
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363TS393_4.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      -       -           -
LGA    I      13      I      13           #
LGA    N      14      N      14          3.162
LGA    I      15      I      15          4.495
LGA    E      16      E      16          1.708
LGA    I      17      I      17          2.338
LGA    A      18      A      18          2.941
LGA    Y      19      -       -           -
LGA    A      20      Y      19          0.771
LGA    F      21      A      20          1.810
LGA    P      22      F      21          3.419
LGA    E      23      P      22          2.704
LGA    R      24      E      23           -
LGA    Y      25      R      24           -
LGA    Y      26      -       -           -
LGA    L      27      Y      25           #
LGA    K      28      Y      26          4.910
LGA    S      29      L      27          2.194
LGA    F      30      K      28          2.123
LGA    Q      31      S      29          3.621
LGA    V      32      F      30          2.360
LGA    D      33      Q      31          2.108
LGA    E      34      V      32          2.417
LGA    G      35      D      33          2.119
LGA    I      36      E      34          2.231
LGA    T      37      G      35           -
LGA    V      38      -       -           -
LGA    Q      39      I      36          3.456
LGA    T      40      T      37           -
LGA    A      41      V      38           #
LGA    I      42      Q      39          3.521
LGA    T      43      T      40          1.959
LGA    -       -      A      41           -
LGA    -       -      I      42           -
LGA    Q      44      T      43          2.154
LGA    S      45      Q      44           #
LGA    G      46      S      45           -
LGA    I      47      G      46           #
LGA    L      48      I      47          4.464
LGA    S      49      L      48          3.124
LGA    Q      50      -       -           -
LGA    F      51      -       -           -
LGA    P      52      S      49          1.069
LGA    E      53      Q      50          3.888
LGA    I      54      F      51           #
LGA    D      55      P      52           -
LGA    L      56      E      53           -
LGA    S      57      I      54           -
LGA    T      58      D      55           -
LGA    N      59      -       -           -
LGA    K      60      -       -           -
LGA    I      61      -       -           -
LGA    G      62      -       -           -
LGA    I      63      L      56           #
LGA    F      64      S      57           -
LGA    -       -      T      58           -
LGA    -       -      N      59           -
LGA    -       -      K      60           -
LGA    S      65      I      61          2.731
LGA    R      66      G      62          2.185
LGA    P      67      I      63          1.072
LGA    I      68      F      64          4.035
LGA    K      69      S      65           #
LGA    L      70      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    T      71      G      77          4.674
LGA    D      72      D      78          4.436
LGA    V      73      R      79           -
LGA    L      74      I      80           -
LGA    K      75      E      81           -
LGA    E      76      I      82           -
LGA    G      77      Y      83           -
LGA    D      78      R      84           -
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      -       -           -
LGA    P      90      -       -           -
LGA    K      91      -       -           -
LGA    E      92      P      85          4.602
LGA    I      93      -       -           -
LGA    R      94      -       -           -
LGA    R      95      L      86          3.775
LGA    E      96      L      87          3.317
LGA    G      97      A      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   80    5.0     35    3.11    20.00     25.753     1.091

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.074888 * X  +  -0.887718 * Y  +   0.454257 * Z  +  20.999563
  Y_new =   0.848592 * X  +  -0.182513 * Y  +  -0.496568 * Z  +  14.488182
  Z_new =   0.523720 * X  +   0.422666 * Y  +   0.739642 * Z  +   4.179083 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.519159   -2.622433  [ DEG:    29.7456   -150.2544 ]
  Theta =  -0.551212   -2.590380  [ DEG:   -31.5821   -148.4179 ]
  Phi   =   1.482775   -1.658818  [ DEG:    84.9567    -95.0433 ]
 
# 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_4                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS393_4.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   35   3.11   20.00  25.753
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS393_4
PFRMAT TS
TARGET T0363
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       4.836 -10.638   2.743  1.00 25.00           C
ATOM      2  CA  ALA     2       3.109  -7.630   1.086  1.00 25.00           C
ATOM      3  CA  HIS     3       3.124  -4.548  -1.082  1.00 25.00           C
ATOM      4  CA  HIS     4       4.753  -2.822  -4.069  1.00 25.00           C
ATOM      5  CA  HIS     5       2.127  -0.090  -3.837  1.00 25.00           C
ATOM      6  CA  HIS     6       1.606   2.614  -1.180  1.00 25.00           C
ATOM      7  CA  HIS     7      -0.312   4.977   0.995  1.00 25.00           C
ATOM      8  CA  HIS     8      -0.458   5.663   4.683  1.00 25.00           C
ATOM      9  CA  SER     9       0.382   7.447   7.916  1.00 25.00           C
ATOM     10  CA  LEU    10       2.511   8.048  11.009  1.00 25.00           C
ATOM     11  CA  ASN    11       5.830   8.228   9.138  1.00 25.00           C
ATOM     12  CA  GLN    12       9.255   9.325   7.952  1.00 25.00           C
ATOM     13  CA  ILE    13      12.831  10.134   6.939  1.00 25.00           C
ATOM     14  CA  ASN    14      15.717  10.863   4.628  1.00 25.00           C
ATOM     15  CA  ILE    15      16.727  14.409   5.489  1.00 25.00           C
ATOM     16  CA  GLU    16      20.267  13.209   4.960  1.00 25.00           C
ATOM     17  CA  ILE    17      23.443  15.159   5.880  1.00 25.00           C
ATOM     18  CA  ALA    18      24.221  18.916   5.467  1.00 25.00           C
ATOM     19  CA  TYR    19      27.603  20.692   5.038  1.00 25.00           C
ATOM     20  CA  ALA    20      28.581  21.137   1.359  1.00 25.00           C
ATOM     21  CA  PHE    21      29.587  24.784   1.390  1.00 25.00           C
ATOM     22  CA  PRO    22      29.190  26.749  -1.851  1.00 25.00           C
ATOM     23  CA  GLU    23      29.554  30.110  -3.647  1.00 25.00           C
ATOM     24  CA  ARG    24      28.370  32.209  -0.710  1.00 25.00           C
ATOM     25  CA  TYR    25      28.093  29.664   2.152  1.00 25.00           C
ATOM     26  CA  TYR    26      25.156  27.326   1.456  1.00 25.00           C
ATOM     27  CA  LEU    27      24.200  23.735   2.257  1.00 25.00           C
ATOM     28  CA  LYS    28      23.552  20.563   0.350  1.00 25.00           C
ATOM     29  CA  SER    29      24.456  16.924   0.708  1.00 25.00           C
ATOM     30  CA  PHE    30      23.803  13.197   1.113  1.00 25.00           C
ATOM     31  CA  GLN    31      23.294   9.836   2.824  1.00 25.00           C
ATOM     32  CA  VAL    32      19.926   8.300   3.454  1.00 25.00           C
ATOM     33  CA  ASP    33      19.889   5.293   5.851  1.00 25.00           C
ATOM     34  CA  GLU    34      21.202   2.531   8.157  1.00 25.00           C
ATOM     35  CA  GLY    35      22.923   3.153  11.541  1.00 25.00           C
ATOM     36  CA  ILE    36      20.569   5.966  12.434  1.00 25.00           C
ATOM     37  CA  THR    37      19.532   8.684   9.897  1.00 25.00           C
ATOM     38  CA  VAL    38      22.604  10.764   8.924  1.00 25.00           C
ATOM     39  CA  GLN    39      24.703   7.898  10.356  1.00 25.00           C
ATOM     40  CA  THR    40      26.321   7.339   6.930  1.00 25.00           C
ATOM     41  CA  ALA    41      27.115  11.076   6.666  1.00 25.00           C
ATOM     42  CA  ILE    42      28.677  11.015  10.163  1.00 25.00           C
ATOM     43  CA  THR    43      30.795   7.976   9.190  1.00 25.00           C
ATOM     44  CA  GLN    44      31.953   9.770   6.011  1.00 25.00           C
ATOM     45  CA  SER    45      32.887  12.863   8.067  1.00 25.00           C
ATOM     46  CA  GLY    46      34.953  15.672   6.693  1.00 25.00           C
ATOM     47  CA  ILE    47      33.169  15.209   3.316  1.00 25.00           C
ATOM     48  CA  LEU    48      36.596  16.164   1.974  1.00 25.00           C
ATOM     49  CA  SER    49      39.272  14.104   3.781  1.00 25.00           C
ATOM     50  CA  GLN    50      36.875  11.124   3.987  1.00 25.00           C
ATOM     51  CA  PHE    51      35.259  11.293   0.547  1.00 25.00           C
ATOM     52  CA  PRO    52      38.602  12.160  -0.906  1.00 25.00           C
ATOM     53  CA  GLU    53      39.148  13.419  -4.434  1.00 25.00           C
ATOM     54  CA  ILE    54      35.556  13.646  -5.744  1.00 25.00           C
ATOM     55  CA  ASP    55      35.181  10.063  -4.472  1.00 25.00           C
ATOM     56  CA  LEU    56      31.355   9.602  -4.705  1.00 25.00           C
ATOM     57  CA  SER    57      30.298   5.984  -5.280  1.00 25.00           C
ATOM     58  CA  THR    58      29.063   5.871  -1.682  1.00 25.00           C
ATOM     59  CA  ASN    59      27.397   9.048  -0.482  1.00 25.00           C
ATOM     60  CA  LYS    60      27.489  12.411  -2.290  1.00 25.00           C
ATOM     61  CA  ILE    61      29.024  14.335   0.591  1.00 25.00           C
ATOM     62  CA  GLY    62      28.057  15.773   3.996  1.00 25.00           C
ATOM     63  CA  ILE    63      28.629  15.752   7.805  1.00 25.00           C
ATOM     64  CA  PHE    64      25.752  16.368  10.272  1.00 25.00           C
ATOM     65  CA  SER    65      27.691  19.460  11.382  1.00 25.00           C
ATOM     66  CA  ARG    66      25.705  22.559  10.279  1.00 25.00           C
ATOM     67  CA  PRO    67      22.711  20.384  11.161  1.00 25.00           C
ATOM     68  CA  ILE    68      20.379  21.237  14.052  1.00 25.00           C
ATOM     69  CA  LYS    69      17.406  22.042  16.235  1.00 25.00           C
ATOM     70  CA  LEU    70      17.619  25.521  14.816  1.00 25.00           C
ATOM     71  CA  THR    71      21.187  26.573  15.544  1.00 25.00           C
ATOM     72  CA  ASP    72      21.909  24.201  18.384  1.00 25.00           C
ATOM     73  CA  VAL    73      24.243  21.154  18.181  1.00 25.00           C
ATOM     74  CA  LEU    74      23.795  17.849  16.284  1.00 25.00           C
ATOM     75  CA  LYS    75      24.291  16.183  19.667  1.00 25.00           C
ATOM     76  CA  GLU    76      21.027  14.845  21.162  1.00 25.00           C
ATOM     77  CA  GLY    77      19.340  15.589  17.827  1.00 25.00           C
ATOM     78  CA  ASP    78      21.563  13.382  15.721  1.00 25.00           C
ATOM     79  CA  ARG    79      21.043  15.705  12.691  1.00 25.00           C
ATOM     80  CA  ILE    80      19.772  16.276   9.158  1.00 25.00           C
ATOM     81  CA  GLU    81      19.312  18.969   6.505  1.00 25.00           C
ATOM     82  CA  ILE    82      19.992  17.966   2.845  1.00 25.00           C
ATOM     83  CA  TYR    83      17.966  15.522   0.738  1.00 25.00           C
ATOM     84  CA  ARG    84      20.442  15.905  -2.101  1.00 25.00           C
ATOM     85  CA  PRO    85      22.297  16.638  -5.324  1.00 25.00           C
ATOM     86  CA  LEU    86      19.411  18.925  -6.229  1.00 25.00           C
ATOM     87  CA  LEU    87      17.985  16.084  -8.276  1.00 25.00           C
ATOM     88  CA  ALA    88      14.854  16.844  -6.238  1.00 25.00           C
ATOM     89  CA  ASP    89      13.355  20.271  -5.725  1.00 25.00           C
ATOM     90  CA  PRO    90      12.534  21.480  -2.161  1.00 25.00           C
ATOM     91  CA  LYS    91       8.799  20.807  -1.652  1.00 25.00           C
ATOM     92  CA  GLU    92       8.217  24.508  -0.853  1.00 25.00           C
ATOM     93  CA  ILE    93      10.125  25.516  -4.016  1.00 25.00           C
ATOM     94  CA  ARG    94       8.015  23.087  -6.093  1.00 25.00           C
ATOM     95  CA  ARG    95       4.495  22.502  -4.813  1.00 25.00           C
ATOM     96  CA  GLU    96       1.710  24.544  -3.130  1.00 25.00           C
ATOM     97  CA  GLY    97      -0.257  21.338  -2.727  1.00 25.00           C
TER
END
