
#######################################################
#                                                     #
#                        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   91 (   91),  selected   91 , name T0299TS393_3-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS393_3-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    T       2      T       2           -
LGA    -       -      R       3           -
LGA    -       -      Y       4           -
LGA    -       -      A       5           -
LGA    -       -      L       6           -
LGA    -       -      L       7           -
LGA    -       -      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    R       3      N      12           #
LGA    Y       4      V      13           -
LGA    A       5      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    L       6      V      20           #
LGA    L       7      M      21           #
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    V       8      L      24          4.959
LGA    R       9      R      25          5.153
LGA    G      10      Q      26           #
LGA    I      11      E      27           #
LGA    N      12      L      28          3.424
LGA    V      13      -       -           -
LGA    G      14      -       -           -
LGA    G      15      -       -           -
LGA    K      16      -       -           -
LGA    N      17      -       -           -
LGA    K      18      -       -           -
LGA    V      19      -       -           -
LGA    V      20      -       -           -
LGA    M      21      -       -           -
LGA    A      22      -       -           -
LGA    E      23      -       -           -
LGA    L      24      -       -           -
LGA    R      25      -       -           -
LGA    Q      26      -       -           -
LGA    E      27      T      29          2.527
LGA    L      28      N      30          0.798
LGA    T      29      L      31           #
LGA    N      30      G      32           -
LGA    L      31      L      33           -
LGA    G      32      E      34           -
LGA    L      33      K      35           -
LGA    E      34      V      36           -
LGA    K      35      E      37           -
LGA    V      36      -       -           -
LGA    E      37      -       -           -
LGA    S      38      -       -           -
LGA    Y      39      S      38           #
LGA    I      40      Y      39           -
LGA    N      41      I      40           -
LGA    S      42      N      41           #
LGA    G      43      S      42          4.399
LGA    N      44      G      43          3.770
LGA    I      45      N      44          4.856
LGA    F      46      I      45          4.445
LGA    F      47      -       -           -
LGA    T      48      -       -           -
LGA    S      49      F      46           #
LGA    I      50      F      47           #
LGA    -       -      T      48           -
LGA    -       -      S      49           -
LGA    -       -      I      50           -
LGA    -       -      D      51           -
LGA    D      51      S      52           #
LGA    S      52      K      53          1.953
LGA    K      53      A      54          3.541
LGA    -       -      Q      55           -
LGA    -       -      L      56           -
LGA    -       -      V      57           -
LGA    A      54      E      58          2.066
LGA    Q      55      K      59          1.417
LGA    L      56      L      60          1.888
LGA    V      57      E      61          1.749
LGA    E      58      T      62          0.525
LGA    K      59      F      63          1.217
LGA    L      60      F      64          2.397
LGA    E      61      A      65          1.359
LGA    T      62      V      66          1.784
LGA    F      63      H      67          3.563
LGA    F      64      Y      68          3.922
LGA    A      65      -       -           -
LGA    V      66      -       -           -
LGA    H      67      -       -           -
LGA    Y      68      -       -           -
LGA    P      69      P      69           #
LGA    F      70      F      70          2.800
LGA    I      71      I      71          4.011
LGA    Q      72      Q      72          3.699
LGA    S      73      S      73          3.380
LGA    F      74      F      74          2.505
LGA    S      75      S      75          4.267
LGA    L      76      L      76          3.284
LGA    L      77      -       -           -
LGA    S      78      L      77          2.309
LGA    A     168      S      78           #
LGA    K     169      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    T     170      I     174          4.197
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    F     171      M     177          1.621
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    D     172      K     180          4.068
LGA    K     173      -       -           -
LGA    I     174      -       -           -
LGA    G     175      -       -           -
LGA    Q     176      -       -           -
LGA    M     177      -       -           -
LGA    L     178      -       -           -
LGA    K     179      -       -           -
LGA    K     180      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     33    3.22    27.27     22.924     0.993

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.342276 * X  +  -0.563926 * Y  +   0.751555 * Z  +  -5.173802
  Y_new =  -0.280345 * X  +   0.702142 * Y  +   0.654525 * Z  +  45.953342
  Z_new =  -0.896802 * X  +  -0.434723 * Y  +   0.082233 * Z  +  -1.660524 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.383843    1.757749  [ DEG:   -79.2884    100.7116 ]
  Theta =   1.112487    2.029106  [ DEG:    63.7408    116.2592 ]
  Phi   =  -0.686255    2.455338  [ DEG:   -39.3195    140.6805 ]
 
# 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: T0299TS393_3-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS393_3-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   91   91   5.0   33   3.22   27.27  22.924
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS393_3-D1
PFRMAT TS
TARGET T0299
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1       5.254  30.058 -18.801  1.00 25.00           C
ATOM      2  CA  THR     2       4.139  32.311 -15.985  1.00 25.00           C
ATOM      3  CA  ARG     3       2.421  35.169 -14.131  1.00 25.00           C
ATOM      4  CA  TYR     4       0.812  38.582 -14.458  1.00 25.00           C
ATOM      5  CA  ALA     5      -2.171  38.863 -12.115  1.00 25.00           C
ATOM      6  CA  LEU     6      -5.328  38.832 -10.057  1.00 25.00           C
ATOM      7  CA  LEU     7      -7.237  41.212  -7.815  1.00 25.00           C
ATOM      8  CA  VAL     8     -10.080  39.371  -6.146  1.00 25.00           C
ATOM      9  CA  ARG     9      -9.716  41.788  -3.186  1.00 25.00           C
ATOM     10  CA  GLY    10     -10.499  38.606  -1.147  1.00 25.00           C
ATOM     11  CA  ILE    11     -11.525  39.276   2.497  1.00 25.00           C
ATOM     12  CA  ASN    12     -14.096  41.655   0.937  1.00 25.00           C
ATOM     13  CA  VAL    13     -15.390  44.852   2.491  1.00 25.00           C
ATOM     14  CA  GLY    14     -16.552  42.482   5.238  1.00 25.00           C
ATOM     15  CA  GLY    15     -17.944  39.265   6.777  1.00 25.00           C
ATOM     16  CA  LYS    16     -21.168  41.196   7.330  1.00 25.00           C
ATOM     17  CA  ASN    17     -20.566  44.904   8.132  1.00 25.00           C
ATOM     18  CA  LYS    18     -17.925  47.358   6.875  1.00 25.00           C
ATOM     19  CA  VAL    19     -18.084  49.413   3.682  1.00 25.00           C
ATOM     20  CA  VAL    20     -21.070  47.336   2.747  1.00 25.00           C
ATOM     21  CA  MET    21     -19.932  45.904  -0.546  1.00 25.00           C
ATOM     22  CA  ALA    22     -22.953  43.680  -1.319  1.00 25.00           C
ATOM     23  CA  GLU    23     -21.119  42.198  -4.338  1.00 25.00           C
ATOM     24  CA  LEU    24     -18.046  41.502  -2.161  1.00 25.00           C
ATOM     25  CA  ARG    25     -20.258  39.791   0.456  1.00 25.00           C
ATOM     26  CA  GLN    26     -21.873  37.647  -2.275  1.00 25.00           C
ATOM     27  CA  GLU    27     -18.411  36.667  -3.589  1.00 25.00           C
ATOM     28  CA  LEU    28     -17.308  35.717  -0.047  1.00 25.00           C
ATOM     29  CA  THR    29     -20.464  33.591   0.392  1.00 25.00           C
ATOM     30  CA  ASN    30     -19.781  31.846  -2.948  1.00 25.00           C
ATOM     31  CA  LEU    31     -16.174  31.143  -1.871  1.00 25.00           C
ATOM     32  CA  GLY    32     -15.740  31.193   1.908  1.00 25.00           C
ATOM     33  CA  LEU    33     -12.229  30.128   0.895  1.00 25.00           C
ATOM     34  CA  GLU    34     -10.899  28.315  -2.206  1.00 25.00           C
ATOM     35  CA  LYS    35     -11.703  31.373  -4.367  1.00 25.00           C
ATOM     36  CA  VAL    36      -9.885  33.643  -1.876  1.00 25.00           C
ATOM     37  CA  GLU    37      -6.842  31.318  -1.939  1.00 25.00           C
ATOM     38  CA  SER    38      -6.847  31.376  -5.769  1.00 25.00           C
ATOM     39  CA  TYR    39      -7.018  35.201  -5.736  1.00 25.00           C
ATOM     40  CA  ILE    40      -4.085  35.336  -3.278  1.00 25.00           C
ATOM     41  CA  ASN    41      -2.063  32.984  -5.525  1.00 25.00           C
ATOM     42  CA  SER    42       1.446  34.256  -5.107  1.00 25.00           C
ATOM     43  CA  GLY    43       0.710  36.572  -8.088  1.00 25.00           C
ATOM     44  CA  ASN    44       1.275  40.010  -6.497  1.00 25.00           C
ATOM     45  CA  ILE    45      -2.486  39.700  -5.748  1.00 25.00           C
ATOM     46  CA  PHE    46      -4.551  41.306  -3.027  1.00 25.00           C
ATOM     47  CA  PHE    47      -5.325  40.346   0.630  1.00 25.00           C
ATOM     48  CA  THR    48      -8.100  42.848   1.499  1.00 25.00           C
ATOM     49  CA  SER    49     -10.781  45.213   0.375  1.00 25.00           C
ATOM     50  CA  ILE    50     -11.089  47.444   3.494  1.00 25.00           C
ATOM     51  CA  ASP    51      -9.193  49.652   5.940  1.00 25.00           C
ATOM     52  CA  SER    52     -12.154  51.012   7.904  1.00 25.00           C
ATOM     53  CA  LYS    53     -12.229  47.646   9.547  1.00 25.00           C
ATOM     54  CA  ALA    54     -12.403  44.872  12.182  1.00 25.00           C
ATOM     55  CA  GLN    55     -13.554  42.377   9.515  1.00 25.00           C
ATOM     56  CA  LEU    56     -10.658  43.432   7.242  1.00 25.00           C
ATOM     57  CA  VAL    57      -8.190  42.975  10.134  1.00 25.00           C
ATOM     58  CA  GLU    58      -9.620  39.493  10.838  1.00 25.00           C
ATOM     59  CA  LYS    59      -9.269  38.574   7.138  1.00 25.00           C
ATOM     60  CA  LEU    60      -5.637  39.789   7.155  1.00 25.00           C
ATOM     61  CA  GLU    61      -4.927  37.702  10.286  1.00 25.00           C
ATOM     62  CA  THR    62      -6.483  34.625   8.618  1.00 25.00           C
ATOM     63  CA  PHE    63      -4.329  35.196   5.502  1.00 25.00           C
ATOM     64  CA  PHE    64      -1.199  35.489   7.688  1.00 25.00           C
ATOM     65  CA  ALA    65      -2.116  32.232   9.481  1.00 25.00           C
ATOM     66  CA  VAL    66      -2.606  30.484   6.108  1.00 25.00           C
ATOM     67  CA  HIS    67       0.804  31.764   4.923  1.00 25.00           C
ATOM     68  CA  TYR    68       4.316  32.540   3.743  1.00 25.00           C
ATOM     69  CA  PRO    69       5.104  32.196   7.475  1.00 25.00           C
ATOM     70  CA  PHE    70       3.654  35.686   8.042  1.00 25.00           C
ATOM     71  CA  ILE    71       3.693  37.508   4.637  1.00 25.00           C
ATOM     72  CA  GLN    72       0.276  39.197   4.638  1.00 25.00           C
ATOM     73  CA  SER    73      -1.763  42.379   5.091  1.00 25.00           C
ATOM     74  CA  PHE    74      -3.364  44.625   2.501  1.00 25.00           C
ATOM     75  CA  SER    75      -6.161  47.209   2.218  1.00 25.00           C
ATOM     76  CA  LEU    76      -5.629  48.781  -1.188  1.00 25.00           C
ATOM     77  CA  LEU    77      -5.429  52.041   0.793  1.00 25.00           C
ATOM     78  CA  SER    78      -9.174  52.842   0.389  1.00 25.00           C
ATOM    168  CA  ALA   168     -12.448  53.289  -6.801  1.00 25.00           C
ATOM    169  CA  LYS   169     -10.608  56.180  -8.513  1.00 25.00           C
ATOM    170  CA  THR   170      -7.735  53.828  -9.451  1.00 25.00           C
ATOM    171  CA  PHE   171     -10.234  51.308 -10.890  1.00 25.00           C
ATOM    172  CA  ASP   172     -11.902  54.089 -12.928  1.00 25.00           C
ATOM    173  CA  LYS   173      -8.485  55.197 -14.257  1.00 25.00           C
ATOM    174  CA  ILE   174      -7.667  51.586 -15.233  1.00 25.00           C
ATOM    175  CA  GLY   175     -11.029  51.286 -17.042  1.00 25.00           C
ATOM    176  CA  GLN   176     -10.342  54.556 -18.914  1.00 25.00           C
ATOM    177  CA  MET   177      -6.879  53.273 -19.932  1.00 25.00           C
ATOM    178  CA  LEU   178      -8.431  50.004 -21.182  1.00 25.00           C
ATOM    179  CA  LYS   179      -9.039  48.830 -24.745  1.00 25.00           C
ATOM    180  CA  LYS   180      -8.674  45.251 -25.982  1.00 25.00           C
TER
END
