
#######################################################
#                                                     #
#                        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   88 (   88),  selected   88 , name T0288TS168_1-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS168_1-D1.T0288_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    V       3      V       3          5.530
LGA    P       4      P       4          2.740
LGA    G       5      G       5          1.996
LGA    K       6      K       6          1.739
LGA    V       7      V       7          0.695
LGA    T       8      T       8          1.696
LGA    L       9      L       9          0.882
LGA    Q      10      Q      10          1.154
LGA    K      11      K      11          1.987
LGA    D      12      D      12          0.820
LGA    A      13      A      13          1.440
LGA    Q      14      Q      14          1.044
LGA    N      15      N      15          0.726
LGA    L      16      L      16          1.301
LGA    I      17      I      17          1.102
LGA    G      18      G      18          1.061
LGA    I      19      I      19          0.342
LGA    S      20      S      20          0.694
LGA    I      21      I      21          1.112
LGA    G      22      G      22          0.957
LGA    G      23      G      23          1.393
LGA    G      24      G      24          2.310
LGA    A      25      -       -           -
LGA    Q      26      A      25          3.456
LGA    Y      27      Q      26          3.959
LGA    C      28      P      29          3.387
LGA    P      29      C      30          3.269
LGA    C      30      -       -           -
LGA    L      31      L      31          1.305
LGA    Y      32      Y      32          1.481
LGA    I      33      I      33          0.734
LGA    V      34      V      34          0.673
LGA    Q      35      Q      35          0.508
LGA    V      36      V      36          0.464
LGA    F      37      F      37          1.435
LGA    D      38      D      38          1.692
LGA    N      39      N      39          0.259
LGA    T      40      T      40          2.134
LGA    P      41      P      41          1.998
LGA    A      42      A      42          0.380
LGA    A      43      A      43          0.289
LGA    L      44      L      44          1.362
LGA    D      45      D      45          1.677
LGA    G      46      G      46          1.149
LGA    T      47      T      47          1.902
LGA    V      48      V      48          1.716
LGA    A      49      A      49          1.100
LGA    A      50      A      50          0.672
LGA    G      51      G      51          0.654
LGA    D      52      D      52          0.846
LGA    E      53      E      53          0.802
LGA    I      54      I      54          0.921
LGA    T      55      T      55          1.312
LGA    G      56      G      56          1.356
LGA    V      57      V      57          4.569
LGA    N      58      N      58          0.937
LGA    G      59      G      59          3.879
LGA    R      60      R      60          3.148
LGA    S      61      S      61          2.481
LGA    I      62      I      62          1.460
LGA    K      63      K      63          2.441
LGA    G      64      G      64          2.068
LGA    K      65      K      65          1.698
LGA    T      66      T      66          0.296
LGA    K      67      K      67          0.483
LGA    V      68      V      68          0.695
LGA    E      69      E      69          0.458
LGA    V      70      V      70          0.770
LGA    A      71      A      71          0.857
LGA    K      72      K      72          0.674
LGA    M      73      M      73          0.930
LGA    I      74      I      74          1.502
LGA    Q      75      Q      75          1.103
LGA    E      76      E      76          0.851
LGA    V      77      V      77          0.559
LGA    K      78      K      78          1.582
LGA    G      79      G      79          2.778
LGA    E      80      E      80          2.333
LGA    V      81      V      81          1.163
LGA    T      82      T      82          1.407
LGA    I      83      I      83          0.981
LGA    H      84      H      84          1.369
LGA    Y      85      Y      85          0.956
LGA    N      86      N      86          1.106
LGA    K      87      K      87          1.047
LGA    L      88      L      88          2.697

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     84    1.80    95.24     88.683     4.431

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.838988 * X  +  -0.543711 * Y  +  -0.021872 * Z  +  27.586084
  Y_new =  -0.542511 * X  +  -0.832666 * Y  +  -0.111128 * Z  +  17.486639
  Z_new =   0.042209 * X  +   0.105101 * Y  +  -0.993565 * Z  +  13.204415 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.036203   -0.105390  [ DEG:   173.9616     -6.0384 ]
  Theta =  -0.042222   -3.099371  [ DEG:    -2.4191   -177.5809 ]
  Phi   =  -0.574000    2.567593  [ DEG:   -32.8878    147.1122 ]
 
# 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: T0288TS168_1-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS168_1-D1.T0288_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   88   86   5.0   84   1.80   95.24  88.683
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS168_1-D1
PFRMAT TS
TARGET T0288
MODEL 1
PARENT N/A
ATOM      1  CA  SER     1      23.967  13.248  32.947  1.00 25.00           C
ATOM      2  CA  MET     2      26.421  11.153  30.975  1.00 25.00           C
ATOM      3  CA  VAL     3      25.905  12.154  27.402  1.00 25.00           C
ATOM      4  CA  PRO     4      24.497  13.300  24.080  1.00 25.00           C
ATOM      5  CA  GLY     5      23.502  16.994  24.289  1.00 25.00           C
ATOM      6  CA  LYS     6      21.571  17.990  21.146  1.00 25.00           C
ATOM      7  CA  VAL     7      20.811  19.954  17.909  1.00 25.00           C
ATOM      8  CA  THR     8      18.340  22.325  16.233  1.00 25.00           C
ATOM      9  CA  LEU     9      20.059  23.996  13.277  1.00 25.00           C
ATOM     10  CA  GLN    10      17.059  25.687  11.711  1.00 25.00           C
ATOM     11  CA  LYS    11      18.922  26.893   8.603  1.00 25.00           C
ATOM     12  CA  ASP    12      19.367  29.553   5.942  1.00 25.00           C
ATOM     13  CA  ALA    13      17.823  30.014   2.477  1.00 25.00           C
ATOM     14  CA  GLN    14      21.306  28.893   1.272  1.00 25.00           C
ATOM     15  CA  ASN    15      20.450  25.491   2.832  1.00 25.00           C
ATOM     16  CA  LEU    16      22.815  24.437   5.633  1.00 25.00           C
ATOM     17  CA  ILE    17      23.563  23.782   9.345  1.00 25.00           C
ATOM     18  CA  GLY    18      26.985  25.164   8.423  1.00 25.00           C
ATOM     19  CA  ILE    19      29.653  22.792   9.756  1.00 25.00           C
ATOM     20  CA  SER    20      32.844  21.482   8.223  1.00 25.00           C
ATOM     21  CA  ILE    21      32.807  17.753   7.714  1.00 25.00           C
ATOM     22  CA  GLY    22      35.951  15.645   7.884  1.00 25.00           C
ATOM     23  CA  GLY    23      36.621  12.118   9.037  1.00 25.00           C
ATOM     24  CA  GLY    24      35.824   8.654  10.501  1.00 25.00           C
ATOM     25  CA  ALA    25      35.214   5.401   8.559  1.00 25.00           C
ATOM     26  CA  GLN    26      38.965   5.539   7.940  1.00 25.00           C
ATOM     27  CA  TYR    27      40.325   6.257  11.449  1.00 25.00           C
ATOM     28  CA  CYS    28      37.511   5.286  13.828  1.00 25.00           C
ATOM     29  CA  PRO    29      33.771   5.077  14.306  1.00 25.00           C
ATOM     30  CA  CYS    30      32.692   8.765  14.590  1.00 25.00           C
ATOM     31  CA  LEU    31      31.778  11.414  12.026  1.00 25.00           C
ATOM     32  CA  TYR    32      33.724  14.676  12.291  1.00 25.00           C
ATOM     33  CA  ILE    33      33.343  18.480  12.787  1.00 25.00           C
ATOM     34  CA  VAL    34      36.294  20.837  12.283  1.00 25.00           C
ATOM     35  CA  GLN    35      35.007  24.378  11.903  1.00 25.00           C
ATOM     36  CA  VAL    36      31.957  26.359  12.969  1.00 25.00           C
ATOM     37  CA  PHE    37      30.446  29.409  11.297  1.00 25.00           C
ATOM     38  CA  ASP    38      30.575  32.836   9.705  1.00 25.00           C
ATOM     39  CA  ASN    39      26.956  33.826  10.385  1.00 25.00           C
ATOM     40  CA  THR    40      26.220  30.808   8.237  1.00 25.00           C
ATOM     41  CA  PRO    41      24.348  28.865  10.986  1.00 25.00           C
ATOM     42  CA  ALA    42      25.551  26.448  13.647  1.00 25.00           C
ATOM     43  CA  ALA    43      26.993  29.674  15.156  1.00 25.00           C
ATOM     44  CA  LEU    44      23.283  30.428  15.824  1.00 25.00           C
ATOM     45  CA  ASP    45      22.087  27.326  17.604  1.00 25.00           C
ATOM     46  CA  GLY    46      25.307  27.689  19.646  1.00 25.00           C
ATOM     47  CA  THR    47      26.260  24.079  19.115  1.00 25.00           C
ATOM     48  CA  VAL    48      29.136  22.616  17.133  1.00 25.00           C
ATOM     49  CA  ALA    49      32.143  23.802  19.167  1.00 25.00           C
ATOM     50  CA  ALA    50      34.824  21.997  17.101  1.00 25.00           C
ATOM     51  CA  GLY    51      36.181  18.416  17.154  1.00 25.00           C
ATOM     52  CA  ASP    52      32.648  17.140  17.778  1.00 25.00           C
ATOM     53  CA  GLU    53      31.475  13.669  16.699  1.00 25.00           C
ATOM     54  CA  ILE    54      28.243  13.952  14.605  1.00 25.00           C
ATOM     55  CA  THR    55      25.888  11.107  15.582  1.00 25.00           C
ATOM     56  CA  GLY    56      22.192  11.201  14.613  1.00 25.00           C
ATOM     57  CA  VAL    57      18.787  12.391  15.822  1.00 25.00           C
ATOM     58  CA  ASN    58      17.331  14.027  12.713  1.00 25.00           C
ATOM     59  CA  GLY    59      17.919  10.636  11.163  1.00 25.00           C
ATOM     60  CA  ARG    60      19.370   7.410   9.889  1.00 25.00           C
ATOM     61  CA  SER    61      22.741   6.309  11.392  1.00 25.00           C
ATOM     62  CA  ILE    62      25.779   8.459  10.845  1.00 25.00           C
ATOM     63  CA  LYS    63      27.785   6.348  13.287  1.00 25.00           C
ATOM     64  CA  GLY    64      28.500   3.228  11.204  1.00 25.00           C
ATOM     65  CA  LYS    65      29.256   5.603   8.420  1.00 25.00           C
ATOM     66  CA  THR    66      31.322   6.981   5.571  1.00 25.00           C
ATOM     67  CA  LYS    67      32.205  10.594   6.252  1.00 25.00           C
ATOM     68  CA  VAL    68      31.233  11.298   2.615  1.00 25.00           C
ATOM     69  CA  GLU    69      27.767   9.787   3.223  1.00 25.00           C
ATOM     70  CA  VAL    70      27.340  11.960   6.347  1.00 25.00           C
ATOM     71  CA  ALA    71      28.352  15.070   4.352  1.00 25.00           C
ATOM     72  CA  LYS    72      25.825  14.167   1.619  1.00 25.00           C
ATOM     73  CA  MET    73      23.088  13.724   4.262  1.00 25.00           C
ATOM     74  CA  ILE    74      23.963  17.132   5.775  1.00 25.00           C
ATOM     75  CA  GLN    75      23.793  18.744   2.307  1.00 25.00           C
ATOM     76  CA  GLU    76      20.375  17.129   1.696  1.00 25.00           C
ATOM     77  CA  VAL    77      17.858  17.426   4.574  1.00 25.00           C
ATOM     78  CA  LYS    78      15.184  20.071   5.057  1.00 25.00           C
ATOM     79  CA  GLY    79      13.238  21.463   8.015  1.00 25.00           C
ATOM     80  CA  GLU    80      15.058  20.984  11.256  1.00 25.00           C
ATOM     81  CA  VAL    81      18.548  20.083  10.200  1.00 25.00           C
ATOM     82  CA  THR    82      19.948  18.290  13.245  1.00 25.00           C
ATOM     83  CA  ILE    83      23.437  17.095  14.169  1.00 25.00           C
ATOM     84  CA  HIS    84      24.157  15.514  17.565  1.00 25.00           C
ATOM     85  CA  TYR    85      27.476  15.659  19.299  1.00 25.00           C
ATOM     86  CA  ASN    86      29.322  13.009  21.291  1.00 25.00           C
ATOM     87  CA  LYS    87      31.152  16.040  22.782  1.00 25.00           C
ATOM     88  CA  LEU    88      34.844  17.110  22.621  1.00 25.00           C
TER
END
