
#######################################################
#                                                     #
#                        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  101 (  101),  selected  101 , name T0304TS599_3-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS599_3-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      17      R      17           -
LGA    P      18      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    W      19      C      24          4.026
LGA    W      20      T      25          0.643
LGA    G      21      V      26          4.855
LGA    L      22      T      27           #
LGA    P      23      P      28           -
LGA    C      24      C      29           -
LGA    T      25      F      30           -
LGA    V      26      G      31           #
LGA    T      27      A      32           -
LGA    P      28      R      33           #
LGA    C      29      L      34           -
LGA    F      30      V      35           -
LGA    G      31      Q      36           -
LGA    A      32      E      37           -
LGA    R      33      G      38           -
LGA    L      34      N      39           -
LGA    V      35      R      40           -
LGA    Q      36      L      41           -
LGA    E      37      H      42           -
LGA    G      38      Y      43           -
LGA    N      39      L      44          3.765
LGA    R      40      A      45          2.216
LGA    -       -      D      46           -
LGA    L      41      R      47          3.027
LGA    H      42      A      48          3.932
LGA    Y      43      G      49           #
LGA    L      44      -       -           -
LGA    A      45      -       -           -
LGA    D      46      I      50          2.232
LGA    R      47      R      51          4.433
LGA    A      48      G      52           #
LGA    G      49      L      53          4.396
LGA    I      50      F      54           #
LGA    R      51      -       -           -
LGA    G      52      -       -           -
LGA    L      53      -       -           -
LGA    F      54      S      55          3.581
LGA    S      55      D      56          2.463
LGA    D      56      -       -           -
LGA    A      57      A      57          3.570
LGA    D      58      D      58          3.225
LGA    A      59      A      59          2.211
LGA    Y      60      Y      60          1.502
LGA    H      61      H      61          1.219
LGA    L      62      L      62          1.460
LGA    D      63      D      63          0.780
LGA    Q      64      Q      64          2.110
LGA    A      65      A      65          3.070
LGA    F      66      F      66          2.568
LGA    P      67      P      67          2.504
LGA    L      68      L      68          2.485
LGA    L      69      L      69          2.069
LGA    M      70      M      70          1.839
LGA    K      71      K      71          1.696
LGA    Q      72      Q      72          1.249
LGA    L      73      L      73          0.865
LGA    E      74      E      74          0.940
LGA    L      75      L      75          0.743
LGA    M      76      M      76          0.479
LGA    L      77      L      77          0.701
LGA    T      78      T      78          1.510
LGA    S      79      S      79          1.677
LGA    G      80      G      80          1.654
LGA    E      81      E      81          1.784
LGA    L      82      L      82          2.250
LGA    N      83      N      83          2.317
LGA    P      84      P      84          3.745
LGA    R      85      R      85          1.225
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    H      86      T     103          3.518
LGA    -       -      L     104           -
LGA    Q      87      S     105           #
LGA    H      88      S     106          5.306
LGA    T      89      C     107          3.762
LGA    V      90      -       -           -
LGA    T      91      -       -           -
LGA    L      92      -       -           -
LGA    Y      93      -       -           -
LGA    A      94      -       -           -
LGA    K      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    T      98      -       -           -
LGA    C      99      -       -           -
LGA    K     100      -       -           -
LGA    A     101      D     108          2.287
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      -       -           -
LGA    D     108      -       -           -
LGA    Y     109      -       -           -
LGA    V     110      -       -           -
LGA    Y     111      Y     109           #
LGA    L     112      V     110           #
LGA    A     113      Y     111          1.239
LGA    V     114      L     112          3.042
LGA    -       -      A     113           -
LGA    Y     115      V     114           #
LGA    P     116      Y     115           -
LGA    -       -      P     116           -
LGA    T     117      T     117           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     47    2.68    63.83     32.551     1.692

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.647198 * X  +  -0.499603 * Y  +   0.575787 * Z  +  42.559200
  Y_new =   0.623783 * X  +  -0.781252 * Y  +   0.023264 * Z  +  24.406961
  Z_new =   0.438212 * X  +   0.374223 * Y  +   0.817268 * Z  +  42.530750 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.429399   -2.712193  [ DEG:    24.6028   -155.3972 ]
  Theta =  -0.453608   -2.687984  [ DEG:   -25.9898   -154.0102 ]
  Phi   =   2.374616   -0.766977  [ DEG:   136.0555    -43.9445 ]
 
# 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: T0304TS599_3-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS599_3-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  101   5.0   47   2.68   63.83  32.551
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS599_3-D1
PFRMAT TS                                                                       
TARGET T0304                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM     17  CA  ARG    17      40.092  36.122  34.874  1.00  0.00              
ATOM     18  CA  PRO    18      37.155  34.087  33.500  1.00  0.00              
ATOM     19  CA  TRP    19      38.028  30.649  34.878  1.00  0.00              
ATOM     20  CA  TRP    20      34.701  29.412  36.027  1.00  0.00              
ATOM     21  CA  GLY    21      35.419  25.963  37.326  1.00  0.00              
ATOM     22  CA  LEU    22      32.133  24.455  38.377  1.00  0.00              
ATOM     23  CA  PRO    23      31.792  22.697  41.671  1.00  0.00              
ATOM     24  CA  CYS    24      28.674  24.151  43.367  1.00  0.00              
ATOM     25  CA  THR    25      29.735  25.102  46.942  1.00  0.00              
ATOM     26  CA  VAL    26      32.882  23.078  47.362  1.00  0.00              
ATOM     27  CA  THR    27      33.999  22.326  50.948  1.00  0.00              
ATOM     28  CA  PRO    28      37.247  20.367  51.078  1.00  0.00              
ATOM     29  CA  CYS    29      36.169  17.596  53.483  1.00  0.00              
ATOM     30  CA  PHE    30      33.372  16.684  51.040  1.00  0.00              
ATOM     31  CA  GLY    31      35.085  16.925  47.717  1.00  0.00              
ATOM     32  CA  ALA    32      34.415  13.371  46.638  1.00  0.00              
ATOM     33  CA  ARG    33      35.719  12.137  49.958  1.00  0.00              
ATOM     34  CA  LEU    34      38.956  14.131  49.424  1.00  0.00              
ATOM     35  CA  VAL    35      39.467  12.725  45.897  1.00  0.00              
ATOM     36  CA  GLN    36      38.685   9.235  47.082  1.00  0.00              
ATOM     37  CA  GLU    37      41.189   9.411  49.987  1.00  0.00              
ATOM     38  CA  GLY    38      44.166  10.941  48.248  1.00  0.00              
ATOM     39  CA  ASN    39      43.816  14.504  49.621  1.00  0.00              
ATOM     40  CA  ARG    40      44.923  16.631  46.696  1.00  0.00              
ATOM     41  CA  LEU    41      42.911  19.672  45.704  1.00  0.00              
ATOM     42  CA  HIS    42      44.615  20.530  42.363  1.00  0.00              
ATOM     43  CA  TYR    43      43.090  23.517  40.639  1.00  0.00              
ATOM     44  CA  LEU    44      44.617  23.181  37.148  1.00  0.00              
ATOM     45  CA  ALA    45      44.634  19.397  36.999  1.00  0.00              
ATOM     46  CA  ASP    46      40.878  18.903  37.603  1.00  0.00              
ATOM     47  CA  ARG    47      39.632  21.770  35.410  1.00  0.00              
ATOM     48  CA  ALA    48      41.790  20.702  32.441  1.00  0.00              
ATOM     49  CA  GLY    49      41.026  16.971  32.626  1.00  0.00              
ATOM     50  CA  ILE    50      44.508  15.521  33.472  1.00  0.00              
ATOM     51  CA  ARG    51      43.233  12.545  35.394  1.00  0.00              
ATOM     52  CA  GLY    52      40.790  11.210  32.878  1.00  0.00              
ATOM     53  CA  LEU    53      38.489  12.427  30.163  1.00  0.00              
ATOM     54  CA  PHE    54      41.020  14.164  27.942  1.00  0.00              
ATOM     55  CA  SER    55      43.309  12.365  25.585  1.00  0.00              
ATOM     56  CA  ASP    56      46.636  10.933  26.695  1.00  0.00              
ATOM     57  CA  ALA    57      48.654  13.787  25.094  1.00  0.00              
ATOM     58  CA  ASP    58      46.516  16.386  26.769  1.00  0.00              
ATOM     59  CA  ALA    59      46.905  14.634  30.180  1.00  0.00              
ATOM     60  CA  TYR    60      50.719  14.750  29.832  1.00  0.00              
ATOM     61  CA  HIS    61      50.564  18.465  28.938  1.00  0.00              
ATOM     62  CA  LEU    62      48.321  19.264  31.965  1.00  0.00              
ATOM     63  CA  ASP    63      50.603  17.368  34.390  1.00  0.00              
ATOM     64  CA  GLN    64      53.573  19.444  33.188  1.00  0.00              
ATOM     65  CA  ALA    65      51.528  22.638  33.706  1.00  0.00              
ATOM     66  CA  PHE    66      50.373  21.763  37.257  1.00  0.00              
ATOM     67  CA  PRO    67      53.854  20.929  38.564  1.00  0.00              
ATOM     68  CA  LEU    68      55.185  24.185  37.111  1.00  0.00              
ATOM     69  CA  LEU    69      52.360  26.217  38.711  1.00  0.00              
ATOM     70  CA  MET    70      52.830  24.680  42.104  1.00  0.00              
ATOM     71  CA  LYS    71      56.581  25.357  41.901  1.00  0.00              
ATOM     72  CA  GLN    72      55.983  29.006  41.059  1.00  0.00              
ATOM     73  CA  LEU    73      53.561  29.336  44.004  1.00  0.00              
ATOM     74  CA  GLU    74      56.079  27.700  46.343  1.00  0.00              
ATOM     75  CA  LEU    75      58.803  30.082  45.158  1.00  0.00              
ATOM     76  CA  MET    76      56.514  33.062  45.806  1.00  0.00              
ATOM     77  CA  LEU    77      55.671  31.811  49.284  1.00  0.00              
ATOM     78  CA  THR    78      59.266  31.283  50.351  1.00  0.00              
ATOM     79  CA  SER    79      60.297  34.686  49.004  1.00  0.00              
ATOM     80  CA  GLY    80      57.735  36.821  50.634  1.00  0.00              
ATOM     81  CA  GLU    81      55.830  37.832  47.555  1.00  0.00              
ATOM     82  CA  LEU    82      52.530  36.848  49.016  1.00  0.00              
ATOM     83  CA  ASN    83      51.426  38.132  52.374  1.00  0.00              
ATOM     84  CA  PRO    84      50.922  36.344  55.654  1.00  0.00              
ATOM     85  CA  ARG    85      47.195  35.842  55.393  1.00  0.00              
ATOM     86  CA  HIS    86      47.470  34.411  51.863  1.00  0.00              
ATOM     87  CA  GLN    87      50.237  31.829  52.405  1.00  0.00              
ATOM     88  CA  HIS    88      48.448  29.875  55.080  1.00  0.00              
ATOM     89  CA  THR    89      44.830  30.026  53.782  1.00  0.00              
ATOM     90  CA  VAL    90      43.554  27.905  50.931  1.00  0.00              
ATOM     91  CA  THR    91      41.042  29.381  48.526  1.00  0.00              
ATOM     92  CA  LEU    92      38.765  27.162  46.552  1.00  0.00              
ATOM     93  CA  TYR    93      37.118  28.612  43.537  1.00  0.00              
ATOM     94  CA  ALA    94      34.079  26.806  42.015  1.00  0.00              
ATOM     95  CA  LYS    95      31.357  28.454  44.061  1.00  0.00              
ATOM     96  CA  GLY    96      33.140  30.027  46.903  1.00  0.00              
ATOM     97  CA  LEU    97      35.189  27.733  49.094  1.00  0.00              
ATOM     98  CA  THR    98      37.422  29.109  51.766  1.00  0.00              
ATOM     99  CA  CYS    99      39.788  26.795  53.564  1.00  0.00              
ATOM    100  CA  LYS   100      41.604  28.053  56.557  1.00  0.00              
ATOM    101  CA  ALA   101      45.111  26.705  56.902  1.00  0.00              
ATOM    102  CA  ASP   102      44.497  25.357  60.336  1.00  0.00              
ATOM    103  CA  THR   103      41.009  23.849  60.237  1.00  0.00              
ATOM    104  CA  LEU   104      41.007  22.045  56.865  1.00  0.00              
ATOM    105  CA  SER   105      44.453  20.666  57.441  1.00  0.00              
ATOM    106  CA  SER   106      43.621  19.343  60.957  1.00  0.00              
ATOM    107  CA  CYS   107      40.465  17.599  59.783  1.00  0.00              
ATOM    108  CA  ASP   108      41.590  16.077  56.525  1.00  0.00              
ATOM    109  CA  TYR   109      40.340  18.584  54.017  1.00  0.00              
ATOM    110  CA  VAL   110      41.913  19.444  50.699  1.00  0.00              
ATOM    111  CA  TYR   111      42.211  23.105  49.607  1.00  0.00              
ATOM    112  CA  LEU   112      42.417  24.093  45.980  1.00  0.00              
ATOM    113  CA  ALA   113      43.872  27.377  45.081  1.00  0.00              
ATOM    114  CA  VAL   114      42.626  29.174  41.925  1.00  0.00              
ATOM    115  CA  TYR   115      44.417  32.340  41.000  1.00  0.00              
ATOM    116  CA  PRO   116      43.670  35.119  38.607  1.00  0.00              
ATOM    117  CA  THR   117      46.443  35.443  36.084  1.00  0.00              
TER                                                                             
END
