
#######################################################
#                                                     #
#                        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 T0304TS393_2-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS393_2-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      W      19           -
LGA    W      20      W      20           -
LGA    G      21      G      21           -
LGA    L      22      L      22           -
LGA    P      23      P      23           -
LGA    C      24      C      24           -
LGA    T      25      T      25           -
LGA    V      26      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    T      27      L      34           #
LGA    P      28      V      35          1.799
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    C      29      R      40          5.062
LGA    F      30      L      41          4.318
LGA    G      31      H      42          4.480
LGA    A      32      Y      43          1.548
LGA    R      33      L      44           #
LGA    L      34      -       -           -
LGA    V      35      -       -           -
LGA    Q      36      A      45          4.253
LGA    E      37      D      46           -
LGA    G      38      R      47           -
LGA    N      39      A      48          3.749
LGA    R      40      G      49          2.493
LGA    L      41      -       -           -
LGA    H      42      -       -           -
LGA    Y      43      I      50          2.795
LGA    L      44      R      51          3.719
LGA    A      45      -       -           -
LGA    D      46      -       -           -
LGA    R      47      -       -           -
LGA    A      48      G      52          1.509
LGA    G      49      L      53          1.395
LGA    I      50      F      54          1.082
LGA    R      51      S      55          1.787
LGA    G      52      D      56          5.232
LGA    L      53      -       -           -
LGA    F      54      -       -           -
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      -       -           -
LGA    D      58      -       -           -
LGA    A      59      -       -           -
LGA    Y      60      -       -           -
LGA    H      61      -       -           -
LGA    L      62      A      57          4.611
LGA    D      63      D      58           #
LGA    -       -      A      59           -
LGA    Q      64      Y      60          4.516
LGA    A      65      H      61          3.336
LGA    F      66      L      62          1.251
LGA    P      67      D      63          1.881
LGA    L      68      Q      64          2.401
LGA    L      69      A      65          1.208
LGA    M      70      F      66          2.261
LGA    K      71      P      67          2.105
LGA    Q      72      L      68          1.059
LGA    L      73      L      69          1.504
LGA    E      74      M      70          1.853
LGA    L      75      K      71          0.848
LGA    M      76      Q      72          0.928
LGA    L      77      L      73          1.603
LGA    T      78      E      74          1.089
LGA    S      79      L      75          3.449
LGA    G      80      M      76          2.479
LGA    -       -      L      77           -
LGA    -       -      T      78           -
LGA    -       -      S      79           -
LGA    -       -      G      80           -
LGA    E      81      E      81          1.320
LGA    L      82      L      82          0.963
LGA    N      83      N      83          2.226
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    P      84      H      86          2.470
LGA    R      85      Q      87          3.822
LGA    H      86      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    Q      87      T     103          1.304
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    H      88      Y     109          4.040
LGA    T      89      V     110          4.860
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    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      -       -           -
LGA    L     112      Y     111           #
LGA    A     113      L     112          3.856
LGA    V     114      A     113          3.802
LGA    Y     115      V     114          3.264
LGA    P     116      Y     115           #
LGA    T     117      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     44    2.94    11.36     28.088     1.447

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.141961 * X  +  -0.952083 * Y  +   0.270895 * Z  +  48.325760
  Y_new =  -0.590089 * X  +   0.301120 * Y  +   0.749081 * Z  +  18.251919
  Z_new =  -0.794759 * X  +  -0.053512 * Y  +  -0.604561 * Z  +  44.840950 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.053309    0.088284  [ DEG:  -174.9417      5.0583 ]
  Theta =   0.918611    2.222982  [ DEG:    52.6325    127.3675 ]
  Phi   =  -1.806885    1.334707  [ DEG:  -103.5269     76.4731 ]
 
# 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: T0304TS393_2-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS393_2-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   44   2.94   11.36  28.088
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS393_2-D1
PFRMAT TS
TARGET T0304
MODEL 2
PARENT N/A
ATOM     17  CA  ARG    17      61.079   8.470  68.950  1.00 25.00           C
ATOM     18  CA  PRO    18      58.686  10.414  66.732  1.00 25.00           C
ATOM     19  CA  TRP    19      56.368  13.476  66.652  1.00 25.00           C
ATOM     20  CA  TRP    20      57.892  16.096  64.331  1.00 25.00           C
ATOM     21  CA  GLY    21      58.045  19.848  64.926  1.00 25.00           C
ATOM     22  CA  LEU    22      57.172  20.119  61.281  1.00 25.00           C
ATOM     23  CA  PRO    23      54.079  22.258  61.489  1.00 25.00           C
ATOM     24  CA  CYS    24      52.974  22.255  57.848  1.00 25.00           C
ATOM     25  CA  THR    25      49.472  21.691  59.225  1.00 25.00           C
ATOM     26  CA  VAL    26      46.780  20.463  56.912  1.00 25.00           C
ATOM     27  CA  THR    27      47.407  23.767  55.046  1.00 25.00           C
ATOM     28  CA  PRO    28      49.845  21.982  52.692  1.00 25.00           C
ATOM     29  CA  CYS    29      52.495  22.374  49.930  1.00 25.00           C
ATOM     30  CA  PHE    30      54.367  20.314  47.379  1.00 25.00           C
ATOM     31  CA  GLY    31      52.966  16.762  47.670  1.00 25.00           C
ATOM     32  CA  ALA    32      49.591  18.161  48.819  1.00 25.00           C
ATOM     33  CA  ARG    33      49.558  20.584  45.853  1.00 25.00           C
ATOM     34  CA  LEU    34      50.337  17.699  43.457  1.00 25.00           C
ATOM     35  CA  VAL    35      47.493  15.634  44.978  1.00 25.00           C
ATOM     36  CA  GLN    36      45.094  18.591  44.569  1.00 25.00           C
ATOM     37  CA  GLU    37      46.164  18.984  40.912  1.00 25.00           C
ATOM     38  CA  GLY    38      45.584  15.246  40.315  1.00 25.00           C
ATOM     39  CA  ASN    39      42.108  15.507  41.902  1.00 25.00           C
ATOM     40  CA  ARG    40      41.288  18.510  39.672  1.00 25.00           C
ATOM     41  CA  LEU    41      42.442  16.562  36.582  1.00 25.00           C
ATOM     42  CA  HIS    42      40.253  13.591  37.609  1.00 25.00           C
ATOM     43  CA  TYR    43      37.253  15.927  38.065  1.00 25.00           C
ATOM     44  CA  LEU    44      37.876  17.442  34.603  1.00 25.00           C
ATOM     45  CA  ALA    45      38.052  13.936  33.073  1.00 25.00           C
ATOM     46  CA  ASP    46      34.761  12.993  34.790  1.00 25.00           C
ATOM     47  CA  ARG    47      33.120  16.183  33.447  1.00 25.00           C
ATOM     48  CA  ALA    48      34.022  19.560  31.810  1.00 25.00           C
ATOM     49  CA  GLY    49      36.751  17.927  29.667  1.00 25.00           C
ATOM     50  CA  ILE    50      40.397  18.440  30.373  1.00 25.00           C
ATOM     51  CA  ARG    51      42.444  18.337  27.117  1.00 25.00           C
ATOM     52  CA  GLY    52      39.833  16.319  25.228  1.00 25.00           C
ATOM     53  CA  LEU    53      41.282  12.901  24.395  1.00 25.00           C
ATOM     54  CA  PHE    54      40.711  11.820  27.937  1.00 25.00           C
ATOM     55  CA  SER    55      41.143   8.126  27.233  1.00 25.00           C
ATOM     56  CA  ASP    56      44.101   5.777  26.598  1.00 25.00           C
ATOM     57  CA  ALA    57      47.927   5.878  26.722  1.00 25.00           C
ATOM     58  CA  ASP    58      47.918   9.298  24.999  1.00 25.00           C
ATOM     59  CA  ALA    59      45.340  10.588  27.520  1.00 25.00           C
ATOM     60  CA  TYR    60      47.490   9.301  30.416  1.00 25.00           C
ATOM     61  CA  HIS    61      50.566  11.038  28.937  1.00 25.00           C
ATOM     62  CA  LEU    62      48.592  14.302  28.602  1.00 25.00           C
ATOM     63  CA  ASP    63      47.447  14.011  32.245  1.00 25.00           C
ATOM     64  CA  GLN    64      51.063  13.427  33.362  1.00 25.00           C
ATOM     65  CA  ALA    65      52.197  16.501  31.379  1.00 25.00           C
ATOM     66  CA  PHE    66      49.432  18.598  32.998  1.00 25.00           C
ATOM     67  CA  PRO    67      50.502  17.375  36.466  1.00 25.00           C
ATOM     68  CA  LEU    68      54.141  18.283  35.690  1.00 25.00           C
ATOM     69  CA  LEU    69      53.052  21.769  34.539  1.00 25.00           C
ATOM     70  CA  MET    70      51.036  22.230  37.763  1.00 25.00           C
ATOM     71  CA  LYS    71      54.070  21.163  39.843  1.00 25.00           C
ATOM     72  CA  GLN    72      56.277  23.652  37.944  1.00 25.00           C
ATOM     73  CA  LEU    73      53.721  26.435  38.572  1.00 25.00           C
ATOM     74  CA  GLU    74      53.647  25.559  42.299  1.00 25.00           C
ATOM     75  CA  LEU    75      57.473  25.661  42.424  1.00 25.00           C
ATOM     76  CA  MET    76      57.463  29.081  40.701  1.00 25.00           C
ATOM     77  CA  LEU    77      54.885  30.371  43.222  1.00 25.00           C
ATOM     78  CA  THR    78      57.035  29.083  46.117  1.00 25.00           C
ATOM     79  CA  SER    79      57.298  32.802  46.956  1.00 25.00           C
ATOM     80  CA  GLY    80      57.496  34.900  43.721  1.00 25.00           C
ATOM     81  CA  GLU    81      54.573  36.938  45.076  1.00 25.00           C
ATOM     82  CA  LEU    82      52.225  36.043  47.934  1.00 25.00           C
ATOM     83  CA  ASN    83      52.098  38.231  51.017  1.00 25.00           C
ATOM     84  CA  PRO    84      48.686  39.884  51.470  1.00 25.00           C
ATOM     85  CA  ARG    85      45.384  38.373  52.552  1.00 25.00           C
ATOM     86  CA  HIS    86      47.351  35.179  53.283  1.00 25.00           C
ATOM     87  CA  GLN    87      46.302  32.492  50.731  1.00 25.00           C
ATOM     88  CA  HIS    88      44.728  29.445  49.006  1.00 25.00           C
ATOM     89  CA  THR    89      43.200  26.303  50.534  1.00 25.00           C
ATOM     90  CA  VAL    90      42.166  22.698  49.695  1.00 25.00           C
ATOM     91  CA  THR    91      44.658  19.838  49.971  1.00 25.00           C
ATOM     92  CA  LEU    92      44.735  16.027  49.984  1.00 25.00           C
ATOM     93  CA  TYR    93      44.342  12.701  48.243  1.00 25.00           C
ATOM     94  CA  ALA    94      41.764  12.444  45.514  1.00 25.00           C
ATOM     95  CA  LYS    95      41.994   8.733  46.251  1.00 25.00           C
ATOM     96  CA  GLY    96      45.553   7.499  46.061  1.00 25.00           C
ATOM     97  CA  LEU    97      46.087  10.139  43.319  1.00 25.00           C
ATOM     98  CA  THR    98      49.641  10.943  44.524  1.00 25.00           C
ATOM     99  CA  CYS    99      49.372  12.003  48.167  1.00 25.00           C
ATOM    100  CA  LYS   100      48.503  12.195  51.895  1.00 25.00           C
ATOM    101  CA  ALA   101      44.801  11.740  52.677  1.00 25.00           C
ATOM    102  CA  ASP   102      41.172  10.934  52.015  1.00 25.00           C
ATOM    103  CA  THR   103      37.514  10.868  50.805  1.00 25.00           C
ATOM    104  CA  LEU   104      34.268  12.251  49.401  1.00 25.00           C
ATOM    105  CA  SER   105      32.007  15.070  50.599  1.00 25.00           C
ATOM    106  CA  SER   106      32.304  16.197  46.924  1.00 25.00           C
ATOM    107  CA  CYS   107      35.954  16.343  45.840  1.00 25.00           C
ATOM    108  CA  ASP   108      36.636  16.899  49.523  1.00 25.00           C
ATOM    109  CA  TYR   109      39.726  14.750  49.073  1.00 25.00           C
ATOM    110  CA  VAL   110      40.863  17.470  46.690  1.00 25.00           C
ATOM    111  CA  TYR   111      40.546  20.945  45.231  1.00 25.00           C
ATOM    112  CA  LEU   112      42.632  22.776  42.615  1.00 25.00           C
ATOM    113  CA  ALA   113      46.323  23.573  42.688  1.00 25.00           C
ATOM    114  CA  VAL   114      46.344  25.145  39.171  1.00 25.00           C
ATOM    115  CA  TYR   115      46.293  28.155  36.870  1.00 25.00           C
ATOM    116  CA  PRO   116      42.736  28.850  38.146  1.00 25.00           C
ATOM    117  CA  THR   117      39.606  31.072  38.350  1.00 25.00           C
TER
END
