
#######################################################
#                                                     #
#                        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   86 (   86),  selected   86 , name T0292TS393_3-D1
# Molecule2: number of CA atoms   77 (  591),  selected   77 , name T0292_D1.pdb
# PARAMETERS: T0292TS393_3-D1.T0292_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    R       2      R       2          2.037
LGA    A       3      A       3          2.794
LGA    E       4      E       4          2.909
LGA    D       5      D       5          4.321
LGA    Y       6      Y       6          2.892
LGA    E       7      E       7          1.724
LGA    V       8      V       8          1.428
LGA    L       9      L       9          2.082
LGA    Y      10      Y      10          1.130
LGA    T      11      T      11          4.449
LGA    I      12      I      12          0.511
LGA    G      13      G      13          1.357
LGA    T      14      T      14          3.795
LGA    G      15      G      15          1.614
LGA    S      16      S      16          3.074
LGA    Y      17      Y      17          2.714
LGA    G      18      G      18          1.529
LGA    R      19      R      19          0.925
LGA    C      20      C      20          0.764
LGA    Q      21      Q      21          1.199
LGA    K      22      K      22          1.227
LGA    I      23      I      23          2.126
LGA    R      24      R      24          1.532
LGA    R      25      R      25          1.048
LGA    K      26      K      26          2.027
LGA    S      27      S      27          1.025
LGA    D      28      D      28          3.037
LGA    G      29      G      29          1.888
LGA    K      30      K      30          2.453
LGA    I      31      I      31          0.495
LGA    L      32      L      32          1.486
LGA    V      33      V      33          1.521
LGA    W      34      W      34          1.836
LGA    K      35      K      35          2.116
LGA    E      36      E      36          0.881
LGA    L      37      L      37          0.747
LGA    D      38      D      38          1.867
LGA    Y      39      Y      39          2.589
LGA    G      40      G      40          0.635
LGA    S      41      S      41          5.606
LGA    M      42      M      42          4.190
LGA    T      43      -       -           -
LGA    E      44      -       -           -
LGA    A      45      -       -           -
LGA    E      46      -       -           -
LGA    K      47      T      43           #
LGA    Q      48      M      49          2.320
LGA    M      49      -       -           -
LGA    L      50      L      50          1.580
LGA    V      51      V      51          0.861
LGA    S      52      S      52          1.546
LGA    E      53      E      53          1.790
LGA    V      54      V      54          1.015
LGA    N      55      N      55          1.825
LGA    L      56      L      56          2.351
LGA    L      57      L      57          1.820
LGA    R      58      R      58          1.604
LGA    E      59      E      59          1.768
LGA    L      60      L      60          1.161
LGA    K      61      K      61          1.199
LGA    H      62      H      62          0.379
LGA    P      63      P      63          0.996
LGA    N      64      N      64          1.562
LGA    I      65      I      65          1.536
LGA    V      66      V      66          0.875
LGA    R      67      R      67          1.719
LGA    Y      68      Y      68          1.228
LGA    Y      69      Y      69          1.437
LGA    D      70      D      70          0.833
LGA    R      71      R      71          0.665
LGA    I      72      I      72          1.354
LGA    I      73      I      73          1.707
LGA    D      74      D      74          3.014
LGA    R      75      -       -           -
LGA    T      76      -       -           -
LGA    N      77      -       -           -
LGA    T      78      -       -           -
LGA    T      79      T      79          0.495
LGA    L      80      L      80          0.728
LGA    Y      81      Y      81          1.355
LGA    I      82      I      82          1.561
LGA    V      83      V      83          1.913
LGA    M      84      M      84          0.634
LGA    E      85      E      85          0.918
LGA    Y      86      Y      86          1.973

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   86   77    5.0     75    2.01    98.67     80.692     3.549

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.872165 * X  +   0.300027 * Y  +   0.386409 * Z  +   6.592917
  Y_new =   0.229949 * X  +  -0.445748 * Y  +   0.865120 * Z  +  14.583611
  Z_new =   0.431800 * X  +   0.843381 * Y  +   0.319775 * Z  +  16.444782 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.208385   -1.933208  [ DEG:    69.2353   -110.7647 ]
  Theta =  -0.446488   -2.695105  [ DEG:   -25.5819   -154.4181 ]
  Phi   =   2.883806   -0.257787  [ DEG:   165.2299    -14.7701 ]
 
# 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: T0292TS393_3-D1                               
REMARK     2: T0292_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0292TS393_3-D1.T0292_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   86   77   5.0   75   2.01   98.67  80.692
REMARK  ---------------------------------------------------------- 
MOLECULE T0292TS393_3-D1
PFRMAT TS
TARGET T0292
MODEL 3
PARENT N/A
ATOM      1  CA  SER     1     -13.382  -6.251   3.204  1.00 25.00           C
ATOM      2  CA  ARG     2     -10.701  -8.374   4.914  1.00 25.00           C
ATOM      3  CA  ALA     3      -9.908  -6.508   8.113  1.00 25.00           C
ATOM      4  CA  GLU     4     -12.257  -8.952   9.834  1.00 25.00           C
ATOM      5  CA  ASP     5     -15.239  -6.641  10.402  1.00 25.00           C
ATOM      6  CA  TYR     6     -14.273  -5.943  13.996  1.00 25.00           C
ATOM      7  CA  GLU     7     -16.183  -2.918  15.287  1.00 25.00           C
ATOM      8  CA  VAL     8     -15.577   0.689  16.192  1.00 25.00           C
ATOM      9  CA  LEU     9     -16.326   3.640  18.444  1.00 25.00           C
ATOM     10  CA  TYR    10     -14.234   6.699  17.724  1.00 25.00           C
ATOM     11  CA  THR    11     -12.283   8.867  20.220  1.00 25.00           C
ATOM     12  CA  ILE    12     -10.074  10.636  17.596  1.00 25.00           C
ATOM     13  CA  GLY    13      -8.261  12.852  15.032  1.00 25.00           C
ATOM     14  CA  THR    14      -6.998  15.805  12.941  1.00 25.00           C
ATOM     15  CA  GLY    15      -6.397  16.353   9.247  1.00 25.00           C
ATOM     16  CA  SER    16      -4.191  15.780   6.193  1.00 25.00           C
ATOM     17  CA  TYR    17      -3.952  12.000   6.744  1.00 25.00           C
ATOM     18  CA  GLY    18      -7.675  11.767   7.461  1.00 25.00           C
ATOM     19  CA  ARG    19      -9.755  10.690  10.504  1.00 25.00           C
ATOM     20  CA  CYS    20      -8.717   8.083  13.092  1.00 25.00           C
ATOM     21  CA  GLN    21      -9.687   5.258  15.443  1.00 25.00           C
ATOM     22  CA  LYS    22     -10.135   2.773  18.225  1.00 25.00           C
ATOM     23  CA  ILE    23     -11.219  -0.805  18.686  1.00 25.00           C
ATOM     24  CA  ARG    24     -11.023  -4.604  18.557  1.00 25.00           C
ATOM     25  CA  ARG    25      -8.911  -6.881  16.358  1.00 25.00           C
ATOM     26  CA  LYS    26     -10.445 -10.262  15.791  1.00 25.00           C
ATOM     27  CA  SER    27      -8.520 -12.481  18.275  1.00 25.00           C
ATOM     28  CA  ASP    28     -10.873 -10.886  20.843  1.00 25.00           C
ATOM     29  CA  GLY    29     -11.535  -7.596  22.722  1.00 25.00           C
ATOM     30  CA  LYS    30      -8.595  -5.235  22.909  1.00 25.00           C
ATOM     31  CA  ILE    31      -7.056  -2.116  21.236  1.00 25.00           C
ATOM     32  CA  LEU    32      -4.635  -1.262  18.385  1.00 25.00           C
ATOM     33  CA  VAL    33      -6.160   1.286  16.098  1.00 25.00           C
ATOM     34  CA  TRP    34      -7.205   1.527  12.404  1.00 25.00           C
ATOM     35  CA  LYS    35      -7.083   4.389   9.904  1.00 25.00           C
ATOM     36  CA  GLU    36      -8.148   6.720   7.092  1.00 25.00           C
ATOM     37  CA  LEU    37      -7.182   8.047   3.725  1.00 25.00           C
ATOM     38  CA  ASP    38      -9.364   9.541   1.016  1.00 25.00           C
ATOM     39  CA  TYR    39      -7.784   9.481  -2.473  1.00 25.00           C
ATOM     40  CA  GLY    40      -9.844   7.631  -5.107  1.00 25.00           C
ATOM     41  CA  SER    41      -9.010   5.980  -8.496  1.00 25.00           C
ATOM     42  CA  MET    42      -5.283   6.501  -7.887  1.00 25.00           C
ATOM     43  CA  THR    43      -3.398   4.087 -10.147  1.00 25.00           C
ATOM     44  CA  GLU    44       0.273   4.987 -10.264  1.00 25.00           C
ATOM     45  CA  ALA    45       0.482   8.544  -8.891  1.00 25.00           C
ATOM     46  CA  GLU    46       0.115   9.525  -5.249  1.00 25.00           C
ATOM     47  CA  LYS    47      -0.732   5.866  -4.500  1.00 25.00           C
ATOM     48  CA  GLN    48       2.957   4.908  -4.877  1.00 25.00           C
ATOM     49  CA  MET    49       3.960   7.737  -2.498  1.00 25.00           C
ATOM     50  CA  LEU    50       1.358   6.551   0.050  1.00 25.00           C
ATOM     51  CA  VAL    51       2.695   2.971  -0.216  1.00 25.00           C
ATOM     52  CA  SER    52       6.268   4.238   0.325  1.00 25.00           C
ATOM     53  CA  GLU    53       5.127   6.216   3.401  1.00 25.00           C
ATOM     54  CA  VAL    54       3.387   3.099   4.788  1.00 25.00           C
ATOM     55  CA  ASN    55       6.569   1.042   4.228  1.00 25.00           C
ATOM     56  CA  LEU    56       8.640   3.711   6.032  1.00 25.00           C
ATOM     57  CA  LEU    57       6.175   3.678   8.963  1.00 25.00           C
ATOM     58  CA  ARG    58       6.395  -0.142   9.138  1.00 25.00           C
ATOM     59  CA  GLU    59      10.221   0.056   9.144  1.00 25.00           C
ATOM     60  CA  LEU    60      11.085   1.041  12.732  1.00 25.00           C
ATOM     61  CA  LYS    61      10.568  -1.359  15.700  1.00 25.00           C
ATOM     62  CA  HIS    62      11.126   0.122  19.198  1.00 25.00           C
ATOM     63  CA  PRO    63       9.152   1.620  22.098  1.00 25.00           C
ATOM     64  CA  ASN    64       9.450   5.216  20.777  1.00 25.00           C
ATOM     65  CA  ILE    65       8.517   4.794  17.112  1.00 25.00           C
ATOM     66  CA  VAL    66       4.967   3.634  17.868  1.00 25.00           C
ATOM     67  CA  ARG    67       4.926   1.192  14.989  1.00 25.00           C
ATOM     68  CA  TYR    68       2.407  -1.295  13.712  1.00 25.00           C
ATOM     69  CA  TYR    69      -0.310  -3.897  14.175  1.00 25.00           C
ATOM     70  CA  ASP    70      -1.327  -3.253  10.601  1.00 25.00           C
ATOM     71  CA  ARG    71      -2.085  -1.940   7.069  1.00 25.00           C
ATOM     72  CA  ILE    72      -4.614  -2.918   4.353  1.00 25.00           C
ATOM     73  CA  ILE    73      -5.596  -1.815   0.847  1.00 25.00           C
ATOM     74  CA  ASP    74      -8.870  -3.686   0.169  1.00 25.00           C
ATOM     75  CA  ARG    75      -9.891  -3.221  -3.473  1.00 25.00           C
ATOM     76  CA  THR    76     -13.496  -2.629  -2.516  1.00 25.00           C
ATOM     77  CA  ASN    77     -13.355   0.827  -4.215  1.00 25.00           C
ATOM     78  CA  THR    78     -11.469   3.619  -2.466  1.00 25.00           C
ATOM     79  CA  THR    79      -9.903   3.830   0.998  1.00 25.00           C
ATOM     80  CA  LEU    80      -6.452   2.859   2.417  1.00 25.00           C
ATOM     81  CA  TYR    81      -5.287   1.941   5.928  1.00 25.00           C
ATOM     82  CA  ILE    82      -2.514   3.428   8.034  1.00 25.00           C
ATOM     83  CA  VAL    83      -2.166   1.629  11.351  1.00 25.00           C
ATOM     84  CA  MET    84      -1.052   2.187  14.932  1.00 25.00           C
ATOM     85  CA  GLU    85      -0.627   2.373  18.685  1.00 25.00           C
ATOM     86  CA  TYR    86      -2.947   5.155  19.879  1.00 25.00           C
TER
END
