
#######################################################
#                                                     #
#                        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 T0283TS599_4-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS599_4-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          3.300
LGA    S       2      S       2          3.487
LGA    F       3      F       3          1.387
LGA    I       4      I       4          2.124
LGA    E       5      E       5          3.927
LGA    K       6      K       6          2.931
LGA    M       7      M       7          0.723
LGA    I       8      I       8          2.918
LGA    G       9      G       9          3.544
LGA    S      10      S      10          1.900
LGA    L      11      L      11          1.025
LGA    N      12      N      12          2.411
LGA    D      13      D      13          2.403
LGA    K      14      K      14          1.076
LGA    R      15      R      15          0.971
LGA    E      16      E      16          1.973
LGA    W      17      W      17          1.776
LGA    K      18      K      18          0.954
LGA    A      19      A      19          0.878
LGA    M      20      M      20          1.707
LGA    E      21      E      21          2.106
LGA    A      22      A      22          1.401
LGA    R      23      R      23          0.828
LGA    A      24      A      24          2.569
LGA    K      25      K      25          2.750
LGA    A      26      A      26          1.294
LGA    L      27      L      27          1.551
LGA    P      28      P      28          1.471
LGA    K      29      K      29          1.115
LGA    E      30      E      30          0.942
LGA    Y      31      Y      31          0.929
LGA    H      32      H      32          0.607
LGA    H      33      H      33          0.537
LGA    A      34      A      34          0.505
LGA    Y      35      Y      35          0.677
LGA    K      36      K      36          0.724
LGA    A      37      A      37          1.290
LGA    I      38      I      38          1.562
LGA    Q      39      Q      39          1.716
LGA    K      40      K      40          1.890
LGA    Y      41      Y      41          1.923
LGA    M      42      M      42          2.184
LGA    W      43      W      43          2.906
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    T      44      G      47          5.061
LGA    S      45      P      48           #
LGA    G      46      T      49          2.933
LGA    G      47      D      50          1.672
LGA    P      48      W      51          1.709
LGA    T      49      -       -           -
LGA    D      50      -       -           -
LGA    W      51      -       -           -
LGA    Q      52      Q      52           #
LGA    D      53      D      53          5.310
LGA    T      54      T      54          3.526
LGA    K      55      K      55          2.123
LGA    R      56      R      56          2.507
LGA    I      57      I      57          1.961
LGA    F      58      F      58          1.472
LGA    G      59      G      59          2.618
LGA    G      60      G      60          2.567
LGA    I      61      I      61          3.961
LGA    L      62      -       -           -
LGA    D      63      L      62           #
LGA    L      64      D      63           -
LGA    F      65      L      64           #
LGA    E      66      F      65          4.765
LGA    E      67      E      66           -
LGA    G      68      E      67           -
LGA    -       -      G      68           -
LGA    -       -      A      69           -
LGA    -       -      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    -       -      K      73           -
LGA    A      69      K      74          4.554
LGA    A      70      V      75          4.744
LGA    -       -      T      76           -
LGA    -       -      D      77           -
LGA    -       -      L      78           -
LGA    E      71      T      79           #
LGA    G      72      G      80           #
LGA    K      73      E      81          1.135
LGA    K      74      D      82          3.882
LGA    V      75      V      83          0.378
LGA    T      76      A      84          2.307
LGA    D      77      A      85           #
LGA    L      78      -       -           -
LGA    T      79      -       -           -
LGA    G      80      F      86           #
LGA    E      81      C      87           -
LGA    D      82      -       -           -
LGA    V      83      D      88          3.566
LGA    A      84      -       -           -
LGA    A      85      -       -           -
LGA    F      86      -       -           -
LGA    C      87      E      89           #
LGA    D      88      L      90           -
LGA    E      89      M      91           -
LGA    -       -      K      92           -
LGA    -       -      D      93           -
LGA    -       -      T      94           -
LGA    L      90      K      95           #
LGA    M      91      T      96           #
LGA    K      92      -       -           -
LGA    D      93      W      97          3.287
LGA    T      94      -       -           -
LGA    K      95      -       -           -
LGA    T      96      -       -           -
LGA    W      97      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     65    2.49    81.54     49.381     2.510

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.645089 * X  +   0.728511 * Y  +  -0.230502 * Z  +  23.706190
  Y_new =  -0.724761 * X  +   0.678921 * Y  +   0.117423 * Z  +  25.391602
  Z_new =   0.242037 * X  +   0.091311 * Y  +   0.965961 * Z  +   4.373631 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.094249   -3.047344  [ DEG:     5.4000   -174.6000 ]
  Theta =  -0.244464   -2.897128  [ DEG:   -14.0068   -165.9932 ]
  Phi   =  -0.843494    2.298099  [ DEG:   -48.3286    131.6714 ]
 
# 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: T0283TS599_4-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS599_4-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   97   5.0   65   2.49   81.54  49.381
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS599_4-D1
PFRMAT TS                                                                       
TARGET T0283                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      24.666   6.235  20.040  1.00  0.00              
ATOM      2  CA  SER     2      28.158   7.033  19.733  1.00  0.00              
ATOM      3  CA  PHE     3      31.347   8.675  19.813  1.00  0.00              
ATOM      4  CA  ILE     4      27.532   8.006  18.645  1.00  0.00              
ATOM      5  CA  GLU     5      26.930  11.754  18.447  1.00  0.00              
ATOM      6  CA  LYS     6      30.062  12.158  16.407  1.00  0.00              
ATOM      7  CA  MET     7      29.049   9.371  14.034  1.00  0.00              
ATOM      8  CA  ILE     8      25.522  10.783  13.504  1.00  0.00              
ATOM      9  CA  GLY     9      26.876  14.205  12.770  1.00  0.00              
ATOM     10  CA  SER    10      29.348  12.935  10.242  1.00  0.00              
ATOM     11  CA  LEU    11      26.801  10.807   8.416  1.00  0.00              
ATOM     12  CA  ASN    12      23.950  13.224   8.042  1.00  0.00              
ATOM     13  CA  ASP    13      26.198  16.028   6.913  1.00  0.00              
ATOM     14  CA  LYS    14      27.797  13.779   4.314  1.00  0.00              
ATOM     15  CA  ARG    15      24.465  12.596   2.918  1.00  0.00              
ATOM     16  CA  GLU    16      23.114  16.170   2.614  1.00  0.00              
ATOM     17  CA  TRP    17      26.260  17.280   0.863  1.00  0.00              
ATOM     18  CA  LYS    18      25.951  14.330  -1.549  1.00  0.00              
ATOM     19  CA  ALA    19      22.351  15.270  -2.349  1.00  0.00              
ATOM     20  CA  MET    20      23.316  18.907  -3.014  1.00  0.00              
ATOM     21  CA  GLU    21      26.111  17.686  -5.313  1.00  0.00              
ATOM     22  CA  ALA    22      23.759  15.404  -7.215  1.00  0.00              
ATOM     23  CA  ARG    23      21.337  18.279  -7.775  1.00  0.00              
ATOM     24  CA  ALA    24      24.247  20.412  -8.944  1.00  0.00              
ATOM     25  CA  LYS    25      25.581  17.857 -11.376  1.00  0.00              
ATOM     26  CA  ALA    26      22.122  17.686 -13.023  1.00  0.00              
ATOM     27  CA  LEU    27      21.733  21.394 -13.375  1.00  0.00              
ATOM     28  CA  PRO    28      22.802  23.684 -16.055  1.00  0.00              
ATOM     29  CA  LYS    29      25.774  25.804 -15.172  1.00  0.00              
ATOM     30  CA  GLU    30      23.707  28.990 -14.735  1.00  0.00              
ATOM     31  CA  TYR    31      21.647  27.306 -12.021  1.00  0.00              
ATOM     32  CA  HIS    32      24.688  25.809 -10.247  1.00  0.00              
ATOM     33  CA  HIS    33      26.337  29.226  -9.745  1.00  0.00              
ATOM     34  CA  ALA    34      23.110  30.657  -8.349  1.00  0.00              
ATOM     35  CA  TYR    35      22.754  27.660  -5.956  1.00  0.00              
ATOM     36  CA  LYS    36      26.307  28.087  -4.744  1.00  0.00              
ATOM     37  CA  ALA    37      25.700  31.824  -4.064  1.00  0.00              
ATOM     38  CA  ILE    38      22.475  31.034  -2.128  1.00  0.00              
ATOM     39  CA  GLN    39      24.312  28.384  -0.071  1.00  0.00              
ATOM     40  CA  LYS    40      27.136  30.848   0.691  1.00  0.00              
ATOM     41  CA  TYR    41      24.602  33.532   1.726  1.00  0.00              
ATOM     42  CA  MET    42      22.690  31.016   3.956  1.00  0.00              
ATOM     43  CA  TRP    43      25.566  29.408   5.780  1.00  0.00              
ATOM     44  CA  THR    44      24.055  27.317   8.478  1.00  0.00              
ATOM     45  CA  SER    45      26.459  25.719  10.995  1.00  0.00              
ATOM     46  CA  GLY    46      24.247  25.718  14.065  1.00  0.00              
ATOM     47  CA  GLY    47      20.908  24.822  12.603  1.00  0.00              
ATOM     48  CA  PRO    48      20.441  21.871  10.222  1.00  0.00              
ATOM     49  CA  THR    49      20.312  19.033  12.678  1.00  0.00              
ATOM     50  CA  ASP    50      17.842  16.644  11.185  1.00  0.00              
ATOM     51  CA  TRP    51      18.959  16.621   7.516  1.00  0.00              
ATOM     52  CA  GLN    52      15.435  16.866   6.252  1.00  0.00              
ATOM     53  CA  ASP    53      14.807  20.131   8.105  1.00  0.00              
ATOM     54  CA  THR    54      18.033  21.748   6.783  1.00  0.00              
ATOM     55  CA  LYS    55      17.431  20.662   3.225  1.00  0.00              
ATOM     56  CA  ARG    56      13.817  21.936   3.172  1.00  0.00              
ATOM     57  CA  ILE    57      15.026  25.347   4.299  1.00  0.00              
ATOM     58  CA  PHE    58      17.742  25.475   1.621  1.00  0.00              
ATOM     59  CA  GLY    59      15.305  24.402  -1.023  1.00  0.00              
ATOM     60  CA  GLY    60      12.884  27.234  -0.099  1.00  0.00              
ATOM     61  CA  ILE    61      15.792  29.723  -0.281  1.00  0.00              
ATOM     62  CA  LEU    62      16.747  28.310  -3.702  1.00  0.00              
ATOM     63  CA  ASP    63      13.159  28.686  -4.917  1.00  0.00              
ATOM     64  CA  LEU    64      13.329  32.387  -4.037  1.00  0.00              
ATOM     65  CA  PHE    65      16.508  32.677  -5.978  1.00  0.00              
ATOM     66  CA  GLU    66      14.917  30.987  -9.040  1.00  0.00              
ATOM     67  CA  GLU    67      12.068  33.498  -8.910  1.00  0.00              
ATOM     68  CA  GLY    68      14.521  36.424  -8.643  1.00  0.00              
ATOM     69  CA  ALA    69      16.541  35.093 -11.642  1.00  0.00              
ATOM     70  CA  ALA    70      13.278  34.970 -13.570  1.00  0.00              
ATOM     71  CA  GLU    71      12.450  38.615 -12.689  1.00  0.00              
ATOM     72  CA  GLY    72      15.917  39.835 -13.663  1.00  0.00              
ATOM     73  CA  LYS    73      17.044  41.029 -10.311  1.00  0.00              
ATOM     74  CA  LYS    74      19.939  39.799  -8.249  1.00  0.00              
ATOM     75  CA  VAL    75      18.922  37.971  -4.981  1.00  0.00              
ATOM     76  CA  THR    76      20.409  40.663  -2.758  1.00  0.00              
ATOM     77  CA  ASP    77      18.587  43.371  -4.796  1.00  0.00              
ATOM     78  CA  LEU    78      15.224  41.570  -4.698  1.00  0.00              
ATOM     79  CA  THR    79      15.285  41.051  -0.962  1.00  0.00              
ATOM     80  CA  GLY    80      16.552  44.549  -0.218  1.00  0.00              
ATOM     81  CA  GLU    81      19.070  45.486   2.399  1.00  0.00              
ATOM     82  CA  ASP    82      17.578  44.247   5.701  1.00  0.00              
ATOM     83  CA  VAL    83      17.510  40.628   4.424  1.00  0.00              
ATOM     84  CA  ALA    84      21.123  40.904   3.236  1.00  0.00              
ATOM     85  CA  ALA    85      22.327  42.180   6.626  1.00  0.00              
ATOM     86  CA  PHE    86      20.498  39.298   8.313  1.00  0.00              
ATOM     87  CA  CYS    87      22.114  36.763   5.937  1.00  0.00              
ATOM     88  CA  ASP    88      25.586  38.186   6.658  1.00  0.00              
ATOM     89  CA  GLU    89      24.934  37.975  10.438  1.00  0.00              
ATOM     90  CA  LEU    90      23.720  34.419  10.281  1.00  0.00              
ATOM     91  CA  MET    91      26.690  33.275   8.277  1.00  0.00              
ATOM     92  CA  LYS    92      29.234  34.860  10.639  1.00  0.00              
ATOM     93  CA  ASP    93      27.547  33.332  13.705  1.00  0.00              
ATOM     94  CA  THR    94      27.419  29.870  12.233  1.00  0.00              
ATOM     95  CA  LYS    95      31.178  29.477  11.811  1.00  0.00              
ATOM     96  CA  THR    96      31.909  30.332  15.477  1.00  0.00              
ATOM     97  CA  TRP    97      29.291  27.895  16.685  1.00  0.00              
TER                                                                             
END
