
#######################################################
#                                                     #
#                        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 T0359TS393_5
# Molecule2: number of CA atoms   93 (  690),  selected   93 , name T0359.pdb
# PARAMETERS: T0359TS393_5.T0359.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           #
LGA    M       2      M       2           #
LGA    S       3      -       -           -
LGA    E       4      S       3          3.182
LGA    T       5      E       4          2.725
LGA    F       6      T       5          3.788
LGA    D       7      F       6          1.455
LGA    V       8      D       7          2.381
LGA    E       9      V       8          1.667
LGA    L      10      E       9          4.643
LGA    T      11      L      10          3.086
LGA    K      12      T      11          0.994
LGA    N      13      K      12          4.300
LGA    V      14      N      13          1.334
LGA    Q      15      V      14          1.993
LGA    -       -      Q      15           -
LGA    G      16      G      16          2.000
LGA    L      17      L      17          1.654
LGA    G      18      G      18          1.655
LGA    I      19      I      19          3.939
LGA    T      20      T      20          2.756
LGA    I      21      I      21          2.172
LGA    A      22      A      22          1.111
LGA    G      23      G      23          2.796
LGA    Y      24      -       -           -
LGA    I      25      Y      24          3.522
LGA    G      26      I      25          2.051
LGA    D      27      -       -           -
LGA    K      28      -       -           -
LGA    K      29      G      26          5.481
LGA    L      30      D      27           -
LGA    E      31      P      32          3.813
LGA    P      32      S      33          1.345
LGA    S      33      G      34          2.511
LGA    G      34      -       -           -
LGA    I      35      I      35          1.235
LGA    F      36      F      36          1.191
LGA    V      37      V      37          1.319
LGA    K      38      K      38          1.426
LGA    S      39      S      39          1.090
LGA    I      40      I      40          1.507
LGA    T      41      T      41          1.357
LGA    K      42      K      42          1.258
LGA    S      43      S      43          1.598
LGA    S      44      S      44          0.844
LGA    A      45      A      45          2.168
LGA    V      46      V      46          2.248
LGA    E      47      E      47          1.669
LGA    H      48      H      48          3.801
LGA    D      49      D      49          1.596
LGA    G      50      G      50          1.880
LGA    R      51      R      51          2.388
LGA    I      52      I      52          0.991
LGA    Q      53      Q      53          0.971
LGA    I      54      I      54          0.848
LGA    G      55      G      55          1.519
LGA    D      56      D      56          1.103
LGA    Q      57      Q      57          0.712
LGA    I      58      I      58          0.718
LGA    I      59      I      59          1.735
LGA    A      60      A      60          2.002
LGA    V      61      V      61          2.327
LGA    D      62      D      62          0.552
LGA    G      63      G      63          0.659
LGA    T      64      T      64          0.921
LGA    N      65      N      65          2.211
LGA    L      66      L      66          2.064
LGA    Q      67      Q      67          1.875
LGA    G      68      G      68          3.442
LGA    F      69      F      69          2.726
LGA    -       -      T      70           -
LGA    T      70      N      71          1.541
LGA    N      71      Q      72          2.385
LGA    Q      72      Q      73           #
LGA    -       -      A      74           -
LGA    -       -      V      75           -
LGA    Q      73      E      76          1.783
LGA    A      74      V      77          2.712
LGA    V      75      L      78          3.339
LGA    E      76      R      79          2.466
LGA    V      77      H      80          3.123
LGA    L      78      T      81          3.494
LGA    R      79      -       -           -
LGA    H      80      -       -           -
LGA    T      81      G      82          2.477
LGA    G      82      Q      83          2.398
LGA    Q      83      T      84          2.147
LGA    T      84      V      85          3.332
LGA    V      85      -       -           -
LGA    L      86      L      86          1.257
LGA    L      87      L      87          1.454
LGA    T      88      T      88          1.387
LGA    L      89      L      89          2.055
LGA    M      90      M      90          2.500
LGA    R      91      R      91          2.247
LGA    R      92      R      92          1.133
LGA    G      93      G      93          1.440
LGA    E      94      E      94          2.005
LGA    T      95      T      95          5.551
LGA    S      96      -       -           -
LGA    V      97      S      96          2.504
LGA    -       -      V      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   93    5.0     84    2.38    63.10     65.761     3.393

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.544872 * X  +   0.801426 * Y  +   0.246638 * Z  +  -4.568601
  Y_new =  -0.196865 * X  +   0.408179 * Y  +  -0.891422 * Z  +  13.902845
  Z_new =  -0.815082 * X  +   0.437157 * Y  +   0.380179 * Z  +  -6.904988 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.854998   -2.286595  [ DEG:    48.9878   -131.0122 ]
  Theta =   0.952870    2.188723  [ DEG:    54.5954    125.4046 ]
  Phi   =  -0.346711    2.794882  [ DEG:   -19.8651    160.1349 ]
 
# 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: T0359TS393_5                                  
REMARK     2: T0359.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS393_5.T0359.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   93   5.0   84   2.38   63.10  65.761
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS393_5
PFRMAT TS
TARGET T0359
MODEL 5
PARENT N/A
ATOM      1  CA  SER     1      10.594   0.344  -0.174  1.00 25.00           C
ATOM      2  CA  MET     2       7.315   0.259   1.728  1.00 25.00           C
ATOM      3  CA  SER     3       4.372   1.963  -0.042  1.00 25.00           C
ATOM      4  CA  GLU     4       5.019   5.042  -2.115  1.00 25.00           C
ATOM      5  CA  THR     5       3.463   8.334  -0.978  1.00 25.00           C
ATOM      6  CA  PHE     6       2.602  12.015  -0.627  1.00 25.00           C
ATOM      7  CA  ASP     7      -0.133  11.706   2.030  1.00 25.00           C
ATOM      8  CA  VAL     8      -1.486  15.186   1.801  1.00 25.00           C
ATOM      9  CA  GLU     9      -3.581  17.858   3.402  1.00 25.00           C
ATOM     10  CA  LEU    10      -3.758  21.004   1.299  1.00 25.00           C
ATOM     11  CA  THR    11      -5.897  23.695   2.921  1.00 25.00           C
ATOM     12  CA  LYS    12      -9.493  24.514   1.949  1.00 25.00           C
ATOM     13  CA  ASN    13      -9.743  28.273   1.560  1.00 25.00           C
ATOM     14  CA  VAL    14     -11.619  30.150  -1.165  1.00 25.00           C
ATOM     15  CA  GLN    15     -11.490  29.482  -4.871  1.00 25.00           C
ATOM     16  CA  GLY    16     -12.511  25.928  -4.055  1.00 25.00           C
ATOM     17  CA  LEU    17      -9.483  23.732  -3.546  1.00 25.00           C
ATOM     18  CA  GLY    18      -7.797  24.751  -6.840  1.00 25.00           C
ATOM     19  CA  ILE    19      -8.758  21.131  -7.771  1.00 25.00           C
ATOM     20  CA  THR    20      -7.503  19.440 -10.985  1.00 25.00           C
ATOM     21  CA  ILE    21      -7.820  15.914 -12.455  1.00 25.00           C
ATOM     22  CA  ALA    22      -6.023  15.308 -15.729  1.00 25.00           C
ATOM     23  CA  GLY    23      -7.741  12.368 -17.434  1.00 25.00           C
ATOM     24  CA  TYR    24      -4.251  10.800 -17.293  1.00 25.00           C
ATOM     25  CA  ILE    25      -5.715   7.314 -16.928  1.00 25.00           C
ATOM     26  CA  GLY    26      -8.162   7.339 -19.889  1.00 25.00           C
ATOM     27  CA  ASP    27      -9.267   3.706 -19.490  1.00 25.00           C
ATOM     28  CA  LYS    28      -5.864   2.695 -20.846  1.00 25.00           C
ATOM     29  CA  LYS    29      -5.034   5.292 -23.431  1.00 25.00           C
ATOM     30  CA  LEU    30      -2.194   6.156 -21.112  1.00 25.00           C
ATOM     31  CA  GLU    31      -0.990   4.039 -18.187  1.00 25.00           C
ATOM     32  CA  PRO    32      -3.811   2.697 -16.014  1.00 25.00           C
ATOM     33  CA  SER    33      -2.452   4.992 -13.369  1.00 25.00           C
ATOM     34  CA  GLY    34      -5.237   5.846 -10.858  1.00 25.00           C
ATOM     35  CA  ILE    35      -5.737   9.463 -12.016  1.00 25.00           C
ATOM     36  CA  PHE    36      -3.359  12.477 -12.268  1.00 25.00           C
ATOM     37  CA  VAL    37      -2.848  15.974 -10.938  1.00 25.00           C
ATOM     38  CA  LYS    38      -2.367  18.321 -13.964  1.00 25.00           C
ATOM     39  CA  SER    39      -1.816  21.926 -12.775  1.00 25.00           C
ATOM     40  CA  ILE    40      -0.691  22.766  -9.300  1.00 25.00           C
ATOM     41  CA  THR    41      -2.254  26.224  -9.932  1.00 25.00           C
ATOM     42  CA  LYS    42      -1.691  29.972  -9.621  1.00 25.00           C
ATOM     43  CA  SER    43      -3.128  31.269  -6.345  1.00 25.00           C
ATOM     44  CA  SER    44      -3.784  28.262  -4.208  1.00 25.00           C
ATOM     45  CA  ALA    45      -4.292  24.762  -2.857  1.00 25.00           C
ATOM     46  CA  VAL    46      -0.691  23.866  -3.804  1.00 25.00           C
ATOM     47  CA  GLU    47       1.162  27.109  -4.650  1.00 25.00           C
ATOM     48  CA  HIS    48       3.353  26.698  -1.536  1.00 25.00           C
ATOM     49  CA  ASP    49       1.552  24.505   1.022  1.00 25.00           C
ATOM     50  CA  GLY    50       3.262  21.641  -0.921  1.00 25.00           C
ATOM     51  CA  ARG    51       3.888  18.197  -2.431  1.00 25.00           C
ATOM     52  CA  ILE    52       0.909  18.723  -4.740  1.00 25.00           C
ATOM     53  CA  GLN    53       3.143  17.851  -7.665  1.00 25.00           C
ATOM     54  CA  ILE    54       2.367  17.908 -11.402  1.00 25.00           C
ATOM     55  CA  GLY    55       2.095  14.345 -12.663  1.00 25.00           C
ATOM     56  CA  ASP    56       1.070  13.176  -9.173  1.00 25.00           C
ATOM     57  CA  GLN    57      -0.768   9.828  -8.680  1.00 25.00           C
ATOM     58  CA  ILE    58      -4.217  10.992  -7.460  1.00 25.00           C
ATOM     59  CA  ILE    59      -6.444   8.394  -5.775  1.00 25.00           C
ATOM     60  CA  ALA    60      -8.921   9.965  -3.294  1.00 25.00           C
ATOM     61  CA  VAL    61     -12.511  11.024  -2.616  1.00 25.00           C
ATOM     62  CA  ASP    62     -11.781  11.386   1.107  1.00 25.00           C
ATOM     63  CA  GLY    63     -11.170   7.852   2.289  1.00 25.00           C
ATOM     64  CA  THR    64     -13.114   6.377  -0.575  1.00 25.00           C
ATOM     65  CA  ASN    65     -11.648   4.599  -3.583  1.00 25.00           C
ATOM     66  CA  LEU    66     -11.344   5.823  -7.137  1.00 25.00           C
ATOM     67  CA  GLN    67      -8.660   3.244  -8.090  1.00 25.00           C
ATOM     68  CA  GLY    68      -8.828   2.269 -11.799  1.00 25.00           C
ATOM     69  CA  PHE    69     -11.372   4.980 -12.606  1.00 25.00           C
ATOM     70  CA  THR    70     -11.113   7.284 -15.656  1.00 25.00           C
ATOM     71  CA  ASN    71     -11.930  10.745 -14.285  1.00 25.00           C
ATOM     72  CA  GLN    72     -15.321  12.514 -14.457  1.00 25.00           C
ATOM     73  CA  GLN    73     -16.405  10.810 -11.203  1.00 25.00           C
ATOM     74  CA  ALA    74     -13.144  11.902  -9.518  1.00 25.00           C
ATOM     75  CA  VAL    75     -13.701  15.498 -10.714  1.00 25.00           C
ATOM     76  CA  GLU    76     -17.276  15.427  -9.341  1.00 25.00           C
ATOM     77  CA  VAL    77     -15.984  14.127  -5.979  1.00 25.00           C
ATOM     78  CA  LEU    78     -13.365  16.920  -5.877  1.00 25.00           C
ATOM     79  CA  ARG    79     -16.074  19.521  -6.632  1.00 25.00           C
ATOM     80  CA  HIS    80     -18.259  18.095  -3.829  1.00 25.00           C
ATOM     81  CA  THR    81     -15.532  17.801  -1.234  1.00 25.00           C
ATOM     82  CA  GLY    82     -16.188  20.544   1.390  1.00 25.00           C
ATOM     83  CA  GLN    83     -13.849  20.950   4.354  1.00 25.00           C
ATOM     84  CA  THR    84     -10.494  19.294   3.648  1.00 25.00           C
ATOM     85  CA  VAL    85     -10.278  17.519   0.232  1.00 25.00           C
ATOM     86  CA  LEU    86      -7.846  14.729   1.136  1.00 25.00           C
ATOM     87  CA  LEU    87      -5.171  13.114  -1.004  1.00 25.00           C
ATOM     88  CA  THR    88      -3.952   9.561  -0.499  1.00 25.00           C
ATOM     89  CA  LEU    89      -1.275   9.027  -3.129  1.00 25.00           C
ATOM     90  CA  MET    90       0.736   6.460  -5.043  1.00 25.00           C
ATOM     91  CA  ARG    91       3.685   8.207  -6.713  1.00 25.00           C
ATOM     92  CA  ARG    92       7.444   7.933  -6.946  1.00 25.00           C
ATOM     93  CA  GLY    93      11.222   8.548  -6.510  1.00 25.00           C
ATOM     94  CA  GLU    94      13.143   5.526  -7.751  1.00 25.00           C
ATOM     95  CA  THR    95      15.171   2.494  -8.957  1.00 25.00           C
ATOM     96  CA  SER    96      15.779   1.939 -12.713  1.00 25.00           C
ATOM     97  CA  VAL    97      12.674   0.899 -14.621  1.00 25.00           C
TER
END
