
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0363TS393_1
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363TS393_1.T0363.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      L      10           -
LGA    A       2      N      11           -
LGA    H       3      Q      12           -
LGA    H       4      -       -           -
LGA    H       5      -       -           -
LGA    H       6      -       -           -
LGA    H       7      -       -           -
LGA    H       8      -       -           -
LGA    S       9      -       -           -
LGA    L      10      -       -           -
LGA    N      11      -       -           -
LGA    Q      12      I      13           #
LGA    I      13      N      14           #
LGA    N      14      -       -           -
LGA    I      15      I      15          2.623
LGA    E      16      E      16          1.651
LGA    I      17      I      17          3.157
LGA    A      18      A      18          2.773
LGA    Y      19      -       -           -
LGA    A      20      Y      19          2.424
LGA    F      21      A      20          1.363
LGA    P      22      F      21          3.631
LGA    E      23      P      22          2.111
LGA    R      24      E      23          3.535
LGA    Y      25      R      24          1.432
LGA    Y      26      Y      25          0.882
LGA    L      27      Y      26          2.998
LGA    K      28      L      27          1.474
LGA    S      29      K      28          1.766
LGA    F      30      S      29          0.953
LGA    Q      31      F      30          2.717
LGA    V      32      Q      31          4.107
LGA    D      33      V      32          1.702
LGA    E      34      D      33          2.635
LGA    G      35      E      34          4.295
LGA    I      36      G      35          4.826
LGA    T      37      -       -           -
LGA    V      38      I      36          4.512
LGA    Q      39      T      37          1.898
LGA    T      40      -       -           -
LGA    A      41      V      38          4.433
LGA    I      42      Q      39          4.054
LGA    T      43      T      40          4.605
LGA    -       -      A      41           -
LGA    Q      44      I      42          3.645
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    S      45      S      45           #
LGA    G      46      G      46           -
LGA    I      47      I      47           -
LGA    -       -      L      48           -
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    L      48      E      53           #
LGA    S      49      I      54          1.824
LGA    Q      50      D      55          2.889
LGA    F      51      L      56          1.003
LGA    P      52      S      57          1.365
LGA    E      53      T      58          1.538
LGA    I      54      N      59          2.832
LGA    D      55      K      60          4.157
LGA    L      56      I      61           #
LGA    S      57      -       -           -
LGA    T      58      -       -           -
LGA    N      59      -       -           -
LGA    K      60      G      62          2.618
LGA    I      61      I      63          3.830
LGA    G      62      -       -           -
LGA    I      63      -       -           -
LGA    F      64      -       -           -
LGA    S      65      -       -           -
LGA    R      66      -       -           -
LGA    P      67      -       -           -
LGA    I      68      -       -           -
LGA    K      69      -       -           -
LGA    L      70      -       -           -
LGA    T      71      -       -           -
LGA    D      72      -       -           -
LGA    V      73      -       -           -
LGA    L      74      -       -           -
LGA    K      75      -       -           -
LGA    E      76      -       -           -
LGA    G      77      -       -           -
LGA    D      78      -       -           -
LGA    R      79      -       -           -
LGA    I      80      -       -           -
LGA    E      81      -       -           -
LGA    I      82      -       -           -
LGA    Y      83      -       -           -
LGA    R      84      -       -           -
LGA    P      85      F      64          5.057
LGA    L      86      S      65           #
LGA    -       -      R      66           -
LGA    -       -      P      67           -
LGA    -       -      I      68           -
LGA    -       -      K      69           -
LGA    -       -      L      70           -
LGA    -       -      T      71           -
LGA    -       -      D      72           -
LGA    -       -      V      73           -
LGA    -       -      L      74           -
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    -       -      G      77           -
LGA    -       -      D      78           -
LGA    -       -      R      79           -
LGA    -       -      I      80           -
LGA    L      87      E      81           #
LGA    A      88      I      82           -
LGA    D      89      Y      83           #
LGA    P      90      -       -           -
LGA    K      91      -       -           -
LGA    E      92      -       -           -
LGA    I      93      -       -           -
LGA    R      94      R      84          3.278
LGA    R      95      P      85          1.782
LGA    E      96      L      86          3.610
LGA    G      97      L      87           -
LGA    -       -      A      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   80    5.0     40    3.04    20.00     29.638     1.274

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.246098 * X  +   0.958946 * Y  +   0.140919 * Z  +  22.158091
  Y_new =  -0.008613 * X  +  -0.147548 * Y  +   0.989017 * Z  +  14.268053
  Z_new =   0.969207 * X  +   0.242181 * Y  +   0.044571 * Z  +   6.116180 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.388795   -1.752798  [ DEG:    79.5721   -100.4279 ]
  Theta =  -1.321989   -1.819604  [ DEG:   -75.7444   -104.2556 ]
  Phi   =  -3.106609    0.034983  [ DEG:  -177.9956      2.0044 ]
 
# 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: T0363TS393_1                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS393_1.T0363.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   80   5.0   40   3.04   20.00  29.638
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS393_1
PFRMAT TS
TARGET T0363
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -5.353  -2.867  23.193  1.00 25.00           C
ATOM      2  CA  ALA     2      -4.742  -1.351  19.743  1.00 25.00           C
ATOM      3  CA  HIS     3      -1.767   1.015  19.849  1.00 25.00           C
ATOM      4  CA  HIS     4      -0.681   1.565  16.245  1.00 25.00           C
ATOM      5  CA  HIS     5      -2.746   4.443  15.027  1.00 25.00           C
ATOM      6  CA  HIS     6       0.275   6.720  15.168  1.00 25.00           C
ATOM      7  CA  HIS     7       0.589  10.535  15.327  1.00 25.00           C
ATOM      8  CA  HIS     8       3.219  11.327  17.983  1.00 25.00           C
ATOM      9  CA  SER     9       6.426  12.200  19.950  1.00 25.00           C
ATOM     10  CA  LEU    10       8.349   9.061  18.956  1.00 25.00           C
ATOM     11  CA  ASN    11       9.804   8.907  15.443  1.00 25.00           C
ATOM     12  CA  GLN    12      12.212   8.648  12.538  1.00 25.00           C
ATOM     13  CA  ILE    13      15.137  10.194  10.631  1.00 25.00           C
ATOM     14  CA  ASN    14      18.198  12.350  11.216  1.00 25.00           C
ATOM     15  CA  ILE    15      20.849  12.862   8.512  1.00 25.00           C
ATOM     16  CA  GLU    16      20.805  15.290   5.523  1.00 25.00           C
ATOM     17  CA  ILE    17      22.692  18.062   3.652  1.00 25.00           C
ATOM     18  CA  ALA    18      25.906  16.778   2.052  1.00 25.00           C
ATOM     19  CA  TYR    19      28.654  17.222  -0.596  1.00 25.00           C
ATOM     20  CA  ALA    20      30.344  20.249   0.969  1.00 25.00           C
ATOM     21  CA  PHE    21      29.542  23.622  -0.614  1.00 25.00           C
ATOM     22  CA  PRO    22      28.649  26.563  -2.806  1.00 25.00           C
ATOM     23  CA  GLU    23      30.009  28.248  -5.883  1.00 25.00           C
ATOM     24  CA  ARG    24      32.781  25.785  -6.667  1.00 25.00           C
ATOM     25  CA  TYR    25      30.116  23.154  -6.232  1.00 25.00           C
ATOM     26  CA  TYR    26      26.782  22.090  -4.643  1.00 25.00           C
ATOM     27  CA  LEU    27      25.298  20.924  -1.301  1.00 25.00           C
ATOM     28  CA  LYS    28      22.553  18.291  -1.351  1.00 25.00           C
ATOM     29  CA  SER    29      21.835  14.705  -0.207  1.00 25.00           C
ATOM     30  CA  PHE    30      20.723  11.735   1.906  1.00 25.00           C
ATOM     31  CA  GLN    31      21.293   9.326   4.757  1.00 25.00           C
ATOM     32  CA  VAL    32      18.947   7.429   7.154  1.00 25.00           C
ATOM     33  CA  ASP    33      20.475   3.960   7.372  1.00 25.00           C
ATOM     34  CA  GLU    34      20.121   3.917  11.163  1.00 25.00           C
ATOM     35  CA  GLY    35      22.779   1.127  11.264  1.00 25.00           C
ATOM     36  CA  ILE    36      25.176   4.071  11.581  1.00 25.00           C
ATOM     37  CA  THR    37      25.272   5.891   8.261  1.00 25.00           C
ATOM     38  CA  VAL    38      23.526   8.758  10.022  1.00 25.00           C
ATOM     39  CA  GLN    39      25.260   9.135  13.415  1.00 25.00           C
ATOM     40  CA  THR    40      28.543   7.864  11.906  1.00 25.00           C
ATOM     41  CA  ALA    41      28.213  10.361   9.021  1.00 25.00           C
ATOM     42  CA  ILE    42      27.589  13.199  11.517  1.00 25.00           C
ATOM     43  CA  THR    43      30.681  12.150  13.519  1.00 25.00           C
ATOM     44  CA  GLN    44      32.775  12.111  10.314  1.00 25.00           C
ATOM     45  CA  SER    45      31.501  15.607   9.408  1.00 25.00           C
ATOM     46  CA  GLY    46      31.243  18.467  11.886  1.00 25.00           C
ATOM     47  CA  ILE    47      31.243  21.496   9.622  1.00 25.00           C
ATOM     48  CA  LEU    48      34.367  20.515   7.667  1.00 25.00           C
ATOM     49  CA  SER    49      38.104  20.160   6.906  1.00 25.00           C
ATOM     50  CA  GLN    50      38.153  16.737   8.625  1.00 25.00           C
ATOM     51  CA  PHE    51      36.102  17.060  11.779  1.00 25.00           C
ATOM     52  CA  PRO    52      39.187  18.942  13.116  1.00 25.00           C
ATOM     53  CA  GLU    53      37.508  21.675  15.135  1.00 25.00           C
ATOM     54  CA  ILE    54      35.623  24.429  13.232  1.00 25.00           C
ATOM     55  CA  ASP    55      33.005  23.697  15.951  1.00 25.00           C
ATOM     56  CA  LEU    56      32.349  20.026  16.516  1.00 25.00           C
ATOM     57  CA  SER    57      29.343  21.353  18.484  1.00 25.00           C
ATOM     58  CA  THR    58      25.751  20.684  17.549  1.00 25.00           C
ATOM     59  CA  ASN    59      24.947  19.564  14.022  1.00 25.00           C
ATOM     60  CA  LYS    60      26.127  20.794  10.603  1.00 25.00           C
ATOM     61  CA  ILE    61      23.680  18.487   8.758  1.00 25.00           C
ATOM     62  CA  GLY    62      25.667  15.476   7.473  1.00 25.00           C
ATOM     63  CA  ILE    63      25.500  12.663   4.912  1.00 25.00           C
ATOM     64  CA  PHE    64      25.869  11.840   1.200  1.00 25.00           C
ATOM     65  CA  SER    65      25.784  12.716  -2.560  1.00 25.00           C
ATOM     66  CA  ARG    66      22.654  10.560  -2.945  1.00 25.00           C
ATOM     67  CA  PRO    67      23.288   7.700  -0.489  1.00 25.00           C
ATOM     68  CA  ILE    68      25.454   5.136  -2.279  1.00 25.00           C
ATOM     69  CA  LYS    69      23.173   3.856  -5.040  1.00 25.00           C
ATOM     70  CA  LEU    70      23.263   6.971  -7.168  1.00 25.00           C
ATOM     71  CA  THR    71      24.673   8.575 -10.262  1.00 25.00           C
ATOM     72  CA  ASP    72      28.272   7.886  -9.079  1.00 25.00           C
ATOM     73  CA  VAL    73      28.290   5.073  -6.581  1.00 25.00           C
ATOM     74  CA  LEU    74      30.136   6.893  -3.803  1.00 25.00           C
ATOM     75  CA  LYS    75      33.848   6.025  -3.592  1.00 25.00           C
ATOM     76  CA  GLU    76      35.105   3.586  -1.057  1.00 25.00           C
ATOM     77  CA  GLY    77      31.659   3.371   0.478  1.00 25.00           C
ATOM     78  CA  ASP    78      29.601   6.470   1.159  1.00 25.00           C
ATOM     79  CA  ARG    79      28.450   8.583   4.146  1.00 25.00           C
ATOM     80  CA  ILE    80      30.704  11.439   3.078  1.00 25.00           C
ATOM     81  CA  GLU    81      29.994  14.857   4.590  1.00 25.00           C
ATOM     82  CA  ILE    82      29.418  18.400   5.671  1.00 25.00           C
ATOM     83  CA  TYR    83      26.888  20.970   4.619  1.00 25.00           C
ATOM     84  CA  ARG    84      23.619  22.600   5.675  1.00 25.00           C
ATOM     85  CA  PRO    85      19.877  21.939   5.647  1.00 25.00           C
ATOM     86  CA  LEU    86      16.655  22.929   7.433  1.00 25.00           C
ATOM     87  CA  LEU    87      16.472  26.533   6.426  1.00 25.00           C
ATOM     88  CA  ALA    88      17.236  25.271   2.931  1.00 25.00           C
ATOM     89  CA  ASP    89      13.560  26.216   2.342  1.00 25.00           C
ATOM     90  CA  PRO    90      13.155  22.841   0.539  1.00 25.00           C
ATOM     91  CA  LYS    91      10.309  24.343  -1.537  1.00 25.00           C
ATOM     92  CA  GLU    92       8.639  20.904  -1.780  1.00 25.00           C
ATOM     93  CA  ILE    93       8.948  20.459   2.012  1.00 25.00           C
ATOM     94  CA  ARG    94       7.392  23.914   2.568  1.00 25.00           C
ATOM     95  CA  ARG    95       4.016  22.335   3.317  1.00 25.00           C
ATOM     96  CA  GLU    96       3.208  20.586   0.041  1.00 25.00           C
ATOM     97  CA  GLY    97       2.101  17.142   1.094  1.00 25.00           C
TER
END
