
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS599_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      -       -           -
LGA    R       8      -       -           -
LGA    L       9      -       -           -
LGA    S      10      -       -           -
LGA    R      11      -       -           -
LGA    I      12      -       -           -
LGA    A      13      -       -           -
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      -       -           -
LGA    G      25      -       -           -
LGA    F      26      -       -           -
LGA    R      27      -       -           -
LGA    E      28      -       -           -
LGA    V      29      -       -           -
LGA    E      30      -       -           -
LGA    L      31      -       -           -
LGA    K      32      -       -           -
LGA    R      33      -       -           -
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      P       7          4.081
LGA    L      73      R       8          2.413
LGA    A      74      L       9          1.913
LGA    L      75      S      10          3.903
LGA    S      76      -       -           -
LGA    K      77      -       -           -
LGA    E      78      R      11           #
LGA    -       -      I      12           -
LGA    -       -      A      13           -
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           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    G      79      H      51          3.035
LGA    V      80      I      52          1.193
LGA    E      81      V      53          1.919
LGA    H      82      P      54          1.304
LGA    V      83      V      55          2.759
LGA    L      84      V      56          2.908
LGA    T      85      A      57          1.739
LGA    S      86      G      58          3.016
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    -       -      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    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    E      87      F      91          4.277
LGA    V      88      S      92          3.836
LGA    A      89      H      93          2.838
LGA    K      90      L      94          2.649
LGA    F      91      G      95          3.103
LGA    S      92      -       -           -
LGA    H      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      -       -           -
LGA    K      96      K      96          1.603
LGA    D      97      D      97          2.123
LGA    E      98      E      98          2.743
LGA    F      99      F      99          2.164
LGA    W     100      W     100          1.012
LGA    S     101      S     101          1.970
LGA    V     102      V     102          2.498
LGA    M     103      M     103          1.865
LGA    D     104      D     104          1.370
LGA    H     105      H     105          2.487
LGA    R     106      R     106          2.385
LGA    N     107      N     107          1.456
LGA    L     108      L     108          1.408

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     30    2.55    46.67     23.651     1.132

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.776419 * X  +  -0.532213 * Y  +   0.337525 * Z  +   0.268110
  Y_new =  -0.630113 * X  +  -0.665342 * Y  +   0.400347 * Z  +  31.990269
  Z_new =   0.011500 * X  +  -0.523515 * Y  +  -0.851939 * Z  +  -7.447102 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.590580    0.551012  [ DEG:  -148.4293     31.5707 ]
  Theta =  -0.011500   -3.130093  [ DEG:    -0.6589   -179.3411 ]
  Phi   =  -0.681752    2.459841  [ DEG:   -39.0615    140.9385 ]
 
# 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_4-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS599_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   30   2.55   46.67  23.651
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS599_4-D1
PFRMAT TS                                                                       
TARGET T0347                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      7  CA  PRO     7       5.533  15.249 -17.568  1.00  0.00              
ATOM      8  CA  ARG     8       1.885  15.671 -16.829  1.00  0.00              
ATOM      9  CA  LEU     9       1.368  19.285 -15.890  1.00  0.00              
ATOM     10  CA  SER    10      -1.973  20.725 -16.432  1.00  0.00              
ATOM     11  CA  ARG    11      -2.426  24.407 -16.574  1.00  0.00              
ATOM     12  CA  ILE    12      -5.897  25.985 -16.105  1.00  0.00              
ATOM     13  CA  ALA    13      -6.730  29.140 -18.010  1.00  0.00              
ATOM     14  CA  ILE    14      -7.623  32.533 -16.952  1.00  0.00              
ATOM     15  CA  ASP    15     -10.696  32.932 -19.178  1.00  0.00              
ATOM     16  CA  LYS    16     -12.299  29.905 -17.565  1.00  0.00              
ATOM     17  CA  LEU    17     -12.009  31.512 -14.098  1.00  0.00              
ATOM     18  CA  ARG    18     -10.076  29.147 -11.909  1.00  0.00              
ATOM     19  CA  PRO    19      -8.517  30.837  -8.833  1.00  0.00              
ATOM     20  CA  THR    20      -4.907  29.912  -9.303  1.00  0.00              
ATOM     21  CA  GLN    21      -5.475  26.585 -10.983  1.00  0.00              
ATOM     22  CA  ILE    22      -2.443  24.360 -11.581  1.00  0.00              
ATOM     23  CA  ALA    23      -2.909  20.660 -11.964  1.00  0.00              
ATOM     24  CA  VAL    24      -0.020  18.305 -11.706  1.00  0.00              
ATOM     25  CA  GLY    25      -0.408  14.758 -12.843  1.00  0.00              
ATOM     26  CA  PHE    26       2.787  12.777 -12.938  1.00  0.00              
ATOM     27  CA  ARG    27       2.076   9.175 -11.874  1.00  0.00              
ATOM     28  CA  GLU    28       4.362   8.857  -8.840  1.00  0.00              
ATOM     29  CA  VAL    29       3.138  12.155  -7.424  1.00  0.00              
ATOM     30  CA  GLU    30      -0.377  11.028  -7.833  1.00  0.00              
ATOM     31  CA  LEU    31       0.263   7.749  -6.084  1.00  0.00              
ATOM     32  CA  LYS    32       1.960   9.446  -3.108  1.00  0.00              
ATOM     33  CA  ARG    33      -0.917  11.867  -2.758  1.00  0.00              
ATOM     34  CA  LYS    34      -3.449   9.024  -2.708  1.00  0.00              
ATOM     35  CA  GLU    35      -1.558   7.373   0.107  1.00  0.00              
ATOM     36  CA  TRP    36      -1.404  10.615   2.033  1.00  0.00              
ATOM     37  CA  ARG    37      -5.086  11.428   1.755  1.00  0.00              
ATOM     51  CA  HIS    51       9.199  13.151   0.267  1.00  0.00              
ATOM     52  CA  ILE    52       8.723  16.490  -1.140  1.00  0.00              
ATOM     53  CA  VAL    53       5.441  17.056  -2.841  1.00  0.00              
ATOM     54  CA  PRO    54       4.401  20.627  -2.922  1.00  0.00              
ATOM     55  CA  VAL    55       0.770  21.304  -2.561  1.00  0.00              
ATOM     56  CA  VAL    56      -0.677  24.500  -3.717  1.00  0.00              
ATOM     57  CA  ALA    57      -3.815  25.729  -2.130  1.00  0.00              
ATOM     58  CA  GLY    58      -5.608  28.557  -3.828  1.00  0.00              
ATOM     59  CA  PRO    59      -7.817  31.095  -2.114  1.00  0.00              
ATOM     60  CA  LYS    60     -10.900  29.161  -3.198  1.00  0.00              
ATOM     61  CA  ASP    61      -9.872  25.971  -1.493  1.00  0.00              
ATOM     62  CA  ARG    62      -8.835  24.137  -4.633  1.00  0.00              
ATOM     63  CA  ALA    63      -5.916  21.855  -4.405  1.00  0.00              
ATOM     64  CA  TYR    64      -3.139  21.958  -7.021  1.00  0.00              
ATOM     65  CA  LEU    65      -0.269  19.450  -6.907  1.00  0.00              
ATOM     66  CA  ILE    66       3.172  20.556  -8.004  1.00  0.00              
ATOM     67  CA  ASP    67       6.160  18.285  -7.479  1.00  0.00              
ATOM     68  CA  HIS    68       8.691  20.623  -5.847  1.00  0.00              
ATOM     69  CA  HIS    69      11.614  20.027  -8.084  1.00  0.00              
ATOM     70  CA  HIS    70       9.881  20.718 -11.360  1.00  0.00              
ATOM     71  CA  LEU    71       8.399  24.041 -10.342  1.00  0.00              
ATOM     72  CA  VAL    72      11.268  25.806  -8.674  1.00  0.00              
ATOM     73  CA  LEU    73      13.674  24.771 -11.392  1.00  0.00              
ATOM     74  CA  ALA    74      11.461  25.894 -14.215  1.00  0.00              
ATOM     75  CA  LEU    75      10.834  29.287 -12.721  1.00  0.00              
ATOM     76  CA  SER    76      14.532  29.831 -12.050  1.00  0.00              
ATOM     77  CA  LYS    77      15.525  28.862 -15.605  1.00  0.00              
ATOM     78  CA  GLU    78      13.020  31.201 -17.119  1.00  0.00              
ATOM     79  CA  GLY    79      14.332  34.060 -15.028  1.00  0.00              
ATOM     80  CA  VAL    80      11.536  34.074 -12.502  1.00  0.00              
ATOM     81  CA  GLU    81      13.008  35.027  -9.193  1.00  0.00              
ATOM     82  CA  HIS    82      10.437  33.933  -6.702  1.00  0.00              
ATOM     83  CA  VAL    83       8.124  30.933  -6.514  1.00  0.00              
ATOM     84  CA  LEU    84       5.410  30.740  -3.961  1.00  0.00              
ATOM     85  CA  THR    85       4.777  27.257  -2.537  1.00  0.00              
ATOM     86  CA  SER    86       1.664  26.613  -0.430  1.00  0.00              
ATOM     87  CA  GLU    87       1.354  23.525   1.485  1.00  0.00              
ATOM     88  CA  VAL    88      -2.064  22.337   2.286  1.00  0.00              
ATOM     89  CA  ALA    89      -1.720  20.368   5.424  1.00  0.00              
ATOM     90  CA  LYS    90       0.287  23.370   6.633  1.00  0.00              
ATOM     91  CA  PHE    91      -2.081  26.122   5.779  1.00  0.00              
ATOM     92  CA  SER    92      -5.320  24.509   6.778  1.00  0.00              
ATOM     93  CA  HIS    93      -3.806  23.209   9.968  1.00  0.00              
ATOM     94  CA  LEU    94      -2.689  26.584  11.144  1.00  0.00              
ATOM     95  CA  GLY    95      -5.347  29.129  10.648  1.00  0.00              
ATOM     96  CA  LYS    96      -4.574  31.850   8.207  1.00  0.00              
ATOM     97  CA  ASP    97      -3.960  34.533  10.800  1.00  0.00              
ATOM     98  CA  GLU    98      -1.542  32.317  12.722  1.00  0.00              
ATOM     99  CA  PHE    99       0.435  31.660   9.669  1.00  0.00              
ATOM    100  CA  TRP   100       0.902  35.177   8.952  1.00  0.00              
ATOM    101  CA  SER   101       1.857  35.933  12.509  1.00  0.00              
ATOM    102  CA  VAL   102       4.652  33.367  12.252  1.00  0.00              
ATOM    103  CA  MET   103       5.991  34.841   9.081  1.00  0.00              
ATOM    104  CA  ASP   104       5.945  38.353  10.496  1.00  0.00              
ATOM    105  CA  HIS   105       7.834  37.174  13.548  1.00  0.00              
ATOM    106  CA  ARG   106      10.475  35.552  11.315  1.00  0.00              
ATOM    107  CA  ASN   107      10.904  38.685   9.188  1.00  0.00              
ATOM    108  CA  LEU   108       9.341  37.575   5.935  1.00  0.00              
TER                                                                             
END
