
#######################################################
#                                                     #
#                        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  104 (  104),  selected  104 , name T0343TS599_4
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS599_4.T0343.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      T       2           -
LGA    T       2      -       -           -
LGA    W       3      W       3           #
LGA    R       4      R       4           #
LGA    E       5      E       5          2.550
LGA    I       6      I       6          2.574
LGA    -       -      L       7           -
LGA    -       -      R       8           -
LGA    L       7      K       9          2.315
LGA    R       8      E      10          5.022
LGA    K       9      -       -           -
LGA    E      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      G      11           #
LGA    D      14      F      12           -
LGA    L      15      L      13           -
LGA    G      16      D      14           -
LGA    E      17      L      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    -       -      I      19           -
LGA    -       -      V      20           -
LGA    -       -      E      21           -
LGA    F      18      L      22          2.728
LGA    I      19      V      23           #
LGA    -       -      Y      24           -
LGA    -       -      I      25           -
LGA    -       -      D      26           -
LGA    -       -      C      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      E      30           -
LGA    -       -      P      31           -
LGA    -       -      I      32           -
LGA    -       -      P      33           -
LGA    V      20      P      34          3.221
LGA    E      21      T      35          0.530
LGA    L      22      L      36          0.444
LGA    V      23      A      37          1.277
LGA    Y      24      I      38          0.199
LGA    I      25      Y      39          0.230
LGA    D      26      D      40          1.225
LGA    C      27      K      41          2.029
LGA    P      28      -       -           -
LGA    C      29      -       -           -
LGA    E      30      -       -           -
LGA    P      31      K      42           #
LGA    I      32      G      43          2.536
LGA    P      33      D      44          2.054
LGA    P      34      E      45          2.028
LGA    T      35      W      46          2.018
LGA    L      36      Y      47          1.271
LGA    A      37      K      48          0.939
LGA    I      38      V      49          1.103
LGA    Y      39      E      50          3.715
LGA    -       -      E      51           -
LGA    D      40      A      52          1.690
LGA    K      41      P      53          3.092
LGA    K      42      N      54          2.617
LGA    -       -      V      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      63           -
LGA    -       -      W      64           -
LGA    -       -      A      65           -
LGA    -       -      I      66           -
LGA    G      43      E      67           #
LGA    D      44      V      68           -
LGA    E      45      L      69           -
LGA    -       -      E      70           -
LGA    -       -      R      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      D      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      N      77           -
LGA    -       -      V      78           -
LGA    -       -      K      79           -
LGA    W      46      L      80           #
LGA    Y      47      V      81          5.406
LGA    K      48      S      82          3.724
LGA    V      49      L      83          2.596
LGA    E      50      D      84          0.780
LGA    E      51      G      85          3.285
LGA    A      52      -       -           -
LGA    P      53      -       -           -
LGA    N      54      -       -           -
LGA    V      55      -       -           -
LGA    Q      56      -       -           -
LGA    N      57      P      86          3.434
LGA    Y      58      A      87          3.005
LGA    R      59      -       -           -
LGA    E      60      -       -           -
LGA    A      61      P      88          1.679
LGA    V      62      -       -           -
LGA    E      63      P      89          3.428
LGA    W      64      K      90          2.644
LGA    A      65      V      91          2.318
LGA    I      66      M      92          2.178
LGA    E      67      K      93          0.585
LGA    V      68      R      94          0.621
LGA    L      69      L      95          1.739
LGA    E      70      S      96          3.168
LGA    R      71      L      97          3.228
LGA    I      72      A      98          2.843
LGA    R      73      L      99          4.658
LGA    -       -      Q     100           -
LGA    D      74      K     101          5.340
LGA    G      75      -       -           -
LGA    E      76      -       -           -
LGA    N      77      -       -           -
LGA    V      78      -       -           -
LGA    K      79      -       -           -
LGA    L      80      -       -           -
LGA    V      81      -       -           -
LGA    S      82      -       -           -
LGA    L      83      -       -           -
LGA    D      84      -       -           -
LGA    G      85      -       -           -
LGA    P      86      -       -           -
LGA    A      87      -       -           -
LGA    P      88      -       -           -
LGA    P      89      -       -           -
LGA    K      90      -       -           -
LGA    V      91      -       -           -
LGA    M      92      -       -           -
LGA    K      93      -       -           -
LGA    R      94      -       -           -
LGA    L      95      -       -           -
LGA    S      96      -       -           -
LGA    L      97      -       -           -
LGA    A      98      -       -           -
LGA    L      99      -       -           -
LGA    Q     100      -       -           -
LGA    K     101      -       -           -
LGA    L     102      -       -           -
LGA    T     103      -       -           -
LGA    E     104      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104   94    5.0     44    2.70    11.36     30.706     1.570

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.686081 * X  +  -0.168674 * Y  +   0.707701 * Z  +  22.813314
  Y_new =  -0.726916 * X  +  -0.198707 * Y  +   0.657349 * Z  +  15.808480
  Z_new =   0.029747 * X  +  -0.965435 * Y  +  -0.258941 * Z  +  11.032629 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.832841    1.308752  [ DEG:  -105.0141     74.9859 ]
  Theta =  -0.029752   -3.111841  [ DEG:    -1.7046   -178.2953 ]
  Phi   =  -0.814290    2.327303  [ DEG:   -46.6554    133.3446 ]
 
# 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: T0343TS599_4                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS599_4.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  104   94   5.0   44   2.70   11.36  30.706
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS599_4
PFRMAT TS                                                                       
TARGET T0343                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      25.135  30.415  21.625  1.00  0.00              
ATOM      2  CA  THR     2      24.022  27.013  21.968  1.00  0.00              
ATOM      3  CA  TRP     3      24.439  23.509  20.992  1.00  0.00              
ATOM      4  CA  ARG     4      25.440  26.966  22.630  1.00  0.00              
ATOM      5  CA  GLU     5      27.874  25.154  24.845  1.00  0.00              
ATOM      6  CA  ILE     6      29.364  23.354  21.905  1.00  0.00              
ATOM      7  CA  LEU     7      29.828  26.444  19.820  1.00  0.00              
ATOM      8  CA  ARG     8      31.513  28.296  22.740  1.00  0.00              
ATOM      9  CA  LYS     9      33.922  25.459  23.550  1.00  0.00              
ATOM     10  CA  GLU    10      34.986  25.160  19.955  1.00  0.00              
ATOM     11  CA  GLY    11      35.409  28.896  19.303  1.00  0.00              
ATOM     12  CA  PHE    12      32.472  28.976  16.903  1.00  0.00              
ATOM     13  CA  LEU    13      29.581  31.128  18.159  1.00  0.00              
ATOM     14  CA  ASP    14      26.385  31.277  16.083  1.00  0.00              
ATOM     15  CA  LEU    15      23.305  29.935  17.800  1.00  0.00              
ATOM     16  CA  GLY    16      20.635  31.391  15.550  1.00  0.00              
ATOM     17  CA  GLU    17      22.350  30.171  12.443  1.00  0.00              
ATOM     18  CA  PHE    18      22.876  26.620  13.736  1.00  0.00              
ATOM     19  CA  ILE    19      19.323  26.251  14.988  1.00  0.00              
ATOM     20  CA  VAL    20      17.677  27.728  11.852  1.00  0.00              
ATOM     21  CA  GLU    21      19.724  25.238   9.850  1.00  0.00              
ATOM     22  CA  LEU    22      20.088  21.913  11.296  1.00  0.00              
ATOM     23  CA  VAL    23      22.231  19.400   9.511  1.00  0.00              
ATOM     24  CA  TYR    24      22.050  15.746  10.466  1.00  0.00              
ATOM     25  CA  ILE    25      24.528  13.332   9.039  1.00  0.00              
ATOM     26  CA  ASP    26      23.792   9.750   9.281  1.00  0.00              
ATOM     27  CA  CYS    27      26.590   7.247   9.400  1.00  0.00              
ATOM     28  CA  PRO    28      25.915   3.522   9.511  1.00  0.00              
ATOM     29  CA  CYS    29      28.644   1.916   7.391  1.00  0.00              
ATOM     30  CA  GLU    30      28.006   0.349   4.052  1.00  0.00              
ATOM     31  CA  PRO    31      27.634   3.272   1.570  1.00  0.00              
ATOM     32  CA  ILE    32      26.815   5.966   4.057  1.00  0.00              
ATOM     33  CA  PRO    33      24.523   8.373   2.296  1.00  0.00              
ATOM     34  CA  PRO    34      21.949   9.672   4.698  1.00  0.00              
ATOM     35  CA  THR    35      21.907  13.302   4.882  1.00  0.00              
ATOM     36  CA  LEU    36      19.014  14.940   6.601  1.00  0.00              
ATOM     37  CA  ALA    37      18.527  18.662   6.424  1.00  0.00              
ATOM     38  CA  ILE    38      16.265  20.308   8.807  1.00  0.00              
ATOM     39  CA  TYR    39      15.114  23.807   8.197  1.00  0.00              
ATOM     40  CA  ASP    40      13.601  25.819  10.862  1.00  0.00              
ATOM     41  CA  LYS    41      11.215  28.410   9.943  1.00  0.00              
ATOM     42  CA  LYS    42      11.586  31.202  12.237  1.00  0.00              
ATOM     43  CA  GLY    43      11.812  28.898  15.310  1.00  0.00              
ATOM     44  CA  ASP    44       8.688  27.171  15.120  1.00  0.00              
ATOM     45  CA  GLU    45       8.217  25.384  12.076  1.00  0.00              
ATOM     46  CA  TRP    46      10.191  22.367  10.996  1.00  0.00              
ATOM     47  CA  TYR    47      10.814  21.698   7.374  1.00  0.00              
ATOM     48  CA  LYS    48      12.539  18.535   6.346  1.00  0.00              
ATOM     49  CA  VAL    49      14.634  18.507   3.373  1.00  0.00              
ATOM     50  CA  GLU    50      16.076  15.382   2.175  1.00  0.00              
ATOM     51  CA  GLU    51      17.671  16.133  -1.208  1.00  0.00              
ATOM     52  CA  ALA    52      15.060  14.738  -3.568  1.00  0.00              
ATOM     53  CA  PRO    53      11.848  16.119  -1.998  1.00  0.00              
ATOM     54  CA  ASN    54       8.895  13.868  -2.884  1.00  0.00              
ATOM     55  CA  VAL    55       6.446  14.410  -0.011  1.00  0.00              
ATOM     56  CA  GLN    56       5.835  10.745   0.881  1.00  0.00              
ATOM     57  CA  ASN    57       9.584  10.123   0.676  1.00  0.00              
ATOM     58  CA  TYR    58      10.357  13.034   3.046  1.00  0.00              
ATOM     59  CA  ARG    59       8.179  11.567   5.724  1.00  0.00              
ATOM     60  CA  GLU    60       9.950   8.200   5.296  1.00  0.00              
ATOM     61  CA  ALA    61      13.453   9.676   5.383  1.00  0.00              
ATOM     62  CA  VAL    62      12.796  11.676   8.537  1.00  0.00              
ATOM     63  CA  GLU    63      11.364   8.617  10.315  1.00  0.00              
ATOM     64  CA  TRP    64      14.282   6.307   9.463  1.00  0.00              
ATOM     65  CA  ALA    65      16.868   8.908  10.578  1.00  0.00              
ATOM     66  CA  ILE    66      15.009   9.569  13.824  1.00  0.00              
ATOM     67  CA  GLU    67      14.760   5.829  14.627  1.00  0.00              
ATOM     68  CA  VAL    68      18.494   5.540  13.981  1.00  0.00              
ATOM     69  CA  LEU    69      19.172   8.433  16.342  1.00  0.00              
ATOM     70  CA  GLU    70      17.009   6.675  18.954  1.00  0.00              
ATOM     71  CA  ARG    71      19.099   3.514  18.458  1.00  0.00              
ATOM     72  CA  ILE    72      22.318   5.545  18.898  1.00  0.00              
ATOM     73  CA  ARG    73      21.032   7.007  22.149  1.00  0.00              
ATOM     74  CA  ASP    74      20.204   3.485  23.368  1.00  0.00              
ATOM     75  CA  GLY    75      23.592   1.888  22.543  1.00  0.00              
ATOM     76  CA  GLU    76      22.813  -0.027  19.342  1.00  0.00              
ATOM     77  CA  ASN    77      25.579   0.948  16.896  1.00  0.00              
ATOM     78  CA  VAL    78      24.309   3.682  14.516  1.00  0.00              
ATOM     79  CA  LYS    79      26.212   6.895  14.321  1.00  0.00              
ATOM     80  CA  LEU    80      24.469  10.212  13.949  1.00  0.00              
ATOM     81  CA  VAL    81      26.644  13.180  12.944  1.00  0.00              
ATOM     82  CA  SER    82      25.371  16.722  13.254  1.00  0.00              
ATOM     83  CA  LEU    83      26.593  19.478  11.008  1.00  0.00              
ATOM     84  CA  ASP    84      24.798  22.847  10.740  1.00  0.00              
ATOM     85  CA  GLY    85      27.717  25.011   9.524  1.00  0.00              
ATOM     86  CA  PRO    86      30.846  23.089   8.837  1.00  0.00              
ATOM     87  CA  ALA    87      33.612  23.346  11.343  1.00  0.00              
ATOM     88  CA  PRO    88      34.010  21.647  14.572  1.00  0.00              
ATOM     89  CA  PRO    89      37.102  19.481  14.390  1.00  0.00              
ATOM     90  CA  LYS    90      35.552  16.294  15.875  1.00  0.00              
ATOM     91  CA  VAL    91      32.642  16.444  13.485  1.00  0.00              
ATOM     92  CA  MET    92      34.890  16.952  10.401  1.00  0.00              
ATOM     93  CA  LYS    93      37.039  14.047  11.471  1.00  0.00              
ATOM     94  CA  ARG    94      34.026  11.804  11.983  1.00  0.00              
ATOM     95  CA  LEU    95      32.712  12.763   8.508  1.00  0.00              
ATOM     96  CA  SER    96      36.034  12.048   6.934  1.00  0.00              
ATOM     97  CA  LEU    97      36.229   8.636   8.602  1.00  0.00              
ATOM     98  CA  ALA    98      32.750   7.634   7.567  1.00  0.00              
ATOM     99  CA  LEU    99      33.428   8.616   4.004  1.00  0.00              
ATOM    100  CA  GLN   100      36.652   6.699   3.847  1.00  0.00              
ATOM    101  CA  LYS   101      35.005   3.524   5.247  1.00  0.00              
ATOM    102  CA  LEU   102      32.247   3.721   2.883  1.00  0.00              
ATOM    103  CA  THR   103      34.974   4.462  -0.238  1.00  0.00              
ATOM    104  CA  GLU   104      35.827   8.093  -2.181  1.00  0.00              
TER                                                                             
END
