
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0347TS168_4-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS168_4-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    P       7      P       7           -
LGA    R       8      R       8           -
LGA    L       9      L       9           -
LGA    S      10      S      10           -
LGA    R      11      R      11           -
LGA    I      12      I      12           -
LGA    A      13      A      13           -
LGA    I      14      I      14           -
LGA    D      15      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    K      16      G      25           #
LGA    L      17      F      26          3.316
LGA    R      18      R      27          3.748
LGA    P      19      E      28          2.363
LGA    T      20      V      29          3.600
LGA    Q      21      E      30          4.458
LGA    I      22      L      31           #
LGA    A      23      K      32           #
LGA    V      24      -       -           -
LGA    G      25      R      33          4.535
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    F      26      L      73          2.113
LGA    R      27      A      74          3.723
LGA    E      28      L      75          2.712
LGA    V      29      S      76          3.227
LGA    E      30      K      77          4.429
LGA    -       -      E      78           -
LGA    L      31      G      79          0.751
LGA    K      32      V      80          1.552
LGA    R      33      E      81          1.114
LGA    K      34      H      82           -
LGA    E      35      -       -           -
LGA    W      36      -       -           -
LGA    R      37      -       -           -
LGA    H      51      -       -           -
LGA    I      52      -       -           -
LGA    V      53      -       -           -
LGA    P      54      -       -           -
LGA    V      55      -       -           -
LGA    V      56      V      83           #
LGA    A      57      L      84          2.944
LGA    G      58      -       -           -
LGA    P      59      -       -           -
LGA    K      60      -       -           -
LGA    D      61      -       -           -
LGA    R      62      -       -           -
LGA    A      63      -       -           -
LGA    Y      64      -       -           -
LGA    L      65      T      85          3.317
LGA    I      66      S      86          2.825
LGA    D      67      E      87          2.642
LGA    H      68      -       -           -
LGA    H      69      -       -           -
LGA    H      70      -       -           -
LGA    L      71      -       -           -
LGA    V      72      -       -           -
LGA    L      73      -       -           -
LGA    A      74      -       -           -
LGA    L      75      -       -           -
LGA    S      76      -       -           -
LGA    K      77      -       -           -
LGA    E      78      -       -           -
LGA    G      79      -       -           -
LGA    V      80      -       -           -
LGA    E      81      -       -           -
LGA    H      82      -       -           -
LGA    V      83      -       -           -
LGA    L      84      -       -           -
LGA    T      85      -       -           -
LGA    S      86      -       -           -
LGA    E      87      V      88          4.997
LGA    V      88      A      89          3.278
LGA    A      89      K      90          3.129
LGA    K      90      -       -           -
LGA    F      91      -       -           -
LGA    S      92      F      91           #
LGA    H      93      S      92          1.293
LGA    -       -      H      93           -
LGA    L      94      L      94          1.821
LGA    G      95      G      95          3.126
LGA    K      96      K      96          4.082
LGA    -       -      D      97           -
LGA    D      97      E      98          2.574
LGA    E      98      F      99          3.544
LGA    F      99      W     100          2.650
LGA    W     100      S     101          0.727
LGA    S     101      V     102          1.506
LGA    V     102      M     103          0.427
LGA    M     103      D     104          1.922
LGA    D     104      H     105          2.998
LGA    H     105      R     106          3.168
LGA    R     106      N     107          2.362
LGA    N     107      L     108           #
LGA    L     108      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     35    2.99    11.43     24.337     1.133

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.830013 * X  +   0.249605 * Y  +   0.498774 * Z  +  10.313690
  Y_new =   0.497338 * X  +   0.073552 * Y  +  -0.864433 * Z  +  36.257286
  Z_new =  -0.252453 * X  +   0.965550 * Y  +  -0.063089 * Z  +  -7.640658 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.636043   -1.505550  [ DEG:    93.7384    -86.2616 ]
  Theta =   0.255214    2.886378  [ DEG:    14.6227    165.3773 ]
  Phi   =   0.539826   -2.601767  [ DEG:    30.9297   -149.0703 ]
 
# 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: T0347TS168_4-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS168_4-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89   89   5.0   35   2.99   11.43  24.337
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS168_4-D1
PFRMAT TS
TARGET T0347
MODEL 4
PARENT N/A
ATOM      7  CA  PRO     7      11.440  75.598 -16.260  1.00 25.00           C
ATOM      8  CA  ARG     8      13.199  72.344 -16.969  1.00 25.00           C
ATOM      9  CA  LEU     9      12.174  69.020 -15.426  1.00 25.00           C
ATOM     10  CA  SER    10       9.269  70.560 -13.511  1.00 25.00           C
ATOM     11  CA  ARG    11       9.847  68.991 -10.147  1.00 25.00           C
ATOM     12  CA  ILE    12      10.390  65.609 -11.896  1.00 25.00           C
ATOM     13  CA  ALA    13      11.733  63.835  -8.779  1.00 25.00           C
ATOM     14  CA  ILE    14       9.402  60.930  -9.745  1.00 25.00           C
ATOM     15  CA  ASP    15       5.902  61.692  -8.391  1.00 25.00           C
ATOM     16  CA  LYS    16       4.652  58.294  -9.643  1.00 25.00           C
ATOM     17  CA  LEU    17       7.276  57.006  -7.253  1.00 25.00           C
ATOM     18  CA  ARG    18      10.909  56.647  -6.002  1.00 25.00           C
ATOM     19  CA  PRO    19      10.459  53.023  -7.177  1.00 25.00           C
ATOM     20  CA  THR    20      10.023  54.182 -10.801  1.00 25.00           C
ATOM     21  CA  GLN    21      12.040  51.168 -12.034  1.00 25.00           C
ATOM     22  CA  ILE    22       9.870  48.822  -9.924  1.00 25.00           C
ATOM     23  CA  ALA    23       6.700  50.416 -11.366  1.00 25.00           C
ATOM     24  CA  VAL    24       8.065  49.975 -14.917  1.00 25.00           C
ATOM     25  CA  GLY    25       8.854  46.300 -14.183  1.00 25.00           C
ATOM     26  CA  PHE    26       5.310  45.783 -12.829  1.00 25.00           C
ATOM     27  CA  ARG    27       3.846  47.403 -15.975  1.00 25.00           C
ATOM     28  CA  GLU    28       5.993  45.123 -18.178  1.00 25.00           C
ATOM     29  CA  VAL    29       4.805  42.060 -16.210  1.00 25.00           C
ATOM     30  CA  GLU    30       1.164  43.170 -16.632  1.00 25.00           C
ATOM     31  CA  LEU    31       1.710  43.613 -20.397  1.00 25.00           C
ATOM     32  CA  LYS    32       3.255  40.114 -20.608  1.00 25.00           C
ATOM     33  CA  ARG    33       0.266  38.653 -18.712  1.00 25.00           C
ATOM     34  CA  LYS    34      -2.147  40.424 -21.101  1.00 25.00           C
ATOM     35  CA  GLU    35      -0.226  39.036 -24.110  1.00 25.00           C
ATOM     36  CA  TRP    36      -0.386  35.513 -22.618  1.00 25.00           C
ATOM     37  CA  ARG    37      -4.158  35.890 -22.069  1.00 25.00           C
ATOM     51  CA  HIS    51      -3.533  33.036  -3.642  1.00 25.00           C
ATOM     52  CA  ILE    52      -1.220  35.991  -4.368  1.00 25.00           C
ATOM     53  CA  VAL    53       1.881  37.231  -6.305  1.00 25.00           C
ATOM     54  CA  PRO    54       5.387  36.942  -7.775  1.00 25.00           C
ATOM     55  CA  VAL    55       8.737  35.316  -6.988  1.00 25.00           C
ATOM     56  CA  VAL    56      10.136  36.545 -10.279  1.00 25.00           C
ATOM     57  CA  ALA    57      11.158  34.026 -12.961  1.00 25.00           C
ATOM     58  CA  GLY    58      12.809  35.629 -15.972  1.00 25.00           C
ATOM     59  CA  PRO    59      12.238  33.496 -19.090  1.00 25.00           C
ATOM     60  CA  LYS    60      15.381  32.163 -20.872  1.00 25.00           C
ATOM     61  CA  ASP    61      18.506  33.845 -19.409  1.00 25.00           C
ATOM     62  CA  ARG    62      18.918  33.661 -15.621  1.00 25.00           C
ATOM     63  CA  ALA    63      15.905  31.288 -15.856  1.00 25.00           C
ATOM     64  CA  TYR    64      12.671  29.604 -14.770  1.00 25.00           C
ATOM     65  CA  LEU    65       9.782  28.900 -12.386  1.00 25.00           C
ATOM     66  CA  ILE    66       8.992  30.788  -9.214  1.00 25.00           C
ATOM     67  CA  ASP    67       7.331  29.113  -6.282  1.00 25.00           C
ATOM     68  CA  HIS    68       3.762  29.494  -7.501  1.00 25.00           C
ATOM     69  CA  HIS    69       0.945  31.604  -5.990  1.00 25.00           C
ATOM     70  CA  HIS    70       1.723  30.196  -2.514  1.00 25.00           C
ATOM     71  CA  LEU    71       5.433  31.021  -2.983  1.00 25.00           C
ATOM     72  CA  VAL    72       4.531  34.588  -4.047  1.00 25.00           C
ATOM     73  CA  LEU    73       2.298  34.970  -0.959  1.00 25.00           C
ATOM     74  CA  ALA    74       5.140  33.717   1.282  1.00 25.00           C
ATOM     75  CA  LEU    75       7.550  36.215  -0.335  1.00 25.00           C
ATOM     76  CA  SER    76       5.035  39.047   0.235  1.00 25.00           C
ATOM     77  CA  LYS    77       4.662  38.011   3.903  1.00 25.00           C
ATOM     78  CA  GLU    78       2.290  40.942   3.973  1.00 25.00           C
ATOM     79  CA  GLY    79       4.438  44.128   3.915  1.00 25.00           C
ATOM     80  CA  VAL    80       7.753  42.459   2.940  1.00 25.00           C
ATOM     81  CA  GLU    81       9.886  44.513   0.551  1.00 25.00           C
ATOM     82  CA  HIS    82      12.821  43.418   2.758  1.00 25.00           C
ATOM     83  CA  VAL    83      12.686  40.209   0.707  1.00 25.00           C
ATOM     84  CA  LEU    84      13.389  39.169  -2.853  1.00 25.00           C
ATOM     85  CA  THR    85      12.190  35.571  -2.166  1.00 25.00           C
ATOM     86  CA  SER    86      11.230  33.893   1.103  1.00 25.00           C
ATOM     87  CA  GLU    87       8.798  30.986   0.736  1.00 25.00           C
ATOM     88  CA  VAL    88       6.414  28.027   0.096  1.00 25.00           C
ATOM     89  CA  ALA    89       3.995  25.300  -1.017  1.00 25.00           C
ATOM     90  CA  LYS    90       3.046  25.239  -4.682  1.00 25.00           C
ATOM     91  CA  PHE    91      -0.394  25.595  -3.131  1.00 25.00           C
ATOM     92  CA  SER    92      -1.931  26.162   0.288  1.00 25.00           C
ATOM     93  CA  HIS    93       0.056  24.530   3.061  1.00 25.00           C
ATOM     94  CA  LEU    94      -2.311  25.498   5.889  1.00 25.00           C
ATOM     95  CA  GLY    95      -2.878  25.603   9.621  1.00 25.00           C
ATOM     96  CA  LYS    96      -2.004  29.355   9.659  1.00 25.00           C
ATOM     97  CA  ASP    97       1.113  29.007  11.858  1.00 25.00           C
ATOM     98  CA  GLU    98       3.346  29.094   8.748  1.00 25.00           C
ATOM     99  CA  PHE    99       1.546  32.241   7.513  1.00 25.00           C
ATOM    100  CA  TRP   100       2.030  33.890  10.935  1.00 25.00           C
ATOM    101  CA  SER   101       5.755  33.001  10.864  1.00 25.00           C
ATOM    102  CA  VAL   102       6.069  34.489   7.350  1.00 25.00           C
ATOM    103  CA  MET   103       4.328  37.691   8.524  1.00 25.00           C
ATOM    104  CA  ASP   104       6.711  37.920  11.514  1.00 25.00           C
ATOM    105  CA  HIS   105       9.717  37.467   9.185  1.00 25.00           C
ATOM    106  CA  ARG   106      11.076  38.347   5.757  1.00 25.00           C
ATOM    107  CA  ASN   107      14.419  36.515   6.233  1.00 25.00           C
ATOM    108  CA  LEU   108      12.312  33.303   6.055  1.00 25.00           C
TER
END
