
#######################################################
#                                                     #
#                        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   94 (   94),  selected   94 , name T0359TS393_1-D1
# Molecule2: number of CA atoms   90 (  669),  selected   90 , name T0359_D1.pdb
# PARAMETERS: T0359TS393_1-D1.T0359_D1.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          6.172
LGA    S       3      S       3          2.292
LGA    E       4      E       4          2.759
LGA    T       5      T       5          1.109
LGA    F       6      F       6          0.525
LGA    D       7      D       7          1.138
LGA    V       8      V       8          1.565
LGA    E       9      E       9          1.377
LGA    L      10      L      10          1.641
LGA    T      11      T      11          2.311
LGA    K      12      K      12          0.551
LGA    N      13      N      13          1.448
LGA    V      14      V      14          1.642
LGA    Q      15      Q      15          4.592
LGA    G      16      G      16          1.539
LGA    L      17      L      17          2.480
LGA    G      18      G      18          0.950
LGA    I      19      I      19          1.180
LGA    T      20      T      20          2.107
LGA    I      21      I      21          2.075
LGA    A      22      A      22          1.548
LGA    G      23      G      23          3.755
LGA    Y      24      Y      24          4.120
LGA    I      25      -       -           -
LGA    G      26      I      25          3.837
LGA    D      27      G      26          4.428
LGA    K      28      D      27           -
LGA    K      29      -       -           -
LGA    L      30      P      32          3.655
LGA    E      31      S      33          3.447
LGA    P      32      -       -           -
LGA    S      33      -       -           -
LGA    G      34      G      34          2.294
LGA    I      35      I      35          1.240
LGA    F      36      F      36          0.858
LGA    V      37      V      37          1.190
LGA    K      38      K      38          2.055
LGA    S      39      S      39          1.302
LGA    I      40      I      40          1.419
LGA    T      41      T      41          1.464
LGA    K      42      K      42          1.411
LGA    S      43      S      43          1.725
LGA    S      44      S      44          2.685
LGA    A      45      A      45          2.410
LGA    V      46      V      46          0.560
LGA    E      47      E      47          1.677
LGA    H      48      H      48          2.308
LGA    D      49      D      49          1.297
LGA    G      50      G      50          3.012
LGA    R      51      R      51          0.992
LGA    I      52      I      52          0.924
LGA    Q      53      Q      53          2.220
LGA    I      54      I      54          1.506
LGA    G      55      G      55          1.579
LGA    D      56      D      56          1.661
LGA    Q      57      Q      57          1.838
LGA    I      58      I      58          1.736
LGA    I      59      I      59          1.167
LGA    A      60      A      60          1.196
LGA    V      61      V      61          1.398
LGA    D      62      D      62          1.093
LGA    G      63      G      63          1.294
LGA    T      64      T      64          1.517
LGA    N      65      N      65          1.385
LGA    L      66      L      66          1.237
LGA    Q      67      Q      67          1.562
LGA    G      68      G      68          2.426
LGA    F      69      F      69          2.206
LGA    T      70      T      70          3.239
LGA    N      71      N      71          3.254
LGA    Q      72      Q      72          2.677
LGA    Q      73      Q      73          2.246
LGA    A      74      A      74          2.642
LGA    V      75      V      75          2.976
LGA    E      76      E      76          2.383
LGA    V      77      V      77          1.809
LGA    L      78      L      78          2.055
LGA    R      79      R      79          2.933
LGA    H      80      H      80          2.670
LGA    T      81      T      81          2.027
LGA    G      82      G      82          1.563
LGA    Q      83      Q      83          2.719
LGA    T      84      T      84          1.851
LGA    V      85      V      85          1.233
LGA    L      86      L      86          0.648
LGA    L      87      L      87          1.110
LGA    T      88      T      88          2.287
LGA    L      89      L      89          2.375
LGA    M      90      M      90          1.336
LGA    R      91      R      91          1.688
LGA    R      92      R      92          2.566
LGA    G      93      G      93          2.671
LGA    E      94      E      94          4.732

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   94   90    5.0     88    2.28    95.45     76.339     3.693

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.532197 * X  +  -0.812049 * Y  +  -0.239463 * Z  +  -4.414406
  Y_new =   0.074229 * X  +  -0.326513 * Y  +   0.942273 * Z  +  13.922263
  Z_new =  -0.843360 * X  +   0.483700 * Y  +   0.234047 * Z  +  -7.214972 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.120138   -2.021455  [ DEG:    64.1792   -115.8208 ]
  Theta =   1.003506    2.138087  [ DEG:    57.4967    122.5033 ]
  Phi   =   3.003010   -0.138582  [ DEG:   172.0598     -7.9402 ]
 
# 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_1-D1                               
REMARK     2: T0359_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS393_1-D1.T0359_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   94   90   5.0   88   2.28   95.45  76.339
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS393_1-D1
PFRMAT TS
TARGET T0359
MODEL 1
PARENT N/A
ATOM      1  CA  SER     1      10.311   1.174  -0.016  1.00 25.00           C
ATOM      2  CA  MET     2       6.568   1.023  -0.575  1.00 25.00           C
ATOM      3  CA  SER     3       6.664   4.246  -2.574  1.00 25.00           C
ATOM      4  CA  GLU     4       5.594   6.293   0.405  1.00 25.00           C
ATOM      5  CA  THR     5       2.049   7.637   0.472  1.00 25.00           C
ATOM      6  CA  PHE     6       1.383  11.374   1.152  1.00 25.00           C
ATOM      7  CA  ASP     7      -1.234  13.595   2.861  1.00 25.00           C
ATOM      8  CA  VAL     8      -2.132  16.871   1.229  1.00 25.00           C
ATOM      9  CA  GLU     9      -4.937  17.763   3.654  1.00 25.00           C
ATOM     10  CA  LEU    10      -6.007  20.435   1.177  1.00 25.00           C
ATOM     11  CA  THR    11      -8.051  23.662   0.949  1.00 25.00           C
ATOM     12  CA  LYS    12     -11.106  24.783  -0.895  1.00 25.00           C
ATOM     13  CA  ASN    13     -11.804  28.449  -0.487  1.00 25.00           C
ATOM     14  CA  VAL    14     -11.855  29.950  -3.963  1.00 25.00           C
ATOM     15  CA  GLN    15     -14.728  28.104  -5.635  1.00 25.00           C
ATOM     16  CA  GLY    16     -12.165  25.641  -7.021  1.00 25.00           C
ATOM     17  CA  LEU    17     -10.080  22.564  -6.297  1.00 25.00           C
ATOM     18  CA  GLY    18      -7.127  24.394  -7.845  1.00 25.00           C
ATOM     19  CA  ILE    19      -6.057  20.999  -9.083  1.00 25.00           C
ATOM     20  CA  THR    20      -6.676  18.729 -12.050  1.00 25.00           C
ATOM     21  CA  ILE    21      -7.277  15.359 -13.642  1.00 25.00           C
ATOM     22  CA  ALA    22      -6.576  14.125 -17.209  1.00 25.00           C
ATOM     23  CA  GLY    23      -3.278  12.820 -18.729  1.00 25.00           C
ATOM     24  CA  TYR    24      -2.611   9.217 -17.569  1.00 25.00           C
ATOM     25  CA  ILE    25      -5.053   6.285 -17.213  1.00 25.00           C
ATOM     26  CA  GLY    26      -7.796   5.082 -19.525  1.00 25.00           C
ATOM     27  CA  ASP    27      -6.607   7.203 -22.459  1.00 25.00           C
ATOM     28  CA  LYS    28      -2.824   7.782 -22.552  1.00 25.00           C
ATOM     29  CA  LYS    29      -2.170   4.054 -22.240  1.00 25.00           C
ATOM     30  CA  LEU    30      -0.668   2.532 -19.049  1.00 25.00           C
ATOM     31  CA  GLU    31      -3.992   1.255 -17.671  1.00 25.00           C
ATOM     32  CA  PRO    32      -4.653   1.250 -13.928  1.00 25.00           C
ATOM     33  CA  SER    33      -2.193   3.955 -13.065  1.00 25.00           C
ATOM     34  CA  GLY    34      -4.821   5.638 -10.954  1.00 25.00           C
ATOM     35  CA  ILE    35      -5.169   9.305 -11.911  1.00 25.00           C
ATOM     36  CA  PHE    36      -2.917  12.346 -12.313  1.00 25.00           C
ATOM     37  CA  VAL    37      -2.273  16.040 -12.103  1.00 25.00           C
ATOM     38  CA  LYS    38      -2.800  17.996 -15.373  1.00 25.00           C
ATOM     39  CA  SER    39      -1.715  21.041 -13.317  1.00 25.00           C
ATOM     40  CA  ILE    40      -1.334  22.594  -9.818  1.00 25.00           C
ATOM     41  CA  THR    41      -1.905  26.316 -10.089  1.00 25.00           C
ATOM     42  CA  LYS    42       0.010  29.542  -9.177  1.00 25.00           C
ATOM     43  CA  SER    43      -2.253  31.654  -6.912  1.00 25.00           C
ATOM     44  CA  SER    44      -5.089  29.231  -7.283  1.00 25.00           C
ATOM     45  CA  ALA    45      -4.984  27.376  -3.915  1.00 25.00           C
ATOM     46  CA  VAL    46      -3.136  24.093  -3.397  1.00 25.00           C
ATOM     47  CA  GLU    47       0.265  24.770  -5.023  1.00 25.00           C
ATOM     48  CA  HIS    48       1.390  26.708  -1.917  1.00 25.00           C
ATOM     49  CA  ASP    49      -0.419  25.507   1.207  1.00 25.00           C
ATOM     50  CA  GLY    50       1.375  22.218   1.175  1.00 25.00           C
ATOM     51  CA  ARG    51       2.489  19.705  -1.428  1.00 25.00           C
ATOM     52  CA  ILE    52       0.966  18.268  -4.636  1.00 25.00           C
ATOM     53  CA  GLN    53       1.708  18.535  -8.375  1.00 25.00           C
ATOM     54  CA  ILE    54       2.337  18.269 -12.175  1.00 25.00           C
ATOM     55  CA  GLY    55       2.961  14.631 -13.129  1.00 25.00           C
ATOM     56  CA  ASP    56       2.047  12.886  -9.872  1.00 25.00           C
ATOM     57  CA  GLN    57       0.370   9.528  -9.401  1.00 25.00           C
ATOM     58  CA  ILE    58      -2.860  10.433  -7.575  1.00 25.00           C
ATOM     59  CA  ILE    59      -4.132   7.292  -5.881  1.00 25.00           C
ATOM     60  CA  ALA    60      -7.015   8.244  -3.562  1.00 25.00           C
ATOM     61  CA  VAL    61     -10.303   9.925  -2.467  1.00 25.00           C
ATOM     62  CA  ASP    62     -11.800  10.646   0.994  1.00 25.00           C
ATOM     63  CA  GLY    63     -12.206   6.902   1.593  1.00 25.00           C
ATOM     64  CA  THR    64     -12.965   5.262  -1.798  1.00 25.00           C
ATOM     65  CA  ASN    65     -10.052   3.807  -3.764  1.00 25.00           C
ATOM     66  CA  LEU    66      -8.580   4.786  -7.140  1.00 25.00           C
ATOM     67  CA  GLN    67      -7.237   1.419  -8.194  1.00 25.00           C
ATOM     68  CA  GLY    68      -9.441   1.309 -11.242  1.00 25.00           C
ATOM     69  CA  PHE    69     -10.784   4.820 -11.721  1.00 25.00           C
ATOM     70  CA  THR    70      -9.827   6.717 -14.837  1.00 25.00           C
ATOM     71  CA  ASN    71     -10.726  10.451 -14.668  1.00 25.00           C
ATOM     72  CA  GLN    72     -14.473  11.235 -14.779  1.00 25.00           C
ATOM     73  CA  GLN    73     -14.961   9.496 -11.401  1.00 25.00           C
ATOM     74  CA  ALA    74     -12.069  11.517  -9.915  1.00 25.00           C
ATOM     75  CA  VAL    75     -13.608  14.756 -11.258  1.00 25.00           C
ATOM     76  CA  GLU    76     -16.991  13.812  -9.729  1.00 25.00           C
ATOM     77  CA  VAL    77     -15.300  13.103  -6.366  1.00 25.00           C
ATOM     78  CA  LEU    78     -13.530  16.495  -6.514  1.00 25.00           C
ATOM     79  CA  ARG    79     -16.860  18.228  -7.276  1.00 25.00           C
ATOM     80  CA  HIS    80     -18.498  16.435  -4.314  1.00 25.00           C
ATOM     81  CA  THR    81     -15.738  17.308  -1.794  1.00 25.00           C
ATOM     82  CA  GLY    82     -16.597  20.735  -0.383  1.00 25.00           C
ATOM     83  CA  GLN    83     -14.538  21.572   2.739  1.00 25.00           C
ATOM     84  CA  THR    84     -11.224  19.691   2.690  1.00 25.00           C
ATOM     85  CA  VAL    85     -10.488  17.347  -0.177  1.00 25.00           C
ATOM     86  CA  LEU    86      -8.439  14.598   1.581  1.00 25.00           C
ATOM     87  CA  LEU    87      -6.890  13.700  -1.768  1.00 25.00           C
ATOM     88  CA  THR    88      -3.680  11.902  -2.748  1.00 25.00           C
ATOM     89  CA  LEU    89      -0.127  13.138  -3.588  1.00 25.00           C
ATOM     90  CA  MET    90       1.938  10.044  -4.420  1.00 25.00           C
ATOM     91  CA  ARG    91       5.048  11.719  -5.783  1.00 25.00           C
ATOM     92  CA  ARG    92       7.318   8.689  -5.609  1.00 25.00           C
ATOM     93  CA  GLY    93      11.072   8.465  -5.128  1.00 25.00           C
ATOM     94  CA  GLU    94      14.515   7.199  -6.045  1.00 25.00           C
TER
END
