
#######################################################
#                                                     #
#                        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  124 (  124),  selected  124 , name T0356TS599_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS599_2-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N       7      N       7           #
LGA    D       8      D       8          2.023
LGA    L       9      L       9          1.787
LGA    R      10      R      10          1.602
LGA    D      11      D      11          1.502
LGA    F      12      F      12          1.345
LGA    L      13      L      13          1.364
LGA    T      14      T      14          1.610
LGA    L      15      L      15          1.136
LGA    L      16      L      16          1.152
LGA    E      17      E      17          1.487
LGA    Q      18      Q      18          2.569
LGA    Q      19      Q      19          2.546
LGA    G      20      G      20          1.279
LGA    E      21      E      21          1.253
LGA    L      22      L      22          3.266
LGA    K      23      K      23          3.505
LGA    R      24      -       -           -
LGA    I      25      -       -           -
LGA    T      26      -       -           -
LGA    L      27      R      24           #
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    P      28      D      40           #
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    V      29      L      43          1.292
LGA    D      30      R      44          1.991
LGA    P      31      A      45          6.442
LGA    H      32      G      46           -
LGA    L      33      G      47           -
LGA    E      34      P      48           -
LGA    I      35      A      49           #
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    T      36      C      64          4.508
LGA    E      37      N      65           #
LGA    I      38      -       -           -
LGA    A      39      -       -           -
LGA    D      40      -       -           -
LGA    R      41      -       -           -
LGA    T      42      -       -           -
LGA    L      43      -       -           -
LGA    R      44      -       -           -
LGA    A      45      -       -           -
LGA    G      46      -       -           -
LGA    G      47      -       -           -
LGA    P      48      -       -           -
LGA    A      49      -       -           -
LGA    L      50      -       -           -
LGA    L      51      -       -           -
LGA    F      52      -       -           -
LGA    E      53      -       -           -
LGA    N      54      -       -           -
LGA    P      55      -       -           -
LGA    K      56      -       -           -
LGA    G      57      -       -           -
LGA    Y      58      -       -           -
LGA    S      59      -       -           -
LGA    M      60      -       -           -
LGA    P      61      -       -           -
LGA    V      62      -       -           -
LGA    L      63      -       -           -
LGA    C      64      -       -           -
LGA    N      65      -       -           -
LGA    L      66      -       -           -
LGA    F      67      L      66           #
LGA    G      68      F      67          1.301
LGA    T      69      G      68          4.297
LGA    P      70      T      69           #
LGA    K      71      P      70          1.745
LGA    R      72      K      71          2.446
LGA    -       -      R      72           -
LGA    V      73      V      73          3.585
LGA    A      74      A      74          3.105
LGA    M      75      M      75          5.320
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    G      76      G      78           #
LGA    M      77      Q      79          2.699
LGA    G      78      E      80          3.497
LGA    Q      79      D      81          3.369
LGA    E      80      -       -           -
LGA    D      81      -       -           -
LGA    V      82      V      82          3.698
LGA    S      83      -       -           -
LGA    A      84      S      83          2.016
LGA    L      85      A      84          2.776
LGA    R      86      L      85          2.912
LGA    E      87      R      86          0.726
LGA    V      88      E      87          2.459
LGA    G      89      V      88          2.945
LGA    K      90      G      89          1.470
LGA    L      91      K      90          2.583
LGA    L      92      L      91          3.795
LGA    A      93      L      92          2.998
LGA    F      94      A      93          2.603
LGA    L      95      F      94          4.260
LGA    K      96      L      95          4.213
LGA    D     314      K      96           -
LGA    A     315      D     314           -
LGA    I     316      A     315           -
LGA    Y     317      I     316           -
LGA    H     318      Y     317           -
LGA    S     319      H     318           -
LGA    T     320      S     319           -
LGA    Y     321      T     320           -
LGA    T     322      Y     321           -
LGA    G     323      T     322           -
LGA    R     324      G     323           -
LGA    P     325      R     324           -
LGA    P     326      P     325           -
LGA    D     327      P     326           -
LGA    E     328      D     327           -
LGA    P     329      E     328           -
LGA    A     330      P     329           -
LGA    V     331      A     330           -
LGA    L     332      V     331           -
LGA    G     333      L     332           -
LGA    V     334      G     333           -
LGA    A     335      V     334           -
LGA    L     336      A     335           -
LGA    N     337      L     336           -
LGA    E     338      N     337           -
LGA    V     339      E     338           -
LGA    F     340      V     339           -
LGA    V     341      F     340           -
LGA    P     342      V     341           -
LGA    I     343      P     342           -
LGA    L     344      I     343           -
LGA    Q     345      L     344           -
LGA    K     346      Q     345           -
LGA    Q     347      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  124  124    5.0     44    2.88    47.73     23.738     1.477

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.510699 * X  +  -0.855357 * Y  +  -0.086901 * Z  +  91.105927
  Y_new =   0.748288 * X  +   0.392434 * Y  +   0.534846 * Z  +  66.680740
  Z_new =  -0.423381 * X  +  -0.338172 * Y  +   0.840469 * Z  +  60.199955 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.382540    2.759052  [ DEG:   -21.9180    158.0820 ]
  Theta =   0.437174    2.704418  [ DEG:    25.0483    154.9518 ]
  Phi   =   0.971920   -2.169673  [ DEG:    55.6869   -124.3131 ]
 
# 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: T0356TS599_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS599_2-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  124  124   5.0   44   2.88   47.73  23.738
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS599_2-D1
PFRMAT TS                                                                       
TARGET T0356                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      7  CA  ASN     7      78.951  79.240  84.751  1.00  0.00              
ATOM      8  CA  ASP     8      76.798  78.809  81.783  1.00  0.00              
ATOM      9  CA  LEU     9      73.683  77.818  83.772  1.00  0.00              
ATOM     10  CA  ARG    10      73.790  79.849  86.674  1.00  0.00              
ATOM     11  CA  ASP    11      73.326  82.593  84.325  1.00  0.00              
ATOM     12  CA  PHE    12      70.228  80.847  82.949  1.00  0.00              
ATOM     13  CA  LEU    13      68.525  79.724  86.587  1.00  0.00              
ATOM     14  CA  THR    14      69.446  83.159  87.726  1.00  0.00              
ATOM     15  CA  LEU    15      68.029  85.290  85.170  1.00  0.00              
ATOM     16  CA  LEU    16      64.972  83.407  85.482  1.00  0.00              
ATOM     17  CA  GLU    17      64.970  83.773  88.981  1.00  0.00              
ATOM     18  CA  GLN    18      64.951  87.304  90.070  1.00  0.00              
ATOM     19  CA  GLN    19      61.851  87.424  87.611  1.00  0.00              
ATOM     20  CA  GLY    20      59.788  84.877  88.748  1.00  0.00              
ATOM     21  CA  GLU    21      59.618  82.609  86.151  1.00  0.00              
ATOM     22  CA  LEU    22      61.610  79.377  86.332  1.00  0.00              
ATOM     23  CA  LYS    23      59.772  78.495  89.549  1.00  0.00              
ATOM     24  CA  ARG    24      56.559  79.135  88.214  1.00  0.00              
ATOM     25  CA  ILE    25      57.139  76.202  85.997  1.00  0.00              
ATOM     26  CA  THR    26      58.343  74.032  88.099  1.00  0.00              
ATOM     27  CA  LEU    27      55.329  74.021  90.707  1.00  0.00              
ATOM     28  CA  PRO    28      52.635  74.097  88.360  1.00  0.00              
ATOM     29  CA  VAL    29      53.015  71.667  85.559  1.00  0.00              
ATOM     30  CA  ASP    30      51.667  68.181  84.714  1.00  0.00              
ATOM     31  CA  PRO    31      51.165  68.776  81.357  1.00  0.00              
ATOM     32  CA  HIS    32      52.720  66.097  79.209  1.00  0.00              
ATOM     33  CA  LEU    33      56.022  67.349  80.037  1.00  0.00              
ATOM     34  CA  GLU    34      57.058  67.029  83.066  1.00  0.00              
ATOM     35  CA  ILE    35      59.238  69.257  84.691  1.00  0.00              
ATOM     36  CA  THR    36      60.762  67.312  87.024  1.00  0.00              
ATOM     37  CA  GLU    37      60.847  64.374  85.166  1.00  0.00              
ATOM     38  CA  ILE    38      62.116  65.821  81.605  1.00  0.00              
ATOM     39  CA  ALA    39      65.107  66.964  83.385  1.00  0.00              
ATOM     40  CA  ASP    40      65.789  63.360  84.336  1.00  0.00              
ATOM     41  CA  ARG    41      65.073  61.582  81.397  1.00  0.00              
ATOM     42  CA  THR    42      67.239  63.856  79.660  1.00  0.00              
ATOM     43  CA  LEU    43      70.314  63.618  81.792  1.00  0.00              
ATOM     44  CA  ARG    44      69.957  59.627  80.995  1.00  0.00              
ATOM     45  CA  ALA    45      69.777  59.869  77.535  1.00  0.00              
ATOM     46  CA  GLY    46      73.223  61.467  77.364  1.00  0.00              
ATOM     47  CA  GLY    47      72.542  64.830  75.675  1.00  0.00              
ATOM     48  CA  PRO    48      74.560  67.340  77.166  1.00  0.00              
ATOM     49  CA  ALA    49      72.418  70.771  76.633  1.00  0.00              
ATOM     50  CA  LEU    50      73.601  73.930  75.502  1.00  0.00              
ATOM     51  CA  LEU    51      70.728  76.703  76.038  1.00  0.00              
ATOM     52  CA  PHE    52      71.104  80.303  74.910  1.00  0.00              
ATOM     53  CA  GLU    53      70.154  83.452  76.164  1.00  0.00              
ATOM     54  CA  ASN    54      70.353  86.123  73.858  1.00  0.00              
ATOM     55  CA  PRO    55      69.963  84.395  71.138  1.00  0.00              
ATOM     56  CA  LYS    56      68.523  86.221  68.252  1.00  0.00              
ATOM     57  CA  GLY    57      71.519  86.016  65.879  1.00  0.00              
ATOM     58  CA  TYR    58      73.841  84.223  68.170  1.00  0.00              
ATOM     59  CA  SER    59      72.997  80.595  66.700  1.00  0.00              
ATOM     60  CA  MET    60      73.387  78.646  69.957  1.00  0.00              
ATOM     61  CA  PRO    61      72.633  74.882  70.852  1.00  0.00              
ATOM     62  CA  VAL    62      69.491  74.419  71.771  1.00  0.00              
ATOM     63  CA  LEU    63      68.072  71.521  74.487  1.00  0.00              
ATOM     64  CA  CYS    64      64.455  71.949  75.439  1.00  0.00              
ATOM     65  CA  ASN    65      63.587  68.865  77.070  1.00  0.00              
ATOM     66  CA  LEU    66      66.967  69.307  78.531  1.00  0.00              
ATOM     67  CA  PHE    67      67.065  72.513  79.572  1.00  0.00              
ATOM     68  CA  GLY    68      63.362  72.954  80.894  1.00  0.00              
ATOM     69  CA  THR    69      60.442  73.264  78.660  1.00  0.00              
ATOM     70  CA  PRO    70      60.286  74.941  75.211  1.00  0.00              
ATOM     71  CA  LYS    71      57.778  77.329  76.531  1.00  0.00              
ATOM     72  CA  ARG    72      59.975  78.439  79.027  1.00  0.00              
ATOM     73  CA  VAL    73      62.889  79.289  76.865  1.00  0.00              
ATOM     74  CA  ALA    74      60.988  81.038  74.413  1.00  0.00              
ATOM     75  CA  MET    75      59.911  83.395  76.799  1.00  0.00              
ATOM     76  CA  GLY    76      63.468  84.036  77.890  1.00  0.00              
ATOM     77  CA  MET    77      64.465  84.498  74.221  1.00  0.00              
ATOM     78  CA  GLY    78      62.130  86.816  73.275  1.00  0.00              
ATOM     79  CA  GLN    79      59.706  85.851  70.900  1.00  0.00              
ATOM     80  CA  GLU    80      56.243  85.761  69.834  1.00  0.00              
ATOM     81  CA  ASP    81      54.736  82.894  68.858  1.00  0.00              
ATOM     82  CA  VAL    82      55.211  79.545  70.169  1.00  0.00              
ATOM     83  CA  SER    83      55.224  78.109  66.468  1.00  0.00              
ATOM     84  CA  ALA    84      58.049  80.469  66.006  1.00  0.00              
ATOM     85  CA  LEU    85      60.226  79.634  68.680  1.00  0.00              
ATOM     86  CA  ARG    86      60.432  76.081  67.380  1.00  0.00              
ATOM     87  CA  GLU    87      61.393  77.376  64.225  1.00  0.00              
ATOM     88  CA  VAL    88      64.039  79.155  65.710  1.00  0.00              
ATOM     89  CA  GLY    89      65.095  75.685  67.187  1.00  0.00              
ATOM     90  CA  LYS    90      64.913  73.915  63.990  1.00  0.00              
ATOM     91  CA  LEU    91      67.268  76.498  62.336  1.00  0.00              
ATOM     92  CA  LEU    92      70.106  76.023  65.106  1.00  0.00              
ATOM     93  CA  ALA    93      69.868  71.950  64.593  1.00  0.00              
ATOM     94  CA  PHE    94      70.182  72.585  60.615  1.00  0.00              
ATOM     95  CA  LEU    95      73.300  74.794  61.073  1.00  0.00              
ATOM     96  CA  LYS    96      75.053  73.223  63.386  1.00  0.00              
ATOM    314  CA  ASP   314     112.832  31.744  41.378  1.00  0.00              
ATOM    315  CA  ALA   315     113.746  34.900  42.253  1.00  0.00              
ATOM    316  CA  ILE   316     110.846  37.525  41.657  1.00  0.00              
ATOM    317  CA  TYR   317     111.240  40.843  41.504  1.00  0.00              
ATOM    318  CA  HIS   318     109.106  43.006  41.173  1.00  0.00              
ATOM    319  CA  SER   319     109.694  46.819  40.697  1.00  0.00              
ATOM    320  CA  THR   320     107.543  48.914  41.193  1.00  0.00              
ATOM    321  CA  TYR   321     107.891  52.705  40.335  1.00  0.00              
ATOM    322  CA  THR   322     106.014  55.832  41.320  1.00  0.00              
ATOM    323  CA  GLY   323     107.229  58.967  39.904  1.00  0.00              
ATOM    324  CA  ARG   324     108.137  61.540  42.857  1.00  0.00              
ATOM    325  CA  PRO   325     110.280  61.457  45.420  1.00  0.00              
ATOM    326  CA  PRO   326     110.467  59.652  48.707  1.00  0.00              
ATOM    327  CA  ASP   327     111.996  62.338  50.677  1.00  0.00              
ATOM    328  CA  GLU   328     115.437  62.175  51.431  1.00  0.00              
ATOM    329  CA  PRO   329     114.750  62.061  55.194  1.00  0.00              
ATOM    330  CA  ALA   330     117.385  60.046  56.688  1.00  0.00              
ATOM    331  CA  VAL   331     115.580  59.409  60.227  1.00  0.00              
ATOM    332  CA  LEU   332     112.478  59.254  58.530  1.00  0.00              
ATOM    333  CA  GLY   333     113.196  57.406  55.368  1.00  0.00              
ATOM    334  CA  VAL   334     115.083  54.650  57.047  1.00  0.00              
ATOM    335  CA  ALA   335     112.336  53.607  59.283  1.00  0.00              
ATOM    336  CA  LEU   336     109.894  53.163  56.547  1.00  0.00              
ATOM    337  CA  ASN   337     112.279  51.031  54.486  1.00  0.00              
ATOM    338  CA  GLU   338     113.313  48.677  56.953  1.00  0.00              
ATOM    339  CA  VAL   339     110.231  47.945  58.360  1.00  0.00              
ATOM    340  CA  PHE   340     108.513  47.103  55.149  1.00  0.00              
ATOM    341  CA  VAL   341     110.769  45.574  53.330  1.00  0.00              
ATOM    342  CA  PRO   342     111.603  43.020  56.069  1.00  0.00              
ATOM    343  CA  ILE   343     108.276  41.874  56.693  1.00  0.00              
ATOM    344  CA  LEU   344     107.595  41.619  52.800  1.00  0.00              
ATOM    345  CA  GLN   345     110.223  39.724  52.367  1.00  0.00              
ATOM    346  CA  LYS   346     109.278  37.416  54.970  1.00  0.00              
ATOM    347  CA  GLN   347     106.243  36.648  53.203  1.00  0.00              
TER                                                                             
END
