
#######################################################
#                                                     #
#                        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 T0347TS599_3-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS599_3-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P       7      P       7           -
LGA    R       8      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    L       9      A      13           #
LGA    S      10      I      14           -
LGA    R      11      D      15           -
LGA    I      12      K      16           -
LGA    A      13      L      17           -
LGA    I      14      -       -           -
LGA    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      R      18           #
LGA    -       -      P      19           -
LGA    G      25      T      20          3.191
LGA    F      26      Q      21          2.535
LGA    R      27      I      22           #
LGA    E      28      A      23           -
LGA    V      29      -       -           -
LGA    E      30      V      24          2.504
LGA    L      31      G      25          3.962
LGA    K      32      -       -           -
LGA    R      33      F      26           #
LGA    K      34      R      27          4.459
LGA    -       -      E      28           -
LGA    E      35      V      29          3.530
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    W      36      R      33          2.838
LGA    R      37      K      34          5.009
LGA    H      51      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      H      51           -
LGA    I      52      I      52          3.850
LGA    V      53      V      53          2.342
LGA    P      54      P      54          1.946
LGA    V      55      V      55          2.463
LGA    V      56      V      56          2.169
LGA    A      57      A      57          2.545
LGA    G      58      G      58          2.982
LGA    P      59      P      59          5.690
LGA    K      60      K      60          1.960
LGA    D      61      D      61          1.524
LGA    R      62      R      62          2.913
LGA    A      63      A      63          3.055
LGA    Y      64      Y      64          1.668
LGA    L      65      L      65          2.129
LGA    I      66      I      66          1.181
LGA    D      67      D      67          0.917
LGA    H      68      H      68           #
LGA    H      69      H      69           -
LGA    H      70      H      70           -
LGA    L      71      L      71           -
LGA    V      72      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           -
LGA    L      73      V      88           #
LGA    A      74      -       -           -
LGA    L      75      -       -           -
LGA    S      76      A      89           #
LGA    K      77      K      90           -
LGA    E      78      F      91           -
LGA    G      79      S      92           -
LGA    V      80      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    E      81      S     101          2.033
LGA    H      82      V     102           #
LGA    -       -      M     103           -
LGA    V      83      D     104          3.203
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    L      84      L     108           #
LGA    T      85      -       -           -
LGA    S      86      -       -           -
LGA    E      87      -       -           -
LGA    V      88      -       -           -
LGA    A      89      -       -           -
LGA    K      90      -       -           -
LGA    F      91      -       -           -
LGA    S      92      -       -           -
LGA    H      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      -       -           -
LGA    K      96      -       -           -
LGA    D      97      -       -           -
LGA    E      98      -       -           -
LGA    F      99      -       -           -
LGA    W     100      -       -           -
LGA    S     101      -       -           -
LGA    V     102      -       -           -
LGA    M     103      -       -           -
LGA    D     104      -       -           -
LGA    H     105      -       -           -
LGA    R     106      -       -           -
LGA    N     107      -       -           -
LGA    L     108      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     26    3.00    61.54     21.172     0.838

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.610883 * X  +   0.743310 * Y  +   0.272601 * Z  +  13.519297
  Y_new =   0.047544 * X  +  -0.378135 * Y  +   0.924529 * Z  +  49.835831
  Z_new =   0.790292 * X  +  -0.551819 * Y  +  -0.266336 * Z  +   2.809469 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.020469    1.121124  [ DEG:  -115.7643     64.2357 ]
  Theta =  -0.911285   -2.230308  [ DEG:   -52.2128   -127.7872 ]
  Phi   =   0.077672   -3.063921  [ DEG:     4.4503   -175.5497 ]
 
# 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: T0347TS599_3-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS599_3-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   26   3.00   61.54  21.172
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS599_3-D1
PFRMAT TS                                                                       
TARGET T0347                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      7  CA  PRO     7       7.925  34.085 -13.813  1.00  0.00              
ATOM      8  CA  ARG     8       9.303  32.954 -10.613  1.00  0.00              
ATOM      9  CA  LEU     9       6.893  30.777  -8.976  1.00  0.00              
ATOM     10  CA  SER    10       7.911  28.374  -6.293  1.00  0.00              
ATOM     11  CA  ARG    11       5.580  25.654  -5.223  1.00  0.00              
ATOM     12  CA  ILE    12       5.710  24.499  -1.634  1.00  0.00              
ATOM     13  CA  ALA    13       3.319  21.990  -0.192  1.00  0.00              
ATOM     14  CA  ILE    14       1.145  23.013   2.733  1.00  0.00              
ATOM     15  CA  ASP    15       2.332  20.426   5.255  1.00  0.00              
ATOM     16  CA  LYS    16       5.893  21.476   4.719  1.00  0.00              
ATOM     17  CA  LEU    17       5.150  25.144   5.142  1.00  0.00              
ATOM     18  CA  ARG    18       3.040  25.383   8.268  1.00  0.00              
ATOM     19  CA  PRO    19      -0.344  26.950   8.618  1.00  0.00              
ATOM     20  CA  THR    20       0.486  30.488   9.723  1.00  0.00              
ATOM     21  CA  GLN    21       2.719  31.256   6.752  1.00  0.00              
ATOM     22  CA  ILE    22       1.826  34.221   4.548  1.00  0.00              
ATOM     23  CA  ALA    23       4.458  36.731   3.314  1.00  0.00              
ATOM     24  CA  VAL    24       3.496  39.982   1.675  1.00  0.00              
ATOM     25  CA  GLY    25       6.325  42.134   0.259  1.00  0.00              
ATOM     26  CA  PHE    26       5.413  45.759  -0.121  1.00  0.00              
ATOM     27  CA  ARG    27       8.539  47.869  -0.444  1.00  0.00              
ATOM     28  CA  GLU    28      10.704  45.939  -2.621  1.00  0.00              
ATOM     29  CA  VAL    29       8.052  45.058  -5.097  1.00  0.00              
ATOM     30  CA  GLU    30       6.796  48.607  -5.470  1.00  0.00              
ATOM     31  CA  LEU    31      10.274  49.980  -6.093  1.00  0.00              
ATOM     32  CA  LYS    32      11.149  47.391  -8.696  1.00  0.00              
ATOM     33  CA  ARG    33       7.863  48.018 -10.603  1.00  0.00              
ATOM     34  CA  LYS    34       8.486  51.764 -10.661  1.00  0.00              
ATOM     35  CA  GLU    35      11.989  51.254 -12.106  1.00  0.00              
ATOM     36  CA  TRP    36      10.694  48.896 -14.712  1.00  0.00              
ATOM     37  CA  ARG    37       7.911  51.112 -15.892  1.00  0.00              
ATOM     51  CA  HIS    51      16.217  40.209  -9.615  1.00  0.00              
ATOM     52  CA  ILE    52      14.202  37.087 -10.001  1.00  0.00              
ATOM     53  CA  VAL    53      11.019  37.548  -8.034  1.00  0.00              
ATOM     54  CA  PRO    54       9.939  34.958  -5.682  1.00  0.00              
ATOM     55  CA  VAL    55       6.363  33.866  -5.456  1.00  0.00              
ATOM     56  CA  VAL    56       5.533  31.125  -3.102  1.00  0.00              
ATOM     57  CA  ALA    57       2.500  29.026  -3.643  1.00  0.00              
ATOM     58  CA  GLY    58       1.381  26.773  -0.804  1.00  0.00              
ATOM     59  CA  PRO    59      -0.596  23.540  -1.149  1.00  0.00              
ATOM     60  CA  LYS    60      -3.835  25.263  -0.327  1.00  0.00              
ATOM     61  CA  ASP    61      -3.595  27.744  -3.150  1.00  0.00              
ATOM     62  CA  ARG    62      -2.498  30.769  -1.071  1.00  0.00              
ATOM     63  CA  ALA    63      -0.017  33.019  -2.802  1.00  0.00              
ATOM     64  CA  TYR    64       2.853  34.515  -0.847  1.00  0.00              
ATOM     65  CA  LEU    65       4.969  37.259  -2.247  1.00  0.00              
ATOM     66  CA  ILE    66       8.418  37.675  -0.891  1.00  0.00              
ATOM     67  CA  ASP    67      10.903  39.894  -2.663  1.00  0.00              
ATOM     68  CA  HIS    68      13.185  41.222   0.009  1.00  0.00              
ATOM     69  CA  HIS    69      15.375  38.103   0.436  1.00  0.00              
ATOM     70  CA  HIS    70      16.898  38.911   3.740  1.00  0.00              
ATOM     71  CA  LEU    71      13.753  40.029   5.425  1.00  0.00              
ATOM     72  CA  VAL    72      11.511  37.167   4.534  1.00  0.00              
ATOM     73  CA  LEU    73      13.942  34.459   5.371  1.00  0.00              
ATOM     74  CA  ALA    74      14.753  35.922   8.768  1.00  0.00              
ATOM     75  CA  LEU    75      11.130  36.322   9.674  1.00  0.00              
ATOM     76  CA  SER    76      10.150  32.774   8.616  1.00  0.00              
ATOM     77  CA  LYS    77      13.019  31.284  10.563  1.00  0.00              
ATOM     78  CA  GLU    78      11.937  33.235  13.619  1.00  0.00              
ATOM     79  CA  GLY    79       8.466  31.571  13.545  1.00  0.00              
ATOM     80  CA  VAL    80       6.650  34.542  12.173  1.00  0.00              
ATOM     81  CA  GLU    81       3.616  33.373  10.288  1.00  0.00              
ATOM     82  CA  HIS    82       2.101  36.554   8.972  1.00  0.00              
ATOM     83  CA  VAL    83       4.281  39.271   7.704  1.00  0.00              
ATOM     84  CA  LEU    84       2.937  42.456   6.214  1.00  0.00              
ATOM     85  CA  THR    85       5.481  44.930   5.011  1.00  0.00              
ATOM     86  CA  SER    86       4.573  48.620   4.972  1.00  0.00              
ATOM     87  CA  GLU    87       6.686  51.040   2.946  1.00  0.00              
ATOM     88  CA  VAL    88       7.222  54.567   4.094  1.00  0.00              
ATOM     89  CA  ALA    89       5.989  56.600   1.227  1.00  0.00              
ATOM     90  CA  LYS    90       2.884  54.632   1.646  1.00  0.00              
ATOM     91  CA  PHE    91       2.500  55.129   5.367  1.00  0.00              
ATOM     92  CA  SER    92       2.984  58.892   5.024  1.00  0.00              
ATOM     93  CA  HIS    93       0.076  59.084   2.640  1.00  0.00              
ATOM     94  CA  LEU    94      -2.166  57.341   5.123  1.00  0.00              
ATOM     95  CA  GLY    95      -1.972  59.037   8.517  1.00  0.00              
ATOM     96  CA  LYS    96      -0.045  57.363  11.249  1.00  0.00              
ATOM     97  CA  ASP    97      -2.956  56.369  13.412  1.00  0.00              
ATOM     98  CA  GLU    98      -4.950  54.705  10.594  1.00  0.00              
ATOM     99  CA  PHE    99      -1.910  52.770   9.479  1.00  0.00              
ATOM    100  CA  TRP   100      -1.162  51.560  13.025  1.00  0.00              
ATOM    101  CA  SER   101      -4.586  50.373  13.571  1.00  0.00              
ATOM    102  CA  VAL   102      -4.649  48.430  10.353  1.00  0.00              
ATOM    103  CA  MET   103      -1.299  46.704  10.824  1.00  0.00              
ATOM    104  CA  ASP   104      -2.124  45.647  14.321  1.00  0.00              
ATOM    105  CA  HIS   105      -5.461  44.212  13.292  1.00  0.00              
ATOM    106  CA  ARG   106      -3.885  41.902  10.811  1.00  0.00              
ATOM    107  CA  ASN   107      -1.411  40.713  13.376  1.00  0.00              
ATOM    108  CA  LEU   108       1.854  41.572  11.885  1.00  0.00              
TER                                                                             
END
