
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363TS393_3.T0363.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    A       2      -       -           -
LGA    H       3      -       -           -
LGA    H       4      -       -           -
LGA    H       5      -       -           -
LGA    H       6      -       -           -
LGA    H       7      -       -           -
LGA    H       8      -       -           -
LGA    S       9      -       -           -
LGA    L      10      L      10          4.925
LGA    N      11      N      11          1.101
LGA    Q      12      Q      12          1.436
LGA    I      13      I      13          3.415
LGA    N      14      N      14          4.401
LGA    I      15      I      15          3.801
LGA    E      16      E      16          1.510
LGA    I      17      I      17          2.503
LGA    A      18      A      18          2.983
LGA    Y      19      Y      19          2.831
LGA    A      20      A      20          4.773
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    F      21      Y      25          4.704
LGA    P      22      Y      26           -
LGA    E      23      -       -           -
LGA    R      24      -       -           -
LGA    Y      25      -       -           -
LGA    Y      26      -       -           -
LGA    L      27      -       -           -
LGA    K      28      -       -           -
LGA    S      29      L      27           #
LGA    F      30      K      28           #
LGA    -       -      S      29           -
LGA    -       -      F      30           -
LGA    -       -      Q      31           -
LGA    -       -      V      32           -
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    -       -      I      36           -
LGA    -       -      T      37           -
LGA    -       -      V      38           -
LGA    -       -      Q      39           -
LGA    -       -      T      40           -
LGA    Q      31      A      41          3.299
LGA    V      32      I      42          4.765
LGA    D      33      T      43           -
LGA    E      34      -       -           -
LGA    G      35      -       -           -
LGA    I      36      -       -           -
LGA    T      37      -       -           -
LGA    V      38      Q      44           #
LGA    Q      39      S      45          2.266
LGA    T      40      -       -           -
LGA    A      41      G      46          1.557
LGA    I      42      I      47          2.604
LGA    T      43      L      48          2.972
LGA    Q      44      S      49          1.216
LGA    S      45      Q      50          4.222
LGA    G      46      F      51          3.233
LGA    I      47      -       -           -
LGA    L      48      -       -           -
LGA    S      49      -       -           -
LGA    Q      50      P      52          2.436
LGA    F      51      E      53          2.015
LGA    P      52      -       -           -
LGA    E      53      I      54           #
LGA    I      54      D      55          4.843
LGA    D      55      L      56           #
LGA    L      56      S      57          3.673
LGA    S      57      T      58          2.242
LGA    T      58      N      59          2.366
LGA    N      59      K      60          4.552
LGA    K      60      I      61           #
LGA    I      61      -       -           -
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      G      62          4.580
LGA    L      86      I      63          2.590
LGA    L      87      F      64          3.585
LGA    A      88      -       -           -
LGA    D      89      S      65           #
LGA    P      90      R      66          3.992
LGA    K      91      -       -           -
LGA    E      92      -       -           -
LGA    I      93      P      67          1.453
LGA    R      94      I      68          1.764
LGA    R      95      K      69          1.972
LGA    E      96      L      70          2.788
LGA    G      97      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           -
LGA    -       -      L      86           -
LGA    -       -      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     36    3.26    33.33     25.600     1.073

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.351106 * X  +  -0.878983 * Y  +   0.322666 * Z  +  23.498461
  Y_new =  -0.933228 * X  +   0.300455 * Y  +  -0.197005 * Z  +  14.479765
  Z_new =   0.076218 * X  +  -0.370291 * Y  +  -0.925784 * Z  +   3.510103 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.761108    0.380485  [ DEG:  -158.1998     21.8002 ]
  Theta =  -0.076292   -3.065301  [ DEG:    -4.3712   -175.6288 ]
  Phi   =  -1.930643    1.210950  [ DEG:  -110.6177     69.3823 ]
 
# 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_3                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS393_3.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   36   3.26   33.33  25.600
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS393_3
PFRMAT TS
TARGET T0363
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -3.786   1.485  -0.789  1.00 25.00           C
ATOM      2  CA  ALA     2      -0.659  -0.494  -0.036  1.00 25.00           C
ATOM      3  CA  HIS     3      -1.992  -1.150   3.498  1.00 25.00           C
ATOM      4  CA  HIS     4      -0.680  -3.496   6.139  1.00 25.00           C
ATOM      5  CA  HIS     5       3.035  -4.339   6.337  1.00 25.00           C
ATOM      6  CA  HIS     6       6.361  -2.555   6.747  1.00 25.00           C
ATOM      7  CA  HIS     7       9.537  -2.672   8.878  1.00 25.00           C
ATOM      8  CA  HIS     8       8.454   0.052  11.201  1.00 25.00           C
ATOM      9  CA  SER     9      10.869  -1.569  13.574  1.00 25.00           C
ATOM     10  CA  LEU    10      13.865  -2.531  11.467  1.00 25.00           C
ATOM     11  CA  ASN    11      16.041   0.440  10.524  1.00 25.00           C
ATOM     12  CA  GLN    12      18.474   2.832   8.818  1.00 25.00           C
ATOM     13  CA  ILE    13      20.216   5.947   7.553  1.00 25.00           C
ATOM     14  CA  ASN    14      21.424   9.545   7.786  1.00 25.00           C
ATOM     15  CA  ILE    15      22.909  10.216   4.388  1.00 25.00           C
ATOM     16  CA  GLU    16      22.944  13.996   4.163  1.00 25.00           C
ATOM     17  CA  ILE    17      25.196  15.785   1.719  1.00 25.00           C
ATOM     18  CA  ALA    18      26.103  19.061  -0.065  1.00 25.00           C
ATOM     19  CA  TYR    19      28.519  22.009  -0.670  1.00 25.00           C
ATOM     20  CA  ALA    20      26.103  22.445  -3.627  1.00 25.00           C
ATOM     21  CA  PHE    21      23.789  24.952  -1.878  1.00 25.00           C
ATOM     22  CA  PRO    22      21.309  27.802  -2.067  1.00 25.00           C
ATOM     23  CA  GLU    23      21.310  31.573  -2.608  1.00 25.00           C
ATOM     24  CA  ARG    24      24.927  31.926  -3.811  1.00 25.00           C
ATOM     25  CA  TYR    25      26.641  31.068  -0.532  1.00 25.00           C
ATOM     26  CA  TYR    26      25.552  28.173   1.745  1.00 25.00           C
ATOM     27  CA  LEU    27      25.777  24.547   2.917  1.00 25.00           C
ATOM     28  CA  LYS    28      27.080  21.426   4.653  1.00 25.00           C
ATOM     29  CA  SER    29      27.034  18.002   6.199  1.00 25.00           C
ATOM     30  CA  PHE    30      27.954  14.536   5.049  1.00 25.00           C
ATOM     31  CA  GLN    31      28.447  12.740   8.368  1.00 25.00           C
ATOM     32  CA  VAL    32      26.888   9.272   8.207  1.00 25.00           C
ATOM     33  CA  ASP    33      26.960   5.526   7.942  1.00 25.00           C
ATOM     34  CA  GLU    34      30.442   3.976   8.457  1.00 25.00           C
ATOM     35  CA  GLY    35      32.196   2.938   5.214  1.00 25.00           C
ATOM     36  CA  ILE    36      30.031   4.442   2.413  1.00 25.00           C
ATOM     37  CA  THR    37      26.804   6.353   2.859  1.00 25.00           C
ATOM     38  CA  VAL    38      28.198   9.890   2.192  1.00 25.00           C
ATOM     39  CA  GLN    39      30.720   9.090   4.962  1.00 25.00           C
ATOM     40  CA  THR    40      33.354   8.179   2.334  1.00 25.00           C
ATOM     41  CA  ALA    41      32.687  11.469   0.490  1.00 25.00           C
ATOM     42  CA  ILE    42      33.055  13.411   3.771  1.00 25.00           C
ATOM     43  CA  THR    43      36.364  11.620   4.488  1.00 25.00           C
ATOM     44  CA  GLN    44      37.617  12.473   0.970  1.00 25.00           C
ATOM     45  CA  SER    45      36.644  16.141   1.487  1.00 25.00           C
ATOM     46  CA  GLY    46      34.813  16.111  -1.883  1.00 25.00           C
ATOM     47  CA  ILE    47      33.274  19.448  -2.618  1.00 25.00           C
ATOM     48  CA  LEU    48      36.644  21.223  -2.076  1.00 25.00           C
ATOM     49  CA  SER    49      39.436  18.604  -2.178  1.00 25.00           C
ATOM     50  CA  GLN    50      40.715  19.802   1.227  1.00 25.00           C
ATOM     51  CA  PHE    51      38.442  22.118   3.209  1.00 25.00           C
ATOM     52  CA  PRO    52      39.804  25.624   2.636  1.00 25.00           C
ATOM     53  CA  GLU    53      39.933  26.015   6.360  1.00 25.00           C
ATOM     54  CA  ILE    54      40.174  24.122   9.629  1.00 25.00           C
ATOM     55  CA  ASP    55      41.330  20.511   9.083  1.00 25.00           C
ATOM     56  CA  LEU    56      38.021  19.455  10.679  1.00 25.00           C
ATOM     57  CA  SER    57      36.987  20.293  14.303  1.00 25.00           C
ATOM     58  CA  THR    58      33.862  21.628  12.574  1.00 25.00           C
ATOM     59  CA  ASN    59      31.604  20.462   9.740  1.00 25.00           C
ATOM     60  CA  LYS    60      31.874  16.835   8.701  1.00 25.00           C
ATOM     61  CA  ILE    61      31.549  18.083   5.106  1.00 25.00           C
ATOM     62  CA  GLY    62      30.625  17.327   1.510  1.00 25.00           C
ATOM     63  CA  ILE    63      29.299  14.843  -1.072  1.00 25.00           C
ATOM     64  CA  PHE    64      26.467  12.480  -2.181  1.00 25.00           C
ATOM     65  CA  SER    65      24.087   9.927  -0.583  1.00 25.00           C
ATOM     66  CA  ARG    66      21.157   9.881  -3.022  1.00 25.00           C
ATOM     67  CA  PRO    67      19.026  12.595  -1.332  1.00 25.00           C
ATOM     68  CA  ILE    68      18.659  14.036  -4.833  1.00 25.00           C
ATOM     69  CA  LYS    69      15.760  12.921  -7.043  1.00 25.00           C
ATOM     70  CA  LEU    70      15.522  16.162  -8.965  1.00 25.00           C
ATOM     71  CA  THR    71      18.242  16.916 -11.452  1.00 25.00           C
ATOM     72  CA  ASP    72      21.201  14.728 -12.363  1.00 25.00           C
ATOM     73  CA  VAL    73      19.152  12.005 -10.747  1.00 25.00           C
ATOM     74  CA  LEU    74      21.541  11.073  -7.884  1.00 25.00           C
ATOM     75  CA  LYS    75      23.822   9.340 -10.439  1.00 25.00           C
ATOM     76  CA  GLU    76      27.535   9.111 -11.233  1.00 25.00           C
ATOM     77  CA  GLY    77      28.315  10.112  -7.617  1.00 25.00           C
ATOM     78  CA  ASP    78      26.263  13.296  -7.209  1.00 25.00           C
ATOM     79  CA  ARG    79      23.513  15.232  -5.491  1.00 25.00           C
ATOM     80  CA  ILE    80      22.116  16.926  -2.325  1.00 25.00           C
ATOM     81  CA  GLU    81      20.558  17.773   1.034  1.00 25.00           C
ATOM     82  CA  ILE    82      22.304  19.088   4.151  1.00 25.00           C
ATOM     83  CA  TYR    83      22.985  20.691   7.590  1.00 25.00           C
ATOM     84  CA  ARG    84      22.850  17.227   9.172  1.00 25.00           C
ATOM     85  CA  PRO    85      24.840  17.812  12.340  1.00 25.00           C
ATOM     86  CA  LEU    86      21.428  18.402  13.880  1.00 25.00           C
ATOM     87  CA  LEU    87      18.772  21.107  13.979  1.00 25.00           C
ATOM     88  CA  ALA    88      19.448  23.541  11.165  1.00 25.00           C
ATOM     89  CA  ASP    89      15.789  24.551  11.526  1.00 25.00           C
ATOM     90  CA  PRO    90      14.082  21.455  10.199  1.00 25.00           C
ATOM     91  CA  LYS    91      10.964  22.645  12.079  1.00 25.00           C
ATOM     92  CA  GLU    92       8.832  20.053  10.234  1.00 25.00           C
ATOM     93  CA  ILE    93      11.347  17.308  11.133  1.00 25.00           C
ATOM     94  CA  ARG    94      11.262  18.398  14.803  1.00 25.00           C
ATOM     95  CA  ARG    95       9.773  16.340  17.698  1.00 25.00           C
ATOM     96  CA  GLU    96       6.576  18.132  16.730  1.00 25.00           C
ATOM     97  CA  GLY    97       5.067  15.979  13.936  1.00 25.00           C
TER
END
