
#######################################################
#                                                     #
#                        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  108 (  108),  selected  108 , name T0291TS393_1-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS393_1-D1.T0291_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       1      T       1          4.138
LGA    Y       2      Y       2          4.139
LGA    V       3      V       3          3.285
LGA    D       4      D       4          4.468
LGA    P       5      P       5          2.608
LGA    H       6      H       6           #
LGA    T       7      -       -           -
LGA    Y       8      -       -           -
LGA    E       9      -       -           -
LGA    D      10      -       -           -
LGA    P      11      -       -           -
LGA    T      12      -       -           -
LGA    Q      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      V      15          2.705
LGA    H      16      H      16          1.406
LGA    E      17      E      17          3.861
LGA    F      18      F      18          1.423
LGA    A      19      A      19          0.731
LGA    K      20      K      20          2.304
LGA    E      21      E      21          2.339
LGA    L      22      L      22          0.883
LGA    D      23      D      23          2.120
LGA    A      24      A      24          2.656
LGA    T      25      T      25          3.086
LGA    N      26      N      26          2.965
LGA    I      27      I      27          2.606
LGA    S      28      S      28          1.676
LGA    I      29      I      29          1.767
LGA    D      30      D      30          1.745
LGA    K      31      K      31          1.579
LGA    V      32      V      32          1.064
LGA    V      33      V      33          2.972
LGA    G      34      G      34          3.884
LGA    A      35      A      35          3.809
LGA    G      36      G      36          3.364
LGA    E      37      E      37          2.427
LGA    F      38      F      38          2.129
LGA    G      39      G      39          2.580
LGA    E      40      E      40          3.262
LGA    V      41      V      41          2.110
LGA    C      42      C      42          1.798
LGA    S      43      S      43          1.208
LGA    G      44      G      44          0.457
LGA    R      45      R      45          1.330
LGA    L      46      L      46          0.256
LGA    K      47      K      47          0.479
LGA    L      48      L      48          1.457
LGA    P      49      P      49          1.618
LGA    S      50      S      50          5.104
LGA    K      51      K      51          1.330
LGA    K      52      K      52          1.169
LGA    E      53      E      53          0.737
LGA    I      54      I      54          0.407
LGA    S      55      S      55          1.210
LGA    V      56      V      56          2.019
LGA    A      57      A      57          1.798
LGA    I      58      I      58          2.366
LGA    K      59      K      59          1.384
LGA    T      60      T      60          1.981
LGA    L      61      L      61          2.215
LGA    K      62      K      62          0.884
LGA    V      63      V      63          0.423
LGA    G      64      G      64          2.520
LGA    Y      65      Y      65          0.940
LGA    T      66      T      66          2.287
LGA    E      67      E      67          1.601
LGA    K      68      K      68          2.016
LGA    Q      69      Q      69          1.613
LGA    R      70      R      70          1.117
LGA    R      71      R      71          1.565
LGA    D      72      D      72          1.702
LGA    F      73      F      73          1.440
LGA    L      74      L      74          1.847
LGA    G      75      G      75          1.355
LGA    E      76      E      76          1.937
LGA    A      77      A      77          1.689
LGA    S      78      S      78          0.830
LGA    I      79      I      79          1.650
LGA    M      80      M      80          2.164
LGA    G      81      G      81          1.742
LGA    Q      82      Q      82          2.488
LGA    F      83      F      83          2.672
LGA    D      84      D      84          3.824
LGA    H      85      H      85          3.085
LGA    P      86      P      86          2.456
LGA    N      87      N      87          1.994
LGA    I      88      I      88          2.186
LGA    I      89      I      89          1.226
LGA    R      90      R      90          1.728
LGA    L      91      L      91          1.582
LGA    E      92      E      92          1.820
LGA    G      93      G      93          1.929
LGA    V      94      V      94          1.551
LGA    V      95      V      95          1.593
LGA    T      96      T      96          1.240
LGA    K      97      K      97          1.211
LGA    S      98      S      98          1.662
LGA    K      99      K      99          1.724
LGA    P     100      P     100          1.530
LGA    V     101      V     101          1.753
LGA    M     102      M     102          1.395
LGA    I     103      I     103          1.888
LGA    V     104      V     104          1.981
LGA    T     105      T     105          2.340
LGA    E     106      E     106          1.638
LGA    Y     107      Y     107          0.542
LGA    M     108      M     108          1.611

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     99    2.17   100.00     82.543     4.352

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.185450 * X  +   0.684488 * Y  +   0.705042 * Z  +  -1.800403
  Y_new =  -0.870549 * X  +  -0.447245 * Y  +   0.205222 * Z  +  10.716112
  Z_new =   0.455799 * X  +  -0.575715 * Y  +   0.678822 * Z  +  55.973179 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.703395    2.438197  [ DEG:   -40.3016    139.6984 ]
  Theta =  -0.473270   -2.668323  [ DEG:   -27.1164   -152.8836 ]
  Phi   =  -1.780686    1.360907  [ DEG:  -102.0258     77.9742 ]
 
# 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: T0291TS393_1-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS393_1-D1.T0291_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  100   5.0   99   2.17  100.00  82.543
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS393_1-D1
PFRMAT TS
TARGET T0291
MODEL 1
PARENT N/A
ATOM      1  CA  THR     1      -2.532  34.165  46.615  1.00 25.00           C
ATOM      2  CA  TYR     2      -4.399  30.948  47.595  1.00 25.00           C
ATOM      3  CA  VAL     3      -7.631  30.250  49.417  1.00 25.00           C
ATOM      4  CA  ASP     4     -10.355  30.282  52.152  1.00 25.00           C
ATOM      5  CA  PRO     5     -13.405  28.607  53.766  1.00 25.00           C
ATOM      6  CA  HIS     6     -14.812  32.065  54.097  1.00 25.00           C
ATOM      7  CA  THR     7     -16.123  33.790  57.275  1.00 25.00           C
ATOM      8  CA  TYR     8     -19.453  32.155  56.441  1.00 25.00           C
ATOM      9  CA  GLU     9     -20.737  35.328  54.780  1.00 25.00           C
ATOM     10  CA  ASP    10     -22.714  33.359  52.281  1.00 25.00           C
ATOM     11  CA  PRO    11     -19.395  31.838  51.280  1.00 25.00           C
ATOM     12  CA  THR    12     -21.455  28.725  50.424  1.00 25.00           C
ATOM     13  CA  GLN    13     -21.352  29.648  46.709  1.00 25.00           C
ATOM     14  CA  ALA    14     -17.554  30.108  46.904  1.00 25.00           C
ATOM     15  CA  VAL    15     -17.203  26.692  48.600  1.00 25.00           C
ATOM     16  CA  HIS    16     -19.349  25.086  45.864  1.00 25.00           C
ATOM     17  CA  GLU    17     -17.182  26.726  43.166  1.00 25.00           C
ATOM     18  CA  PHE    18     -14.015  25.430  44.887  1.00 25.00           C
ATOM     19  CA  ALA    19     -15.510  21.907  45.035  1.00 25.00           C
ATOM     20  CA  LYS    20     -16.384  22.094  41.311  1.00 25.00           C
ATOM     21  CA  GLU    21     -19.925  20.754  41.904  1.00 25.00           C
ATOM     22  CA  LEU    22     -21.483  17.286  41.516  1.00 25.00           C
ATOM     23  CA  ASP    23     -25.342  17.149  41.536  1.00 25.00           C
ATOM     24  CA  ALA    24     -26.466  14.236  43.722  1.00 25.00           C
ATOM     25  CA  THR    25     -28.420  12.654  40.834  1.00 25.00           C
ATOM     26  CA  ASN    26     -25.247  12.585  38.691  1.00 25.00           C
ATOM     27  CA  ILE    27     -23.821   9.158  39.536  1.00 25.00           C
ATOM     28  CA  SER    28     -23.457   5.954  41.513  1.00 25.00           C
ATOM     29  CA  ILE    29     -22.741   3.058  43.895  1.00 25.00           C
ATOM     30  CA  ASP    30     -21.124  -0.147  45.111  1.00 25.00           C
ATOM     31  CA  LYS    31     -19.616  -1.506  48.348  1.00 25.00           C
ATOM     32  CA  VAL    32     -17.460  -0.798  51.459  1.00 25.00           C
ATOM     33  CA  VAL    33     -13.661  -0.644  50.931  1.00 25.00           C
ATOM     34  CA  GLY    34     -13.434   0.587  54.534  1.00 25.00           C
ATOM     35  CA  ALA    35     -14.493   0.569  58.227  1.00 25.00           C
ATOM     36  CA  GLY    36     -14.050   3.668  60.387  1.00 25.00           C
ATOM     37  CA  GLU    37     -14.539   7.177  61.795  1.00 25.00           C
ATOM     38  CA  PHE    38     -17.667   9.141  61.012  1.00 25.00           C
ATOM     39  CA  GLY    39     -18.181   6.774  58.133  1.00 25.00           C
ATOM     40  CA  GLU    40     -16.456   4.414  55.719  1.00 25.00           C
ATOM     41  CA  VAL    41     -15.768   4.257  52.014  1.00 25.00           C
ATOM     42  CA  CYS    42     -17.753   3.545  48.801  1.00 25.00           C
ATOM     43  CA  SER    43     -15.305   2.580  46.007  1.00 25.00           C
ATOM     44  CA  GLY    44     -17.622   3.464  43.122  1.00 25.00           C
ATOM     45  CA  ARG    45     -18.724   4.820  39.712  1.00 25.00           C
ATOM     46  CA  LEU    46     -18.366   8.567  39.115  1.00 25.00           C
ATOM     47  CA  LYS    47     -19.523   9.221  35.580  1.00 25.00           C
ATOM     48  CA  LEU    48     -18.020  12.735  36.069  1.00 25.00           C
ATOM     49  CA  PRO    49     -18.311  14.395  32.665  1.00 25.00           C
ATOM     50  CA  SER    50     -21.615  12.717  31.785  1.00 25.00           C
ATOM     51  CA  LYS    51     -19.685   9.844  30.085  1.00 25.00           C
ATOM     52  CA  LYS    52     -16.157   8.543  30.701  1.00 25.00           C
ATOM     53  CA  GLU    53     -15.421   6.826  33.995  1.00 25.00           C
ATOM     54  CA  ILE    54     -13.065   6.967  36.960  1.00 25.00           C
ATOM     55  CA  SER    55     -13.731   6.025  40.573  1.00 25.00           C
ATOM     56  CA  VAL    56     -14.712   8.795  42.952  1.00 25.00           C
ATOM     57  CA  ALA    57     -15.039   7.821  46.625  1.00 25.00           C
ATOM     58  CA  ILE    58     -18.427   9.276  47.441  1.00 25.00           C
ATOM     59  CA  LYS    59     -18.442   9.055  51.287  1.00 25.00           C
ATOM     60  CA  THR    60     -22.054   8.865  52.418  1.00 25.00           C
ATOM     61  CA  LEU    61     -21.040  10.256  55.853  1.00 25.00           C
ATOM     62  CA  LYS    62     -23.907   9.659  58.342  1.00 25.00           C
ATOM     63  CA  VAL    63     -27.519  10.119  59.327  1.00 25.00           C
ATOM     64  CA  GLY    64     -27.580  10.465  63.144  1.00 25.00           C
ATOM     65  CA  TYR    65     -26.034  13.888  62.814  1.00 25.00           C
ATOM     66  CA  THR    66     -26.575  17.620  62.470  1.00 25.00           C
ATOM     67  CA  GLU    67     -25.959  21.389  62.358  1.00 25.00           C
ATOM     68  CA  LYS    68     -22.580  21.854  64.100  1.00 25.00           C
ATOM     69  CA  GLN    69     -21.462  18.391  62.908  1.00 25.00           C
ATOM     70  CA  ARG    70     -22.524  19.253  59.331  1.00 25.00           C
ATOM     71  CA  ARG    71     -20.568  22.540  59.516  1.00 25.00           C
ATOM     72  CA  ASP    72     -17.480  20.661  60.779  1.00 25.00           C
ATOM     73  CA  PHE    73     -17.802  18.150  57.905  1.00 25.00           C
ATOM     74  CA  LEU    74     -18.074  21.025  55.391  1.00 25.00           C
ATOM     75  CA  GLY    75     -14.950  22.661  56.888  1.00 25.00           C
ATOM     76  CA  GLU    76     -13.059  19.341  56.633  1.00 25.00           C
ATOM     77  CA  ALA    77     -14.133  18.982  52.974  1.00 25.00           C
ATOM     78  CA  SER    78     -12.946  22.551  52.251  1.00 25.00           C
ATOM     79  CA  ILE    79      -9.578  21.794  53.911  1.00 25.00           C
ATOM     80  CA  MET    80      -9.229  18.612  51.809  1.00 25.00           C
ATOM     81  CA  GLY    81     -10.012  20.598  48.629  1.00 25.00           C
ATOM     82  CA  GLN    82      -7.384  23.214  49.585  1.00 25.00           C
ATOM     83  CA  PHE    83      -4.137  21.420  48.610  1.00 25.00           C
ATOM     84  CA  ASP    84      -2.351  19.687  45.700  1.00 25.00           C
ATOM     85  CA  HIS    85       0.958  18.143  44.620  1.00 25.00           C
ATOM     86  CA  PRO    86       1.212  14.566  43.304  1.00 25.00           C
ATOM     87  CA  ASN    87       0.678  13.220  46.883  1.00 25.00           C
ATOM     88  CA  ILE    88      -1.982  14.863  49.077  1.00 25.00           C
ATOM     89  CA  ILE    89      -4.992  12.824  47.899  1.00 25.00           C
ATOM     90  CA  ARG    90      -6.248  14.854  44.937  1.00 25.00           C
ATOM     91  CA  LEU    91      -9.945  15.516  45.531  1.00 25.00           C
ATOM     92  CA  GLU    92     -12.667  13.935  43.450  1.00 25.00           C
ATOM     93  CA  GLY    93     -14.735  16.801  44.734  1.00 25.00           C
ATOM     94  CA  VAL    94     -17.924  17.559  46.757  1.00 25.00           C
ATOM     95  CA  VAL    95     -21.530  16.702  47.400  1.00 25.00           C
ATOM     96  CA  THR    96     -24.202  17.637  49.934  1.00 25.00           C
ATOM     97  CA  LYS    97     -27.698  18.806  48.934  1.00 25.00           C
ATOM     98  CA  SER    98     -29.922  16.173  50.375  1.00 25.00           C
ATOM     99  CA  LYS    99     -30.082  12.555  51.456  1.00 25.00           C
ATOM    100  CA  PRO   100     -26.862  13.177  53.337  1.00 25.00           C
ATOM    101  CA  VAL   101     -23.334  14.603  53.817  1.00 25.00           C
ATOM    102  CA  MET   102     -20.488  13.758  51.457  1.00 25.00           C
ATOM    103  CA  ILE   103     -16.771  14.564  51.384  1.00 25.00           C
ATOM    104  CA  VAL   104     -15.290  13.099  48.267  1.00 25.00           C
ATOM    105  CA  THR   105     -11.855  11.608  48.557  1.00 25.00           C
ATOM    106  CA  GLU   106     -10.148   9.909  45.616  1.00 25.00           C
ATOM    107  CA  TYR   107      -9.470   6.537  43.998  1.00 25.00           C
ATOM    108  CA  MET   108      -7.176   3.692  45.089  1.00 25.00           C
TER
END
