
#######################################################
#                                                     #
#                        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   85 (   85),  selected   85 , name T0335TS393_1
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS393_1.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    S       3      S       3           #
LGA    N       4      N       4          1.411
LGA    A       5      A       5          1.961
LGA    K       6      K       6          1.924
LGA    I       7      I       7          1.377
LGA    A       8      A       8          1.258
LGA    R       9      R       9          2.138
LGA    I      10      I      10          2.061
LGA    N      11      N      11          1.381
LGA    E      12      E      12          1.812
LGA    L      13      L      13          3.092
LGA    A      14      A      14          2.283
LGA    A      15      A      15          1.282
LGA    K      16      K      16          2.797
LGA    A      17      A      17          3.753
LGA    K      18      K      18          1.864
LGA    A      19      A      19          2.138
LGA    G      20      G      20          1.524
LGA    V      21      V      21          1.361
LGA    I      22      I      22          1.581
LGA    T      23      T      23          1.600
LGA    E      24      E      24          1.330
LGA    E      25      E      25          0.512
LGA    E      26      E      26          0.729
LGA    K      27      K      27          1.103
LGA    A      28      A      28          0.523
LGA    E      29      E      29          0.795
LGA    Q      30      Q      30          1.551
LGA    Q      31      Q      31          1.177
LGA    K      32      K      32          1.483
LGA    L      33      L      33          1.544
LGA    R      34      R      34          1.314
LGA    Q      35      Q      35          0.648
LGA    E      36      E      36          1.871
LGA    Y      37      Y      37          2.086
LGA    L      38      L      38          0.764
LGA    K      39      K      39          2.102
LGA    G      40      G      40          3.140
LGA    F      41      F      41          0.915
LGA    R      42      -       -           -
LGA    S      43      -       -           -
LGA    S      44      R      42          1.905
LGA    M      45      -       -           -
LGA    K      46      -       -           -
LGA    N      47      -       -           -
LGA    T      48      -       -           -
LGA    L      49      -       -           -
LGA    K      50      -       -           -
LGA    S      51      -       -           -
LGA    V      52      -       -           -
LGA    K      53      -       -           -
LGA    I      54      -       -           -
LGA    I      55      -       -           -
LGA    D      56      -       -           -
LGA    P      57      -       -           -
LGA    E      58      -       -           -
LGA    G      59      -       -           -
LGA    N      60      -       -           -
LGA    D      61      -       -           -
LGA    V      62      -       -           -
LGA    T      63      -       -           -
LGA    P      64      -       -           -
LGA    E      65      -       -           -
LGA    K      66      -       -           -
LGA    L      67      -       -           -
LGA    K      68      -       -           -
LGA    R      69      -       -           -
LGA    E      70      -       -           -
LGA    Q      71      -       -           -
LGA    R      72      -       -           -
LGA    N      73      -       -           -
LGA    N      74      -       -           -
LGA    K      75      -       -           -
LGA    L      76      -       -           -
LGA    H      77      -       -           -
LGA    L      78      -       -           -
LGA    E      79      -       -           -
LGA    H      80      -       -           -
LGA    H      81      -       -           -
LGA    H      82      -       -           -
LGA    H      83      -       -           -
LGA    H      84      -       -           -
LGA    H      85      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   42    5.0     39    1.79    97.44     84.463     2.063

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.249247 * X  +   0.375692 * Y  +   0.892598 * Z  +   4.442441
  Y_new =   0.887553 * X  +  -0.457370 * Y  +  -0.055332 * Z  +   1.699225
  Z_new =   0.387460 * X  +   0.806020 * Y  +  -0.447445 * Z  +  -6.697079 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.077569   -1.064024  [ DEG:   119.0359    -60.9641 ]
  Theta =  -0.397875   -2.743718  [ DEG:   -22.7965   -157.2035 ]
  Phi   =   1.297023   -1.844570  [ DEG:    74.3139   -105.6861 ]
 
# 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: T0335TS393_1                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS393_1.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   42   5.0   39   1.79   97.44  84.463
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS393_1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -1.230 -18.624 -10.153  1.00 25.00           C
ATOM      2  CA  ILE     2      -3.717 -15.828 -10.626  1.00 25.00           C
ATOM      3  CA  SER     3      -1.492 -13.179 -12.121  1.00 25.00           C
ATOM      4  CA  ASN     4      -0.673  -9.982 -10.264  1.00 25.00           C
ATOM      5  CA  ALA     5       0.607 -10.558  -6.701  1.00 25.00           C
ATOM      6  CA  LYS     6       1.965  -6.979  -6.585  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.407  -5.632  -7.798  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.217  -7.664  -5.103  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.837  -6.292  -2.436  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.476  -2.721  -3.668  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.255  -3.321  -3.518  1.00 25.00           C
ATOM     12  CA  GLU    12      -4.925  -4.668   0.052  1.00 25.00           C
ATOM     13  CA  LEU    13      -2.882  -1.587   1.052  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.544   0.704  -0.476  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.284  -1.159   1.445  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.292  -0.789   4.695  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.865   2.960   4.036  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.627   3.302   3.404  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.369   1.449   6.672  1.00 25.00           C
ATOM     20  CA  GLY    20     -11.482   2.216  10.198  1.00 25.00           C
ATOM     21  CA  VAL    21      -8.699   4.052  12.102  1.00 25.00           C
ATOM     22  CA  ILE    22      -5.185   3.941  10.511  1.00 25.00           C
ATOM     23  CA  THR    23      -1.901   4.465  12.439  1.00 25.00           C
ATOM     24  CA  GLU    24       1.404   6.077  11.356  1.00 25.00           C
ATOM     25  CA  GLU    25       3.293   2.810  10.705  1.00 25.00           C
ATOM     26  CA  GLU    26       0.387   1.528   8.564  1.00 25.00           C
ATOM     27  CA  LYS    27       0.376   4.801   6.575  1.00 25.00           C
ATOM     28  CA  ALA    28       4.154   4.506   6.023  1.00 25.00           C
ATOM     29  CA  GLU    29       3.722   0.896   4.820  1.00 25.00           C
ATOM     30  CA  GLN    30       0.963   2.005   2.406  1.00 25.00           C
ATOM     31  CA  GLN    31       3.223   4.791   1.064  1.00 25.00           C
ATOM     32  CA  LYS    32       6.066   2.275   0.560  1.00 25.00           C
ATOM     33  CA  LEU    33       3.688  -0.077  -1.306  1.00 25.00           C
ATOM     34  CA  ARG    34       2.539   2.816  -3.538  1.00 25.00           C
ATOM     35  CA  GLN    35       6.185   3.723  -4.280  1.00 25.00           C
ATOM     36  CA  GLU    36       6.937   0.076  -5.174  1.00 25.00           C
ATOM     37  CA  TYR    37       3.899  -0.004  -7.506  1.00 25.00           C
ATOM     38  CA  LEU    38       5.072   3.232  -9.185  1.00 25.00           C
ATOM     39  CA  LYS    39       8.571   1.748  -9.655  1.00 25.00           C
ATOM     40  CA  GLY    40       7.052  -1.412 -11.195  1.00 25.00           C
ATOM     41  CA  PHE    41       4.949   0.729 -13.574  1.00 25.00           C
ATOM     42  CA  ARG    42       8.068   2.706 -14.591  1.00 25.00           C
ATOM     43  CA  SER    43       9.956  -0.561 -15.242  1.00 25.00           C
ATOM     44  CA  SER    44       7.051  -1.843 -17.383  1.00 25.00           C
ATOM     45  CA  MET    45       7.040   1.430 -19.372  1.00 25.00           C
ATOM     46  CA  LYS    46      10.819   1.136 -19.924  1.00 25.00           C
ATOM     47  CA  ASN    47      10.386  -2.474 -21.127  1.00 25.00           C
ATOM     48  CA  THR    48       7.627  -1.366 -23.541  1.00 25.00           C
ATOM     49  CA  LEU    49       9.886   1.419 -24.883  1.00 25.00           C
ATOM     50  CA  LYS    50       7.958   4.668 -24.688  1.00 25.00           C
ATOM     51  CA  SER    51       4.435   3.706 -23.604  1.00 25.00           C
ATOM     52  CA  VAL    52       1.557   4.064 -21.104  1.00 25.00           C
ATOM     53  CA  LYS    53      -1.325   1.621 -21.503  1.00 25.00           C
ATOM     54  CA  ILE    54      -3.133   2.427 -18.212  1.00 25.00           C
ATOM     55  CA  ILE    55      -5.946   3.371 -15.808  1.00 25.00           C
ATOM     56  CA  ASP    56      -4.888   6.376 -13.735  1.00 25.00           C
ATOM     57  CA  PRO    57      -7.723   8.764 -14.350  1.00 25.00           C
ATOM     58  CA  GLU    58      -8.584  12.288 -15.360  1.00 25.00           C
ATOM     59  CA  GLY    59      -6.553  13.324 -18.408  1.00 25.00           C
ATOM     60  CA  ASN    60      -3.896  14.188 -15.825  1.00 25.00           C
ATOM     61  CA  ASP    61      -2.159  12.112 -13.221  1.00 25.00           C
ATOM     62  CA  VAL    62      -0.176   9.227 -14.815  1.00 25.00           C
ATOM     63  CA  THR    63       2.613  11.851 -14.885  1.00 25.00           C
ATOM     64  CA  PRO    64       5.914  10.183 -15.943  1.00 25.00           C
ATOM     65  CA  GLU    65       7.769  13.124 -14.339  1.00 25.00           C
ATOM     66  CA  LYS    66       8.060  11.179 -11.052  1.00 25.00           C
ATOM     67  CA  LEU    67       9.431   8.143 -12.941  1.00 25.00           C
ATOM     68  CA  LYS    68      11.991  10.371 -14.715  1.00 25.00           C
ATOM     69  CA  ARG    69      13.059  11.862 -11.353  1.00 25.00           C
ATOM     70  CA  GLU    70      13.454   8.345  -9.891  1.00 25.00           C
ATOM     71  CA  GLN    71      15.576   7.304 -12.903  1.00 25.00           C
ATOM     72  CA  ARG    72      17.770  10.411 -12.463  1.00 25.00           C
ATOM     73  CA  ASN    73      18.213   9.603  -8.746  1.00 25.00           C
ATOM     74  CA  ASN    74      19.192   6.005  -9.620  1.00 25.00           C
ATOM     75  CA  LYS    75      22.876   6.318  -8.855  1.00 25.00           C
ATOM     76  CA  LEU    76      23.287   2.624  -9.895  1.00 25.00           C
ATOM     77  CA  HIS    77      22.628  -0.083  -7.258  1.00 25.00           C
ATOM     78  CA  LEU    78      24.333  -2.117  -4.613  1.00 25.00           C
ATOM     79  CA  GLU    79      22.289  -5.361  -4.918  1.00 25.00           C
ATOM     80  CA  HIS    80      19.164  -5.775  -2.793  1.00 25.00           C
ATOM     81  CA  HIS    81      17.184  -3.830  -0.191  1.00 25.00           C
ATOM     82  CA  HIS    82      17.681  -1.782   2.906  1.00 25.00           C
ATOM     83  CA  HIS    83      17.366  -4.380   5.641  1.00 25.00           C
ATOM     84  CA  HIS    84      14.351  -5.251   7.838  1.00 25.00           C
ATOM     85  CA  HIS    85      15.631  -8.774   8.742  1.00 25.00           C
TER
END
