L      73      K      88           #
LGA    K      74      H      89          1.694
LGA    A      75      N      90          5.290
LGA    V      76      F      91          4.525
LGA    L      77      C      92          2.806
LGA    R      78      -       -           -
LGA    K      79      -       -           -
LGA    L      80      M      93          3.420
LGA    I      81      -       -           -
LGA    E      82      -       -           -
LGA    D      83      L      94          4.592
LGA    A      84      G      95          5.071
LGA    D      85      V      96           -
LGA    K      86      C      97           -
LGA    E      87      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    K      88      D     117          4.196
LGA    H      89      K     290          1.746
LGA    N      90      Y     291          2.197
LGA    F      91      M     292          2.579
LGA    C      92      A     293          4.076
LGA    M      93      C     294          3.283
LGA    -       -      L     295           -
LGA    L      94      K     296          3.221
LGA    G      95      D     297          4.175
LGA    V      96      H     298           #
LGA    C      97      -       -           -
LGA    S      98      -       -           -
LGA    N      99      -       -           -
LGA    M     100      -       -           -
LGA    R     101      -       -           -
LGA    A     102      -       -           -
LGA    D     103      -       -           -
LGA    L     104      -       -           -
LGA    E     105      -       -           -
LGA    A     106      -       -           -
LGA    I     107      -       -           -
LGA    L     108      -       -           -
LGA    P     109      -       -           -
LGA    E     110      -       -           -
LGA    R     111      -       -           -
LGA    F     112      -       -           -
LGA    I     113      -       -           -
LGA    F     114      -       -           -
LGA    T     115      -       -           -
LGA    E     116      -       -           -
LGA    D     117      -       -           -
LGA    K     290      -       -           -
LGA    Y     291      -       -           -
LGA    M     292      -       -           -
LGA    A     293      -       -           -
LGA    C     294      -       -           -
LGA    L     295      -       -           -
LGA    K     296      -       -           -
LGA    D     297      -       -           -
LGA    H     298      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  126  126    5.0     48    3.00    35.42     22.825     1.548

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.328057 * X  +   0.762082 * Y  +  -0.558220 * Z  +  17.566301
  Y_new =  -0.345850 * X  +  -0.646788 * Y  +  -0.679745 * Z  +  84.035118
  Z_new =  -0.879071 * X  +  -0.029934 * Y  +   0.475750 * Z  + -13.155563 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.062838    3.078755  [ DEG:    -3.6003    176.3997 ]
  Theta =   1.073910    2.067683  [ DEG:    61.5305    118.4695 ]
  Phi   =  -2.329797    0.811796  [ DEG:  -133.4875     46.5125 ]
 
# 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: T0372TS599_1-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS599_1-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  126  126   5.0   48   3.00   35.42  22.825
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS599_1-D1
PFRMAT TS                                                                       
TARGET T0372                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      41.852  54.634  -5.395  1.00  0.00              
ATOM      2  CA  ILE     2      40.060  51.827  -3.666  1.00  0.00              
ATOM      3  CA  PRO     3      36.276  51.409  -1.892  1.00  0.00              
ATOM      4  CA  PHE     4      35.720  52.109   1.610  1.00  0.00              
ATOM      5  CA  LYS     5      34.662  50.147   4.638  1.00  0.00              
ATOM      6  CA  ASP     6      37.389  47.892   5.933  1.00  0.00              
ATOM      7  CA  ILE     7      40.430  49.543   4.446  1.00  0.00              
ATOM      8  CA  THR     8      43.280  49.558   6.954  1.00  0.00              
ATOM      9  CA  LEU     9      45.830  52.389   7.067  1.00  0.00              
ATOM     10  CA  ALA    10      48.613  51.713   9.488  1.00  0.00              
ATOM     11  CA  ASP    11      49.683  54.988  10.966  1.00  0.00              
ATOM     12  CA  ARG    12      47.428  54.891  14.081  1.00  0.00              
ATOM     13  CA  ASP    13      47.479  58.627  14.642  1.00  0.00              
ATOM     14  CA  THR    14      46.564  59.275  11.041  1.00  0.00              
ATOM     15  CA  ILE    15      43.751  56.791  10.996  1.00  0.00              
ATOM     16  CA  THR    16      42.194  58.211  14.148  1.00  0.00              
ATOM     17  CA  ALA    17      42.444  61.691  12.593  1.00  0.00              
ATOM     18  CA  PHE    18      40.788  60.470   9.409  1.00  0.00              
ATOM     19  CA  THR    19      37.897  58.794  11.305  1.00  0.00              
ATOM     20  CA  MET    20      37.308  61.914  13.336  1.00  0.00              
ATOM     21  CA  LYS    21      37.189  64.110  10.273  1.00  0.00              
ATOM     22  CA  SER    22      34.721  61.977   8.399  1.00  0.00              
ATOM     23  CA  ASP    23      32.227  61.768  11.331  1.00  0.00              
ATOM     24  CA  ARG    24      32.175  58.034  11.571  1.00  0.00              
ATOM     25  CA  ARG    25      30.756  56.434  14.703  1.00  0.00              
ATOM     26  CA  ASN    26      32.983  53.500  15.481  1.00  0.00              
ATOM     27  CA  CYS    27      30.763  50.496  15.466  1.00  0.00              
ATOM     28  CA  ASP    28      33.377  47.746  15.470  1.00  0.00              
ATOM     29  CA  LEU    29      36.255  49.858  14.502  1.00  0.00              
ATOM     30  CA  SER    30      39.744  49.200  15.580  1.00  0.00              
ATOM     31  CA  PHE    31      41.797  52.065  14.217  1.00  0.00              
ATOM     32  CA  SER    32      43.611  50.111  11.616  1.00  0.00              
ATOM     33  CA  ASN    33      40.551  48.502  10.174  1.00  0.00              
ATOM     34  CA  LEU    34      37.929  51.129  10.041  1.00  0.00              
ATOM     35  CA  CYS    35      34.320  50.457  10.385  1.00  0.00              
ATOM     36  CA  SER    36      31.680  53.025  10.157  1.00  0.00              
ATOM     37  CA  TRP    37      28.198  52.677  11.463  1.00  0.00              
ATOM     38  CA  ARG    38      25.192  54.705  10.749  1.00  0.00              
ATOM     39  CA  PHE    39      22.097  53.220  12.356  1.00  0.00              
ATOM     40  CA  LEU    40      20.405  51.802   9.295  1.00  0.00              
ATOM     41  CA  TYR    41      23.541  50.654   7.415  1.00  0.00              
ATOM     42  CA  ASP    42      22.332  50.414   3.937  1.00  0.00              
ATOM     43  CA  THR    43      24.843  51.012   1.361  1.00  0.00              
ATOM     44  CA  GLN    44      23.940  51.907  -2.193  1.00  0.00              
ATOM     45  CA  PHE    45      26.315  51.696  -4.876  1.00  0.00              
ATOM     46  CA  ALA    46      25.774  53.311  -8.253  1.00  0.00              
ATOM     47  CA  VAL    47      27.943  52.490 -11.221  1.00  0.00              
ATOM     48  CA  ILE    48      28.166  54.733 -14.198  1.00  0.00              
ATOM     49  CA  ASP    49      30.749  53.988 -16.887  1.00  0.00              
ATOM     50  CA  ASP    50      34.003  54.772 -15.102  1.00  0.00              
ATOM     51  CA  PHE    51      32.572  56.659 -12.144  1.00  0.00              
ATOM     52  CA  LEU    52      31.590  55.104  -8.881  1.00  0.00              
ATOM     53  CA  VAL    53      28.979  56.551  -6.580  1.00  0.00              
ATOM     54  CA  PHE    54      28.454  55.558  -3.290  1.00  0.00              
ATOM     55  CA  LYS    55      25.598  56.337  -1.053  1.00  0.00              
ATOM     56  CA  PHE    56      25.515  55.931   2.602  1.00  0.00              
ATOM     57  CA  TRP    57      22.475  56.182   4.647  1.00  0.00              
ATOM     58  CA  ALA    58      22.813  57.165   8.315  1.00  0.00              
ATOM     59  CA  GLY    59      20.170  59.523   9.565  1.00  0.00              
ATOM     60  CA  GLU    60      21.249  62.452   7.478  1.00  0.00              
ATOM     61  CA  GLN    61      22.312  60.966   4.235  1.00  0.00              
ATOM     62  CA  LEU    62      25.961  60.798   3.330  1.00  0.00              
ATOM     63  CA  ALA    63      27.037  60.888  -0.324  1.00  0.00              
ATOM     64  CA  TYR    64      30.397  59.640  -1.384  1.00  0.00              
ATOM     65  CA  MET    65      31.711  60.180  -4.916  1.00  0.00              
ATOM     66  CA  MET    66      34.604  58.076  -6.044  1.00  0.00              
ATOM     67  CA  PRO    67      36.418  58.491  -9.385  1.00  0.00              
ATOM     68  CA  VAL    68      36.884  55.044 -10.754  1.00  0.00              
ATOM     69  CA  GLY    69      39.819  54.352 -12.961  1.00  0.00              
ATOM     70  CA  ASN    70      38.829  52.688 -16.162  1.00  0.00              
ATOM     71  CA  GLY    71      40.444  49.334 -15.718  1.00  0.00              
ATOM     72  CA  ASP    72      39.932  48.591 -12.071  1.00  0.00              
ATOM     73  CA  LEU    73      36.305  49.274 -11.475  1.00  0.00              
ATOM     74  CA  LYS    74      34.955  45.769 -11.618  1.00  0.00              
ATOM     75  CA  ALA    75      37.476  44.522  -9.070  1.00  0.00              
ATOM     76  CA  VAL    76      36.721  47.338  -6.703  1.00  0.00              
ATOM     77  CA  LEU    77      33.043  46.821  -6.822  1.00  0.00              
ATOM     78  CA  ARG    78      33.325  43.118  -6.230  1.00  0.00              
ATOM     79  CA  LYS    79      35.562  43.588  -3.231  1.00  0.00              
ATOM     80  CA  LEU    80      33.165  46.194  -1.788  1.00  0.00              
ATOM     81  CA  ILE    81      30.194  43.836  -2.170  1.00  0.00              
ATOM     82  CA  GLU    82      32.108  41.117  -0.455  1.00  0.00              
ATOM     83  CA  ASP    83      33.121  43.373   2.418  1.00  0.00              
ATOM     84  CA  ALA    84      29.625  44.521   3.047  1.00  0.00              
ATOM     85  CA  ASP    85      28.461  40.948   3.120  1.00  0.00              
ATOM     86  CA  LYS    86      31.124  39.884   5.605  1.00  0.00              
ATOM     87  CA  GLU    87      30.311  42.806   7.942  1.00  0.00              
ATOM     88  CA  LYS    88      26.557  42.394   7.635  1.00  0.00              
ATOM     89  CA  HIS    89      25.967  45.595   5.692  1.00  0.00              
ATOM     90  CA  ASN    90      23.424  45.685   3.010  1.00  0.00              
ATOM     91  CA  PHE    91      24.858  46.863  -0.184  1.00  0.00              
ATOM     92  CA  CYS    92      22.649  47.436  -3.179  1.00  0.00              
ATOM     93  CA  MET    93      24.193  47.769  -6.556  1.00  0.00              
ATOM     94  CA  LEU    94      22.463  50.002  -9.145  1.00  0.00              
ATOM     95  CA  GLY    95      23.564  50.378 -12.635  1.00  0.00              
ATOM     96  CA  VAL    96      23.011  53.868 -13.819  1.00  0.00              
ATOM     97  CA  CYS    97      21.920  54.677 -17.271  1.00  0.00              
ATOM     98  CA  SER    98      23.708  57.509 -18.988  1.00  0.00              
ATOM     99  CA  ASN    99      20.960  60.062 -18.591  1.00  0.00              
ATOM    100  CA  MET   100      20.703  59.505 -14.877  1.00  0.00              
ATOM    101  CA  ARG   101      24.401  59.710 -14.334  1.00  0.00              
ATOM    102  CA  ALA   102      24.609  62.932 -16.243  1.00  0.00              
ATOM    103  CA  ASP   103      21.743  64.520 -14.295  1.00  0.00              
ATOM    104  CA  LEU   104      23.245  63.560 -10.934  1.00  0.00              
ATOM    105  CA  GLU   105      26.605  64.934 -11.918  1.00  0.00              
ATOM    106  CA  ALA   106      25.033  68.198 -12.948  1.00  0.00              
ATOM    107  CA  ILE   107      23.052  68.782  -9.817  1.00  0.00              
ATOM    108  CA  LEU   108      25.696  67.590  -7.348  1.00  0.00              
ATOM    109  CA  PRO   109      28.544  69.151  -9.225  1.00  0.00              
ATOM    110  CA  GLU   110      27.442  72.798  -9.306  1.00  0.00              
ATOM    111  CA  ARG   111      27.027  73.138  -5.597  1.00  0.00              
ATOM    112  CA  PHE   112      29.682  70.798  -4.594  1.00  0.00              
ATOM    113  CA  ILE   113      31.621  70.184  -1.520  1.00  0.00              
ATOM    114  CA  PHE   114      34.878  68.359  -1.828  1.00  0.00              
ATOM    115  CA  THR   115      36.257  66.397   1.121  1.00  0.00              
ATOM    116  CA  GLU   116      39.215  64.142   0.503  1.00  0.00              
ATOM    117  CA  ASP   117      39.892  61.145   2.608  1.00  0.00              
ATOM    290  CA  LYS   290      19.126 106.800 -37.850  1.00  0.00              
ATOM    291  CA  TYR   291      22.241 106.909 -35.706  1.00  0.00              
ATOM    292  CA  MET   292      23.397 103.526 -34.463  1.00  0.00              
ATOM    293  CA  ALA   293      27.015 103.124 -33.309  1.00  0.00              
ATOM    294  CA  CYS   294      27.942 100.658 -30.627  1.00  0.00              
ATOM    295  CA  LEU   295      31.523 100.419 -29.436  1.00  0.00              
ATOM    296  CA  LYS   296      31.260  97.254 -27.399  1.00  0.00              
ATOM    297  CA  ASP   297      32.759  97.916 -23.972  1.00  0.00              
ATOM    298  CA  HIS   298      31.117 101.345 -23.802  1.00  0.00              
TER                                                                             
END
