
#######################################################
#                                                     #
#                        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 T0363TS599_3
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363TS599_3.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      -       -           -
LGA    H       4      -       -           -
LGA    H       5      -       -           -
LGA    H       6      -       -           -
LGA    H       7      -       -           -
LGA    H       8      -       -           -
LGA    S       9      -       -           -
LGA    L      10      -       -           -
LGA    N      11      Q      12          5.213
LGA    Q      12      I      13          3.353
LGA    -       -      N      14           -
LGA    I      13      I      15          1.725
LGA    N      14      E      16          1.467
LGA    I      15      I      17          2.048
LGA    E      16      A      18          2.022
LGA    I      17      Y      19          2.059
LGA    A      18      A      20          2.290
LGA    Y      19      F      21          0.902
LGA    A      20      P      22          0.582
LGA    F      21      -       -           -
LGA    P      22      -       -           -
LGA    E      23      -       -           -
LGA    R      24      -       -           -
LGA    Y      25      E      23          2.610
LGA    Y      26      R      24          2.234
LGA    L      27      Y      25          2.850
LGA    K      28      Y      26          1.832
LGA    S      29      L      27          2.891
LGA    -       -      K      28           -
LGA    F      30      S      29          4.995
LGA    Q      31      F      30          2.750
LGA    V      32      Q      31          5.956
LGA    D      33      V      32          2.083
LGA    -       -      D      33           -
LGA    E      34      E      34          2.440
LGA    G      35      G      35          1.475
LGA    I      36      I      36          1.239
LGA    T      37      T      37          2.516
LGA    V      38      V      38          2.604
LGA    Q      39      Q      39          3.082
LGA    T      40      T      40          2.701
LGA    A      41      A      41          1.474
LGA    I      42      I      42          1.673
LGA    T      43      T      43          2.977
LGA    Q      44      Q      44          2.986
LGA    S      45      S      45          2.030
LGA    G      46      G      46          1.567
LGA    I      47      I      47          1.047
LGA    L      48      L      48          0.816
LGA    S      49      S      49          1.120
LGA    Q      50      Q      50          2.318
LGA    F      51      F      51          2.593
LGA    P      52      P      52          2.403
LGA    E      53      E      53          3.646
LGA    I      54      I      54          2.538
LGA    -       -      D      55           -
LGA    D      55      L      56          0.876
LGA    L      56      S      57           #
LGA    S      57      T      58           -
LGA    T      58      N      59           #
LGA    N      59      -       -           -
LGA    K      60      K      60          2.055
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      I      61          3.210
LGA    L      74      G      62          1.531
LGA    K      75      I      63          0.298
LGA    E      76      F      64          3.899
LGA    G      77      S      65           #
LGA    D      78      R      66           -
LGA    R      79      P      67           -
LGA    I      80      I      68           -
LGA    E      81      K      69           -
LGA    I      82      L      70           -
LGA    Y      83      T      71           -
LGA    R      84      D      72           -
LGA    P      85      V      73           -
LGA    L      86      L      74           -
LGA    L      87      K      75           -
LGA    A      88      E      76           -
LGA    D      89      G      77           -
LGA    P      90      D      78           -
LGA    K      91      R      79           -
LGA    E      92      I      80           -
LGA    I      93      E      81           -
LGA    R      94      I      82           -
LGA    R      95      Y      83           -
LGA    E      96      R      84           -
LGA    G      97      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     46    2.59    54.35     39.300     1.709

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.265014 * X  +   0.884892 * Y  +  -0.383057 * Z  +  28.282747
  Y_new =   0.799001 * X  +   0.020859 * Y  +   0.600967 * Z  +  21.382639
  Z_new =   0.539781 * X  +  -0.465328 * Y  +  -0.701502 * Z  +   5.868902 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.555903    0.585690  [ DEG:  -146.4424     33.5575 ]
  Theta =  -0.570177   -2.571415  [ DEG:   -32.6688   -147.3312 ]
  Phi   =   1.250533   -1.891060  [ DEG:    71.6502   -108.3498 ]
 
# 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: T0363TS599_3                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS599_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   46   2.59   54.35  39.300
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS599_3
PFRMAT TS                                                                       
TARGET T0363                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      28.744   9.899  18.414  1.00  0.00              
ATOM      2  CA  ALA     2      25.522   8.599  17.231  1.00  0.00              
ATOM      3  CA  HIS     3      22.281   7.198  19.519  1.00  0.00              
ATOM      4  CA  HIS     4      19.149   5.983  22.053  1.00  0.00              
ATOM      5  CA  HIS     5      15.072   7.012  21.933  1.00  0.00              
ATOM      6  CA  HIS     6      12.484   8.617  19.576  1.00  0.00              
ATOM      7  CA  HIS     7      13.580  10.866  17.029  1.00  0.00              
ATOM      8  CA  HIS     8      11.779  13.088  14.586  1.00  0.00              
ATOM      9  CA  SER     9      13.794  11.823  11.515  1.00  0.00              
ATOM     10  CA  LEU    10      16.829   9.912  12.771  1.00  0.00              
ATOM     11  CA  ASN    11      16.344   6.884  10.382  1.00  0.00              
ATOM     12  CA  GLN    12      16.996   9.141   7.459  1.00  0.00              
ATOM     13  CA  ILE    13      19.321  12.052   7.948  1.00  0.00              
ATOM     14  CA  ASN    14      20.152  14.157   5.018  1.00  0.00              
ATOM     15  CA  ILE    15      23.102  16.479   4.966  1.00  0.00              
ATOM     16  CA  GLU    16      23.611  18.810   2.065  1.00  0.00              
ATOM     17  CA  ILE    17      26.794  20.474   1.406  1.00  0.00              
ATOM     18  CA  ALA    18      27.221  23.070  -1.279  1.00  0.00              
ATOM     19  CA  TYR    19      30.575  24.241  -2.342  1.00  0.00              
ATOM     20  CA  ALA    20      31.060  27.297  -4.271  1.00  0.00              
ATOM     21  CA  PHE    21      34.372  27.989  -5.843  1.00  0.00              
ATOM     22  CA  PRO    22      34.795  31.007  -8.004  1.00  0.00              
ATOM     23  CA  GLU    23      31.928  29.917 -10.288  1.00  0.00              
ATOM     24  CA  ARG    24      32.017  26.154 -10.107  1.00  0.00              
ATOM     25  CA  TYR    25      29.351  24.627  -8.129  1.00  0.00              
ATOM     26  CA  TYR    26      29.975  21.528  -6.341  1.00  0.00              
ATOM     27  CA  LEU    27      27.113  19.711  -4.716  1.00  0.00              
ATOM     28  CA  LYS    28      27.743  17.247  -2.011  1.00  0.00              
ATOM     29  CA  SER    29      24.978  15.217  -0.646  1.00  0.00              
ATOM     30  CA  PHE    30      25.494  13.230   2.489  1.00  0.00              
ATOM     31  CA  GLN    31      23.104  10.557   3.582  1.00  0.00              
ATOM     32  CA  VAL    32      23.313   9.312   7.104  1.00  0.00              
ATOM     33  CA  ASP    33      21.581   6.126   8.168  1.00  0.00              
ATOM     34  CA  GLU    34      20.218   5.970  11.643  1.00  0.00              
ATOM     35  CA  GLY    35      22.727   4.870  14.179  1.00  0.00              
ATOM     36  CA  ILE    36      25.739   5.820  12.160  1.00  0.00              
ATOM     37  CA  THR    37      28.558   7.956  13.431  1.00  0.00              
ATOM     38  CA  VAL    38      29.325  11.157  11.597  1.00  0.00              
ATOM     39  CA  GLN    39      32.739   9.800  10.603  1.00  0.00              
ATOM     40  CA  THR    40      31.231   6.790   8.926  1.00  0.00              
ATOM     41  CA  ALA    41      28.509   8.828   7.125  1.00  0.00              
ATOM     42  CA  ILE    42      30.941  11.370   5.927  1.00  0.00              
ATOM     43  CA  THR    43      33.321   8.794   4.546  1.00  0.00              
ATOM     44  CA  GLN    44      30.703   6.918   2.684  1.00  0.00              
ATOM     45  CA  SER    45      29.387  10.057   1.073  1.00  0.00              
ATOM     46  CA  GLY    46      32.824  11.302  -0.037  1.00  0.00              
ATOM     47  CA  ILE    47      32.544  14.470   2.008  1.00  0.00              
ATOM     48  CA  LEU    48      35.993  14.132   3.678  1.00  0.00              
ATOM     49  CA  SER    49      37.673  13.546   0.376  1.00  0.00              
ATOM     50  CA  GLN    50      36.079  16.727  -1.011  1.00  0.00              
ATOM     51  CA  PHE    51      36.513  18.979   2.009  1.00  0.00              
ATOM     52  CA  PRO    52      39.740  17.943   3.765  1.00  0.00              
ATOM     53  CA  GLU    53      39.793  20.620   6.439  1.00  0.00              
ATOM     54  CA  ILE    54      36.246  20.026   7.573  1.00  0.00              
ATOM     55  CA  ASP    55      35.709  18.051  10.721  1.00  0.00              
ATOM     56  CA  LEU    56      32.720  15.735  10.167  1.00  0.00              
ATOM     57  CA  SER    57      31.625  15.162  13.760  1.00  0.00              
ATOM     58  CA  THR    58      31.495  18.883  14.630  1.00  0.00              
ATOM     59  CA  ASN    59      29.954  19.872  11.367  1.00  0.00              
ATOM     60  CA  LYS    60      31.226  23.278  10.390  1.00  0.00              
ATOM     61  CA  ILE    61      28.939  25.164   8.051  1.00  0.00              
ATOM     62  CA  GLY    62      30.402  28.173   6.275  1.00  0.00              
ATOM     63  CA  ILE    63      28.172  30.727   4.609  1.00  0.00              
ATOM     64  CA  PHE    64      29.810  33.441   2.470  1.00  0.00              
ATOM     65  CA  SER    65      27.987  36.792   1.798  1.00  0.00              
ATOM     66  CA  ARG    66      26.939  37.479   5.425  1.00  0.00              
ATOM     67  CA  PRO    67      30.135  36.332   7.029  1.00  0.00              
ATOM     68  CA  ILE    68      29.387  33.079   8.720  1.00  0.00              
ATOM     69  CA  LYS    69      31.598  31.899  11.617  1.00  0.00              
ATOM     70  CA  LEU    70      33.417  28.568  11.264  1.00  0.00              
ATOM     71  CA  THR    71      31.841  27.060  14.338  1.00  0.00              
ATOM     72  CA  ASP    72      28.274  27.219  12.913  1.00  0.00              
ATOM     73  CA  VAL    73      26.826  23.785  13.562  1.00  0.00              
ATOM     74  CA  LEU    74      25.152  21.701  10.977  1.00  0.00              
ATOM     75  CA  LYS    75      21.802  20.063  11.869  1.00  0.00              
ATOM     76  CA  GLU    76      20.119  17.103  10.098  1.00  0.00              
ATOM     77  CA  GLY    77      18.466  18.275   6.881  1.00  0.00              
ATOM     78  CA  ASP    78      20.502  21.267   6.461  1.00  0.00              
ATOM     79  CA  ARG    79      22.076  22.916   3.616  1.00  0.00              
ATOM     80  CA  ILE    80      25.592  24.242   4.241  1.00  0.00              
ATOM     81  CA  GLU    81      27.157  26.717   1.894  1.00  0.00              
ATOM     82  CA  ILE    82      30.796  27.010   1.602  1.00  0.00              
ATOM     83  CA  TYR    83      32.175  29.888  -0.354  1.00  0.00              
ATOM     84  CA  ARG    84      35.587  29.732  -1.567  1.00  0.00              
ATOM     85  CA  PRO    85      35.855  32.383  -4.185  1.00  0.00              
ATOM     86  CA  LEU    86      33.756  34.892  -2.267  1.00  0.00              
ATOM     87  CA  LEU    87      35.418  34.645   1.112  1.00  0.00              
ATOM     88  CA  ALA    88      33.521  37.166   3.304  1.00  0.00              
ATOM     89  CA  ASP    89      35.617  38.956   5.878  1.00  0.00              
ATOM     90  CA  PRO    90      33.606  41.751   7.548  1.00  0.00              
ATOM     91  CA  LYS    91      35.892  44.546   6.408  1.00  0.00              
ATOM     92  CA  GLU    92      35.821  43.290   2.828  1.00  0.00              
ATOM     93  CA  ILE    93      32.087  42.961   2.573  1.00  0.00              
ATOM     94  CA  ARG    94      31.424  46.493   3.923  1.00  0.00              
ATOM     95  CA  ARG    95      34.219  47.872   1.104  1.00  0.00              
ATOM     96  CA  GLU    96      31.520  47.780   3.481  1.00  0.00              
ATOM     97  CA  GLY    97      27.833  47.473   2.824  1.00  0.00              
TER                                                                             
END
