
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS393_4-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          2.966
LGA    Y       2      Y       2          2.941
LGA    V       3      V       3          2.698
LGA    D       4      D       4          3.727
LGA    P       5      P       5          1.779
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          1.838
LGA    H      16      H      16          0.729
LGA    E      17      E      17          2.892
LGA    F      18      F      18          2.149
LGA    A      19      A      19          1.653
LGA    K      20      K      20          3.598
LGA    E      21      E      21          2.750
LGA    L      22      L      22          2.503
LGA    -       -      D      23           -
LGA    -       -      A      24           -
LGA    -       -      T      25           -
LGA    D      23      N      26           #
LGA    A      24      -       -           -
LGA    T      25      -       -           -
LGA    N      26      -       -           -
LGA    I      27      -       -           -
LGA    S      28      -       -           -
LGA    I      29      I      27           #
LGA    -       -      S      28           -
LGA    D      30      I      29          3.370
LGA    K      31      D      30          2.417
LGA    V      32      K      31          1.221
LGA    V      33      V      32          3.910
LGA    G      34      V      33          2.282
LGA    A      35      G      34          1.951
LGA    G      36      A      35          3.961
LGA    E      37      G      36          1.341
LGA    -       -      E      37           -
LGA    F      38      F      38          2.479
LGA    G      39      G      39          3.233
LGA    E      40      E      40          1.958
LGA    V      41      V      41          1.270
LGA    C      42      C      42          1.102
LGA    S      43      S      43          1.844
LGA    G      44      G      44          2.968
LGA    R      45      R      45          4.486
LGA    L      46      L      46          3.850
LGA    K      47      K      47          4.881
LGA    L      48      L      48          4.721
LGA    P      49      P      49          1.812
LGA    S      50      S      50          0.831
LGA    K      51      K      51          1.223
LGA    K      52      K      52          5.091
LGA    E      53      E      53          4.548
LGA    I      54      I      54          4.099
LGA    S      55      S      55          2.866
LGA    V      56      V      56          1.339
LGA    A      57      A      57          1.675
LGA    I      58      I      58          1.418
LGA    K      59      K      59          1.120
LGA    T      60      T      60          1.221
LGA    L      61      L      61          1.274
LGA    K      62      K      62          0.777
LGA    V      63      V      63          1.959
LGA    G      64      G      64          0.859
LGA    Y      65      Y      65          0.893
LGA    T      66      T      66          1.035
LGA    E      67      E      67          1.477
LGA    K      68      K      68          1.135
LGA    Q      69      Q      69          0.528
LGA    R      70      R      70          0.676
LGA    R      71      R      71          0.559
LGA    D      72      D      72          0.404
LGA    F      73      F      73          0.575
LGA    L      74      L      74          1.029
LGA    G      75      G      75          0.800
LGA    E      76      E      76          1.226
LGA    A      77      A      77          1.241
LGA    S      78      S      78          1.498
LGA    I      79      I      79          1.970
LGA    M      80      M      80          1.935
LGA    G      81      G      81          2.136
LGA    Q      82      Q      82          2.999
LGA    F      83      F      83          4.370
LGA    D      84      D      84          4.144
LGA    H      85      H      85          3.549
LGA    P      86      P      86          2.805
LGA    N      87      N      87          2.186
LGA    I      88      I      88          2.552
LGA    I      89      I      89          2.486
LGA    R      90      R      90          2.202
LGA    L      91      L      91          1.645
LGA    E      92      E      92          1.430
LGA    G      93      G      93          1.522
LGA    V      94      V      94          0.882
LGA    V      95      V      95          1.858
LGA    T      96      T      96          1.570
LGA    K      97      K      97          0.694
LGA    S      98      S      98          0.879
LGA    K      99      K      99          2.553
LGA    P     100      P     100          1.062
LGA    V     101      V     101          0.969
LGA    M     102      M     102          0.730
LGA    I     103      I     103          1.302
LGA    V     104      V     104          2.200
LGA    T     105      T     105          0.961
LGA    E     106      E     106          1.019
LGA    Y     107      Y     107          0.666
LGA    M     108      M     108          0.911

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     92    2.35    92.39     68.112     3.761

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.671224 * X  +   0.424367 * Y  +   0.607760 * Z  +  -1.192814
  Y_new =  -0.591321 * X  +   0.800962 * Y  +   0.093799 * Z  +   9.137267
  Z_new =  -0.446988 * X  +  -0.422341 * Y  +   0.788562 * Z  +  55.172230 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.491708    2.649885  [ DEG:   -28.1728    151.8272 ]
  Theta =   0.463395    2.678198  [ DEG:    26.5506    153.4494 ]
  Phi   =  -0.722196    2.419397  [ DEG:   -41.3788    138.6212 ]
 
# 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_4-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS393_4-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   92   2.35   92.39  68.112
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS393_4-D1
PFRMAT TS
TARGET T0291
MODEL 4
PARENT N/A
ATOM      1  CA  THR     1      -1.871  33.485  47.797  1.00 25.00           C
ATOM      2  CA  TYR     2      -3.261  29.986  48.638  1.00 25.00           C
ATOM      3  CA  VAL     3      -6.794  30.060  50.031  1.00 25.00           C
ATOM      4  CA  ASP     4      -9.634  29.406  52.534  1.00 25.00           C
ATOM      5  CA  PRO     5     -12.872  29.010  54.516  1.00 25.00           C
ATOM      6  CA  HIS     6     -14.335  32.518  54.546  1.00 25.00           C
ATOM      7  CA  THR     7     -13.583  32.770  58.219  1.00 25.00           C
ATOM      8  CA  TYR     8     -17.104  31.526  58.714  1.00 25.00           C
ATOM      9  CA  GLU     9     -18.887  34.419  57.003  1.00 25.00           C
ATOM     10  CA  ASP    10     -20.774  33.150  53.952  1.00 25.00           C
ATOM     11  CA  PRO    11     -18.833  29.952  54.289  1.00 25.00           C
ATOM     12  CA  THR    12     -20.733  26.943  52.874  1.00 25.00           C
ATOM     13  CA  GLN    13     -21.615  28.946  49.731  1.00 25.00           C
ATOM     14  CA  ALA    14     -17.943  29.954  49.314  1.00 25.00           C
ATOM     15  CA  VAL    15     -16.874  26.294  49.678  1.00 25.00           C
ATOM     16  CA  HIS    16     -19.452  25.252  47.045  1.00 25.00           C
ATOM     17  CA  GLU    17     -18.162  27.967  44.672  1.00 25.00           C
ATOM     18  CA  PHE    18     -14.567  26.760  45.206  1.00 25.00           C
ATOM     19  CA  ALA    19     -15.640  23.158  44.471  1.00 25.00           C
ATOM     20  CA  LYS    20     -17.399  24.310  41.268  1.00 25.00           C
ATOM     21  CA  GLU    21     -19.800  21.344  41.740  1.00 25.00           C
ATOM     22  CA  LEU    22     -19.793  17.590  40.981  1.00 25.00           C
ATOM     23  CA  ASP    23     -18.948  15.002  38.263  1.00 25.00           C
ATOM     24  CA  ALA    24     -16.302  12.465  37.354  1.00 25.00           C
ATOM     25  CA  THR    25     -14.251  12.489  34.120  1.00 25.00           C
ATOM     26  CA  ASN    26     -14.814   8.723  33.707  1.00 25.00           C
ATOM     27  CA  ILE    27     -15.932   5.060  34.181  1.00 25.00           C
ATOM     28  CA  SER    28     -17.478   2.724  36.802  1.00 25.00           C
ATOM     29  CA  ILE    29     -19.726   1.830  39.664  1.00 25.00           C
ATOM     30  CA  ASP    30     -20.668   0.189  43.013  1.00 25.00           C
ATOM     31  CA  LYS    31     -20.492  -0.884  46.657  1.00 25.00           C
ATOM     32  CA  VAL    32     -17.172  -1.166  48.496  1.00 25.00           C
ATOM     33  CA  VAL    33     -14.606  -0.693  51.183  1.00 25.00           C
ATOM     34  CA  GLY    34     -13.347   0.290  54.615  1.00 25.00           C
ATOM     35  CA  ALA    35     -14.919   1.023  58.030  1.00 25.00           C
ATOM     36  CA  GLY    36     -13.607   4.579  57.548  1.00 25.00           C
ATOM     37  CA  GLU    37     -14.708   6.751  60.544  1.00 25.00           C
ATOM     38  CA  PHE    38     -17.944   8.653  59.882  1.00 25.00           C
ATOM     39  CA  GLY    39     -19.247   5.163  59.107  1.00 25.00           C
ATOM     40  CA  GLU    40     -20.387   3.634  55.840  1.00 25.00           C
ATOM     41  CA  VAL    41     -17.619   4.316  53.301  1.00 25.00           C
ATOM     42  CA  CYS    42     -16.502   3.776  49.720  1.00 25.00           C
ATOM     43  CA  SER    43     -17.434   3.291  46.047  1.00 25.00           C
ATOM     44  CA  GLY    44     -19.453   5.600  43.718  1.00 25.00           C
ATOM     45  CA  ARG    45     -21.769   6.466  40.781  1.00 25.00           C
ATOM     46  CA  LEU    46     -21.442  10.244  40.366  1.00 25.00           C
ATOM     47  CA  LYS    47     -23.894   9.920  37.425  1.00 25.00           C
ATOM     48  CA  LEU    48     -22.355  12.380  34.965  1.00 25.00           C
ATOM     49  CA  PRO    49     -20.338  14.135  32.248  1.00 25.00           C
ATOM     50  CA  SER    50     -17.183  13.965  30.181  1.00 25.00           C
ATOM     51  CA  LYS    51     -18.380  10.550  29.150  1.00 25.00           C
ATOM     52  CA  LYS    52     -20.662   8.679  31.529  1.00 25.00           C
ATOM     53  CA  GLU    53     -20.548   7.047  34.926  1.00 25.00           C
ATOM     54  CA  ILE    54     -17.474   7.830  37.097  1.00 25.00           C
ATOM     55  CA  SER    55     -14.029   7.245  38.684  1.00 25.00           C
ATOM     56  CA  VAL    56     -13.520   6.321  42.339  1.00 25.00           C
ATOM     57  CA  ALA    57     -14.477   7.454  45.872  1.00 25.00           C
ATOM     58  CA  ILE    58     -17.756   8.183  47.671  1.00 25.00           C
ATOM     59  CA  LYS    59     -17.210   9.144  51.281  1.00 25.00           C
ATOM     60  CA  THR    60     -20.328   8.948  53.537  1.00 25.00           C
ATOM     61  CA  LEU    61     -21.691  10.800  56.560  1.00 25.00           C
ATOM     62  CA  LYS    62     -24.735  10.089  58.735  1.00 25.00           C
ATOM     63  CA  VAL    63     -28.315  11.184  57.818  1.00 25.00           C
ATOM     64  CA  GLY    64     -28.953  12.014  61.482  1.00 25.00           C
ATOM     65  CA  TYR    65     -26.024  14.407  61.317  1.00 25.00           C
ATOM     66  CA  THR    66     -26.086  17.054  64.029  1.00 25.00           C
ATOM     67  CA  GLU    67     -25.228  19.950  61.736  1.00 25.00           C
ATOM     68  CA  LYS    68     -21.908  20.278  63.617  1.00 25.00           C
ATOM     69  CA  GLN    69     -20.701  16.969  62.113  1.00 25.00           C
ATOM     70  CA  ARG    70     -21.673  18.177  58.612  1.00 25.00           C
ATOM     71  CA  ARG    71     -19.776  21.454  59.188  1.00 25.00           C
ATOM     72  CA  ASP    72     -16.696  19.495  60.346  1.00 25.00           C
ATOM     73  CA  PHE    73     -16.896  17.286  57.224  1.00 25.00           C
ATOM     74  CA  LEU    74     -17.141  20.399  55.007  1.00 25.00           C
ATOM     75  CA  GLY    75     -14.089  21.915  56.755  1.00 25.00           C
ATOM     76  CA  GLU    76     -12.138  18.662  56.222  1.00 25.00           C
ATOM     77  CA  ALA    77     -13.102  18.664  52.515  1.00 25.00           C
ATOM     78  CA  SER    78     -11.951  22.302  52.192  1.00 25.00           C
ATOM     79  CA  ILE    79      -8.621  21.424  53.867  1.00 25.00           C
ATOM     80  CA  MET    80      -8.161  18.477  51.464  1.00 25.00           C
ATOM     81  CA  GLY    81      -8.885  20.766  48.481  1.00 25.00           C
ATOM     82  CA  GLN    82      -6.327  23.305  49.776  1.00 25.00           C
ATOM     83  CA  PHE    83      -3.498  20.814  50.076  1.00 25.00           C
ATOM     84  CA  ASP    84      -2.765  20.053  46.411  1.00 25.00           C
ATOM     85  CA  HIS    85       0.670  18.746  45.544  1.00 25.00           C
ATOM     86  CA  PRO    86       1.601  15.752  43.305  1.00 25.00           C
ATOM     87  CA  ASN    87       2.276  14.135  46.666  1.00 25.00           C
ATOM     88  CA  ILE    88      -0.603  15.247  48.956  1.00 25.00           C
ATOM     89  CA  ILE    89      -4.330  14.326  49.160  1.00 25.00           C
ATOM     90  CA  ARG    90      -6.599  14.451  46.150  1.00 25.00           C
ATOM     91  CA  LEU    91      -9.780  16.549  45.743  1.00 25.00           C
ATOM     92  CA  GLU    92     -12.628  15.319  43.599  1.00 25.00           C
ATOM     93  CA  GLY    93     -15.490  16.938  45.478  1.00 25.00           C
ATOM     94  CA  VAL    94     -19.213  16.670  46.292  1.00 25.00           C
ATOM     95  CA  VAL    95     -22.868  15.841  45.477  1.00 25.00           C
ATOM     96  CA  THR    96     -24.330  17.671  48.506  1.00 25.00           C
ATOM     97  CA  LYS    97     -27.967  18.620  47.897  1.00 25.00           C
ATOM     98  CA  SER    98     -29.964  15.395  48.347  1.00 25.00           C
ATOM     99  CA  LYS    99     -29.735  11.976  50.127  1.00 25.00           C
ATOM    100  CA  PRO   100     -27.187  12.673  52.887  1.00 25.00           C
ATOM    101  CA  VAL   101     -23.551  13.669  52.255  1.00 25.00           C
ATOM    102  CA  MET   102     -20.710  12.905  49.844  1.00 25.00           C
ATOM    103  CA  ILE   103     -17.424  14.511  50.888  1.00 25.00           C
ATOM    104  CA  VAL   104     -14.999  12.906  48.482  1.00 25.00           C
ATOM    105  CA  THR   105     -11.692  11.810  47.067  1.00 25.00           C
ATOM    106  CA  GLU   106      -9.025  10.309  44.728  1.00 25.00           C
ATOM    107  CA  TYR   107      -8.992   6.558  44.455  1.00 25.00           C
ATOM    108  CA  MET   108      -5.669   4.928  45.314  1.00 25.00           C
TER
END
