
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS599_1.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      W       3           -
LGA    -       -      R       4           -
LGA    -       -      E       5           -
LGA    -       -      I       6           -
LGA    -       -      L       7           -
LGA    -       -      R       8           -
LGA    -       -      K       9           -
LGA    -       -      E      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      D      14           -
LGA    -       -      L      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    -       -      I      19           -
LGA    -       -      V      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      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    -       -      P      34           -
LGA    -       -      T      35           -
LGA    -       -      L      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Y      39           -
LGA    W       3      D      40          2.575
LGA    R       4      K      41          4.425
LGA    E       5      K      42          4.540
LGA    I       6      -       -           -
LGA    L       7      -       -           -
LGA    R       8      -       -           -
LGA    K       9      -       -           -
LGA    E      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    D      14      -       -           -
LGA    L      15      G      43          3.037
LGA    G      16      D      44          3.623
LGA    E      17      -       -           -
LGA    F      18      E      45          3.522
LGA    I      19      W      46          2.469
LGA    V      20      Y      47           #
LGA    E      21      -       -           -
LGA    L      22      K      48          1.424
LGA    V      23      V      49          1.460
LGA    Y      24      E      50          1.862
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    P      34      -       -           -
LGA    T      35      E      51           #
LGA    L      36      A      52          1.631
LGA    A      37      P      53           #
LGA    I      38      -       -           -
LGA    Y      39      -       -           -
LGA    D      40      -       -           -
LGA    K      41      -       -           -
LGA    K      42      -       -           -
LGA    G      43      -       -           -
LGA    D      44      -       -           -
LGA    E      45      -       -           -
LGA    W      46      -       -           -
LGA    Y      47      -       -           -
LGA    K      48      -       -           -
LGA    V      49      -       -           -
LGA    E      50      -       -           -
LGA    E      51      -       -           -
LGA    A      52      -       -           -
LGA    P      53      -       -           -
LGA    N      54      -       -           -
LGA    V      55      -       -           -
LGA    Q      56      -       -           -
LGA    N      57      -       -           -
LGA    Y      58      -       -           -
LGA    R      59      N      54          4.331
LGA    E      60      V      55          1.460
LGA    A      61      -       -           -
LGA    V      62      -       -           -
LGA    E      63      Q      56          4.313
LGA    W      64      E      63          3.008
LGA    A      65      W      64          3.887
LGA    I      66      A      65          3.713
LGA    E      67      I      66          1.011
LGA    V      68      E      67          3.338
LGA    L      69      V      68          2.144
LGA    E      70      L      69          2.145
LGA    -       -      E      70           -
LGA    -       -      R      71           -
LGA    R      71      I      72           #
LGA    I      72      R      73          1.569
LGA    R      73      D      74           #
LGA    D      74      -       -           -
LGA    G      75      -       -           -
LGA    E      76      -       -           -
LGA    N      77      -       -           -
LGA    V      78      -       -           -
LGA    K      79      G      75          3.071
LGA    L      80      E      76           #
LGA    -       -      N      77           -
LGA    -       -      V      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    V      81      V      81          3.142
LGA    S      82      S      82          2.039
LGA    L      83      L      83          1.625
LGA    D      84      D      84          1.094
LGA    G      85      G      85          1.209
LGA    P      86      P      86          1.840
LGA    A      87      A      87           #
LGA    P      88      -       -           -
LGA    P      89      -       -           -
LGA    K      90      -       -           -
LGA    V      91      -       -           -
LGA    M      92      P      88          1.528
LGA    K      93      P      89          1.864
LGA    R      94      K      90          1.418
LGA    L      95      V      91          1.478
LGA    S      96      M      92          0.912
LGA    L      97      K      93          0.685
LGA    A      98      R      94          2.277
LGA    L      99      L      95          2.352
LGA    Q     100      S      96          1.161
LGA    K     101      L      97          1.598
LGA    L     102      A      98          2.151
LGA    T     103      L      99          2.195
LGA    E     104      Q     100          2.088
LGA    -       -      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104   94    5.0     42    2.54    19.05     29.543     1.591

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.659898 * X  +  -0.746936 * Y  +   0.081370 * Z  +  16.428875
  Y_new =   0.637224 * X  +   0.613748 * Y  +   0.466109 * Z  +  18.169111
  Z_new =  -0.398094 * X  +  -0.255734 * Y  +   0.880977 * Z  +  10.615934 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.282520    2.859073  [ DEG:   -16.1872    163.8128 ]
  Theta =   0.409439    2.732154  [ DEG:    23.4591    156.5409 ]
  Phi   =   0.767920   -2.373673  [ DEG:    43.9986   -136.0014 ]
 
# 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_1                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS599_1.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   42   2.54   19.05  29.543
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS599_1
PFRMAT TS                                                                       
TARGET T0343                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      28.112   9.504   3.223  1.00  0.00              
ATOM      2  CA  THR     2      28.782   7.415   6.805  1.00  0.00              
ATOM      3  CA  TRP     3      25.287   7.061   7.510  1.00  0.00              
ATOM      4  CA  ARG     4      26.028   6.237   3.544  1.00  0.00              
ATOM      5  CA  GLU     5      27.431   2.889   4.750  1.00  0.00              
ATOM      6  CA  ILE     6      24.312   2.361   6.853  1.00  0.00              
ATOM      7  CA  LEU     7      21.952   3.175   3.937  1.00  0.00              
ATOM      8  CA  ARG     8      23.834   0.756   1.659  1.00  0.00              
ATOM      9  CA  LYS     9      23.663  -2.072   4.235  1.00  0.00              
ATOM     10  CA  GLU    10      19.911  -1.512   4.584  1.00  0.00              
ATOM     11  CA  GLY    11      19.168  -1.439   0.819  1.00  0.00              
ATOM     12  CA  PHE    12      18.051   2.174   0.736  1.00  0.00              
ATOM     13  CA  LEU    13      20.735   4.073  -1.111  1.00  0.00              
ATOM     14  CA  ASP    14      21.018   7.837  -0.650  1.00  0.00              
ATOM     15  CA  LEU    15      23.901   9.316   1.345  1.00  0.00              
ATOM     16  CA  GLY    16      24.882  12.131  -0.981  1.00  0.00              
ATOM     17  CA  GLU    17      21.335  13.382  -1.288  1.00  0.00              
ATOM     18  CA  PHE    18      20.662  13.436   2.478  1.00  0.00              
ATOM     19  CA  ILE    19      23.928  15.126   3.272  1.00  0.00              
ATOM     20  CA  VAL    20      23.749  17.838   0.613  1.00  0.00              
ATOM     21  CA  GLU    21      20.270  18.751   1.895  1.00  0.00              
ATOM     22  CA  LEU    22      19.861  18.720   5.530  1.00  0.00              
ATOM     23  CA  VAL    23      16.553  19.506   6.970  1.00  0.00              
ATOM     24  CA  TYR    24      16.230  20.231  10.635  1.00  0.00              
ATOM     25  CA  ILE    25      12.872  20.382  12.239  1.00  0.00              
ATOM     26  CA  ASP    26      12.522  22.113  15.491  1.00  0.00              
ATOM     27  CA  CYS    27       9.434  21.559  17.497  1.00  0.00              
ATOM     28  CA  PRO    28       9.415  22.998  21.047  1.00  0.00              
ATOM     29  CA  CYS    29       7.353  20.653  23.292  1.00  0.00              
ATOM     30  CA  GLU    30       4.577  23.015  24.505  1.00  0.00              
ATOM     31  CA  PRO    31       2.249  24.059  21.634  1.00  0.00              
ATOM     32  CA  ILE    32       4.588  23.649  18.730  1.00  0.00              
ATOM     33  CA  PRO    33       5.995  26.775  17.144  1.00  0.00              
ATOM     34  CA  PRO    34       6.826  25.623  13.650  1.00  0.00              
ATOM     35  CA  THR    35      10.570  26.226  13.170  1.00  0.00              
ATOM     36  CA  LEU    36      12.126  24.747  10.108  1.00  0.00              
ATOM     37  CA  ALA    37      15.822  25.025   9.545  1.00  0.00              
ATOM     38  CA  ILE    38      17.179  24.315   6.155  1.00  0.00              
ATOM     39  CA  TYR    39      20.879  23.746   5.755  1.00  0.00              
ATOM     40  CA  ASP    40      22.444  23.475   2.410  1.00  0.00              
ATOM     41  CA  LYS    41      25.693  21.628   2.353  1.00  0.00              
ATOM     42  CA  LYS    42      27.255  22.630  -0.832  1.00  0.00              
ATOM     43  CA  GLY    43      26.805  26.347  -0.364  1.00  0.00              
ATOM     44  CA  ASP    44      27.093  26.446   3.475  1.00  0.00              
ATOM     45  CA  GLU    45      23.897  28.398   3.748  1.00  0.00              
ATOM     46  CA  TRP    46      21.450  28.269   6.468  1.00  0.00              
ATOM     47  CA  TYR    47      17.847  28.891   5.594  1.00  0.00              
ATOM     48  CA  LYS    48      15.219  29.428   8.218  1.00  0.00              
ATOM     49  CA  VAL    49      11.719  28.779   7.402  1.00  0.00              
ATOM     50  CA  GLU    50       9.194  29.933   9.624  1.00  0.00              
ATOM     51  CA  GLU    51       5.884  30.165   7.854  1.00  0.00              
ATOM     52  CA  ALA    52       5.606  33.970   7.455  1.00  0.00              
ATOM     53  CA  PRO    53       9.101  34.804   6.198  1.00  0.00              
ATOM     54  CA  ASN    54      10.009  38.395   7.079  1.00  0.00              
ATOM     55  CA  VAL    55      13.813  38.351   6.972  1.00  0.00              
ATOM     56  CA  GLN    56      14.600  40.073  10.292  1.00  0.00              
ATOM     57  CA  ASN    57      12.069  37.848  12.102  1.00  0.00              
ATOM     58  CA  TYR    58      13.552  34.771  10.543  1.00  0.00              
ATOM     59  CA  ARG    59      17.093  35.327  11.673  1.00  0.00              
ATOM     60  CA  GLU    60      15.955  35.917  15.305  1.00  0.00              
ATOM     61  CA  ALA    61      13.717  32.906  15.354  1.00  0.00              
ATOM     62  CA  VAL    62      16.452  30.532  13.982  1.00  0.00              
ATOM     63  CA  GLU    63      18.774  31.346  16.899  1.00  0.00              
ATOM     64  CA  TRP    64      15.943  30.661  19.387  1.00  0.00              
ATOM     65  CA  ALA    65      15.196  27.402  17.578  1.00  0.00              
ATOM     66  CA  ILE    66      18.811  26.216  17.700  1.00  0.00              
ATOM     67  CA  GLU    67      18.898  26.612  21.466  1.00  0.00              
ATOM     68  CA  VAL    68      15.668  24.594  21.446  1.00  0.00              
ATOM     69  CA  LEU    69      17.390  21.893  19.346  1.00  0.00              
ATOM     70  CA  GLU    70      19.948  21.471  22.132  1.00  0.00              
ATOM     71  CA  ARG    71      17.063  21.040  24.581  1.00  0.00              
ATOM     72  CA  ILE    72      15.426  18.415  22.273  1.00  0.00              
ATOM     73  CA  ARG    73      18.691  16.486  22.059  1.00  0.00              
ATOM     74  CA  ASP    74      18.320  16.298  25.878  1.00  0.00              
ATOM     75  CA  GLY    75      14.870  14.842  25.863  1.00  0.00              
ATOM     76  CA  GLU    76      12.519  17.647  26.733  1.00  0.00              
ATOM     77  CA  ASN    77       9.543  17.290  24.395  1.00  0.00              
ATOM     78  CA  VAL    78      10.161  18.685  20.861  1.00  0.00              
ATOM     79  CA  LYS    79      10.371  16.448  17.867  1.00  0.00              
ATOM     80  CA  LEU    80      13.075  17.219  15.279  1.00  0.00              
ATOM     81  CA  VAL    81      12.870  15.650  11.870  1.00  0.00              
ATOM     82  CA  SER    82      15.578  16.020   9.290  1.00  0.00              
ATOM     83  CA  LEU    83      14.864  15.695   5.613  1.00  0.00              
ATOM     84  CA  ASP    84      17.191  15.846   2.803  1.00  0.00              
ATOM     85  CA  GLY    85      15.416  14.581  -0.130  1.00  0.00              
ATOM     86  CA  PRO    86      12.399  12.682  -1.263  1.00  0.00              
ATOM     87  CA  ALA    87      13.129   9.027  -0.865  1.00  0.00              
ATOM     88  CA  PRO    88      11.408   6.266   0.564  1.00  0.00              
ATOM     89  CA  PRO    89       9.500   5.905   3.752  1.00  0.00              
ATOM     90  CA  LYS    90      11.599   3.031   5.212  1.00  0.00              
ATOM     91  CA  VAL    91      14.749   5.161   4.975  1.00  0.00              
ATOM     92  CA  MET    92      13.018   8.090   6.715  1.00  0.00              
ATOM     93  CA  LYS    93      11.777   5.771   9.462  1.00  0.00              
ATOM     94  CA  ARG    94      15.357   4.513  10.078  1.00  0.00              
ATOM     95  CA  LEU    95      16.557   8.136  10.219  1.00  0.00              
ATOM     96  CA  SER    96      13.835   9.106  12.662  1.00  0.00              
ATOM     97  CA  LEU    97      14.649   6.163  15.024  1.00  0.00              
ATOM     98  CA  ALA    98      18.348   7.067  14.912  1.00  0.00              
ATOM     99  CA  LEU    99      17.619  10.695  15.730  1.00  0.00              
ATOM    100  CA  GLN   100      15.414   9.782  18.623  1.00  0.00              
ATOM    101  CA  LYS   101      18.065   7.466  20.075  1.00  0.00              
ATOM    102  CA  LEU   102      20.771  10.106  19.645  1.00  0.00              
ATOM    103  CA  THR   103      18.464  10.609  22.326  1.00  0.00              
ATOM    104  CA  GLU   104      16.824   8.598  24.795  1.00  0.00              
TER                                                                             
END
