
#######################################################
#                                                     #
#                        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 T0335TS168_2
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS168_2.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    I       2      -       -           -
LGA    S       3      -       -           -
LGA    N       4      -       -           -
LGA    A       5      -       -           -
LGA    K       6      M       1           #
LGA    -       -      I       2           -
LGA    I       7      S       3          1.941
LGA    A       8      N       4          2.891
LGA    -       -      A       5           -
LGA    R       9      K       6          0.921
LGA    I      10      I       7          1.648
LGA    N      11      A       8          1.488
LGA    E      12      R       9          0.708
LGA    L      13      I      10          0.789
LGA    A      14      N      11          1.019
LGA    A      15      E      12          1.125
LGA    K      16      L      13          1.284
LGA    A      17      A      14          1.404
LGA    K      18      A      15          0.858
LGA    A      19      K      16          0.994
LGA    G      20      A      17          2.940
LGA    V      21      K      18          6.403
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    I      22      I      22          3.112
LGA    T      23      T      23          1.644
LGA    E      24      E      24          1.264
LGA    E      25      E      25          1.071
LGA    E      26      E      26          1.223
LGA    K      27      K      27          1.002
LGA    A      28      A      28          1.026
LGA    E      29      E      29          0.834
LGA    Q      30      Q      30          0.489
LGA    Q      31      Q      31          1.505
LGA    K      32      K      32          1.048
LGA    L      33      L      33          0.375
LGA    R      34      R      34          0.483
LGA    Q      35      Q      35          0.942
LGA    E      36      E      36          0.584
LGA    Y      37      Y      37          0.708
LGA    L      38      L      38          1.125
LGA    K      39      K      39          1.305
LGA    G      40      G      40          1.507
LGA    F      41      F      41          1.339
LGA    R      42      R      42          3.862
LGA    S      43      -       -           -
LGA    S      44      -       -           -
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     36    1.85    63.89     79.664     1.845

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.324466 * X  +  -0.542281 * Y  +   0.775018 * Z  +   5.603961
  Y_new =  -0.920604 * X  +  -0.369250 * Y  +   0.127051 * Z  +   1.669153
  Z_new =   0.217278 * X  +  -0.754709 * Y  +  -0.619035 * Z  +  -8.155830 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.257752    0.883841  [ DEG:  -129.3596     50.6403 ]
  Theta =  -0.219025   -2.922568  [ DEG:   -12.5492   -167.4508 ]
  Phi   =  -1.231942    1.909651  [ DEG:   -70.5851    109.4149 ]
 
# 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: T0335TS168_2                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS168_2.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   36   1.85   63.89  79.664
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS168_2
PFRMAT TS
TARGET T0335
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1       1.985 -20.802 -10.586  1.00 25.00           C
ATOM      2  CA  ILE     2       4.056 -17.593 -10.631  1.00 25.00           C
ATOM      3  CA  SER     3       1.139 -15.533 -12.006  1.00 25.00           C
ATOM      4  CA  ASN     4       2.268 -11.928 -11.370  1.00 25.00           C
ATOM      5  CA  ALA     5       3.956 -11.343  -7.983  1.00 25.00           C
ATOM      6  CA  LYS     6       4.040  -7.572  -8.648  1.00 25.00           C
ATOM      7  CA  ILE     7       0.321  -7.627  -9.566  1.00 25.00           C
ATOM      8  CA  ALA     8      -0.471  -9.539  -6.344  1.00 25.00           C
ATOM      9  CA  ARG     9       1.521  -6.981  -4.307  1.00 25.00           C
ATOM     10  CA  ILE    10      -0.379  -4.118  -5.998  1.00 25.00           C
ATOM     11  CA  ASN    11      -3.712  -5.831  -5.210  1.00 25.00           C
ATOM     12  CA  GLU    12      -2.655  -6.260  -1.554  1.00 25.00           C
ATOM     13  CA  LEU    13      -1.691  -2.558  -1.374  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.083  -1.576  -2.854  1.00 25.00           C
ATOM     15  CA  ALA    15      -6.871  -3.779  -0.282  1.00 25.00           C
ATOM     16  CA  LYS    16      -4.858  -2.156   2.543  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.770   1.323   1.229  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.467   0.331   1.098  1.00 25.00           C
ATOM     19  CA  ALA    19      -9.272  -0.964   4.697  1.00 25.00           C
ATOM     20  CA  GLY    20      -9.387   1.295   7.739  1.00 25.00           C
ATOM     21  CA  VAL    21      -6.712   0.018  10.108  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.026   1.463   7.892  1.00 25.00           C
ATOM     23  CA  THR    23      -3.254   4.676   9.752  1.00 25.00           C
ATOM     24  CA  GLU    24       0.542   5.329   9.937  1.00 25.00           C
ATOM     25  CA  GLU    25       3.587   3.048   9.496  1.00 25.00           C
ATOM     26  CA  GLU    26       1.464   0.559   7.506  1.00 25.00           C
ATOM     27  CA  LYS    27       0.174   3.397   5.282  1.00 25.00           C
ATOM     28  CA  ALA    28       3.763   4.595   4.687  1.00 25.00           C
ATOM     29  CA  GLU    29       4.825   1.033   3.762  1.00 25.00           C
ATOM     30  CA  GLN    30       1.885   0.766   1.321  1.00 25.00           C
ATOM     31  CA  GLN    31       2.864   4.113  -0.262  1.00 25.00           C
ATOM     32  CA  LYS    32       6.481   2.911  -0.627  1.00 25.00           C
ATOM     33  CA  LEU    33       5.265  -0.326  -2.275  1.00 25.00           C
ATOM     34  CA  ARG    34       3.088   1.693  -4.693  1.00 25.00           C
ATOM     35  CA  GLN    35       6.078   3.922  -5.563  1.00 25.00           C
ATOM     36  CA  GLU    36       8.235   0.822  -6.199  1.00 25.00           C
ATOM     37  CA  TYR    37       5.514  -0.637  -8.464  1.00 25.00           C
ATOM     38  CA  LEU    38       5.321   2.663 -10.398  1.00 25.00           C
ATOM     39  CA  LYS    39       9.127   2.668 -10.817  1.00 25.00           C
ATOM     40  CA  GLY    40       9.016  -0.941 -12.095  1.00 25.00           C
ATOM     41  CA  PHE    41       6.266  -0.000 -14.588  1.00 25.00           C
ATOM     42  CA  ARG    42       8.350   2.976 -15.802  1.00 25.00           C
ATOM     43  CA  SER    43      11.395   0.695 -16.243  1.00 25.00           C
ATOM     44  CA  SER    44       9.272  -1.795 -18.232  1.00 25.00           C
ATOM     45  CA  MET    45       7.983   1.043 -20.457  1.00 25.00           C
ATOM     46  CA  LYS    46      11.572   2.240 -21.051  1.00 25.00           C
ATOM     47  CA  ASN    47      12.632  -1.321 -21.977  1.00 25.00           C
ATOM     48  CA  THR    48       9.693  -1.588 -24.418  1.00 25.00           C
ATOM     49  CA  LEU    49      10.672   1.759 -26.001  1.00 25.00           C
ATOM     50  CA  LYS    50       7.235   3.356 -25.426  1.00 25.00           C
ATOM     51  CA  SER    51       4.066   3.561 -23.397  1.00 25.00           C
ATOM     52  CA  VAL    52       3.217   2.064 -19.993  1.00 25.00           C
ATOM     53  CA  LYS    53       0.730   0.260 -17.762  1.00 25.00           C
ATOM     54  CA  ILE    54      -1.291   3.257 -16.508  1.00 25.00           C
ATOM     55  CA  ILE    55      -2.835   5.769 -14.206  1.00 25.00           C
ATOM     56  CA  ASP    56      -2.731   8.814 -16.398  1.00 25.00           C
ATOM     57  CA  PRO    57      -6.297   9.990 -16.895  1.00 25.00           C
ATOM     58  CA  GLU    58      -5.692  13.629 -15.977  1.00 25.00           C
ATOM     59  CA  GLY    59      -4.635  14.807 -19.448  1.00 25.00           C
ATOM     60  CA  ASN    60      -1.133  16.248 -19.416  1.00 25.00           C
ATOM     61  CA  ASP    61       0.276  15.289 -16.017  1.00 25.00           C
ATOM     62  CA  VAL    62       0.911  12.036 -14.223  1.00 25.00           C
ATOM     63  CA  THR    63       3.684  10.591 -16.360  1.00 25.00           C
ATOM     64  CA  PRO    64       6.732  10.771 -18.579  1.00 25.00           C
ATOM     65  CA  GLU    65       8.842  13.768 -17.472  1.00 25.00           C
ATOM     66  CA  LYS    66       9.267  12.217 -13.996  1.00 25.00           C
ATOM     67  CA  LEU    67      10.345   8.901 -15.580  1.00 25.00           C
ATOM     68  CA  LYS    68      12.883  10.746 -17.775  1.00 25.00           C
ATOM     69  CA  ARG    69      14.260  12.564 -14.699  1.00 25.00           C
ATOM     70  CA  GLU    70      14.579   9.230 -12.843  1.00 25.00           C
ATOM     71  CA  GLN    71      16.427   7.713 -15.834  1.00 25.00           C
ATOM     72  CA  ARG    72      18.801  10.717 -15.921  1.00 25.00           C
ATOM     73  CA  ASN    73      19.465  10.334 -12.169  1.00 25.00           C
ATOM     74  CA  ASN    74      20.197   6.606 -12.655  1.00 25.00           C
ATOM     75  CA  LYS    75      23.527   4.712 -12.402  1.00 25.00           C
ATOM     76  CA  LEU    76      23.014   4.862  -8.580  1.00 25.00           C
ATOM     77  CA  HIS    77      22.005   1.181  -9.026  1.00 25.00           C
ATOM     78  CA  LEU    78      23.866   0.626  -5.722  1.00 25.00           C
ATOM     79  CA  GLU    79      23.041   3.779  -3.802  1.00 25.00           C
ATOM     80  CA  HIS    80      19.995   2.035  -2.319  1.00 25.00           C
ATOM     81  CA  HIS    81      19.293  -1.719  -2.053  1.00 25.00           C
ATOM     82  CA  HIS    82      17.050  -1.126   0.955  1.00 25.00           C
ATOM     83  CA  HIS    83      17.241  -1.177   4.790  1.00 25.00           C
ATOM     84  CA  HIS    84      14.527  -3.449   6.223  1.00 25.00           C
ATOM     85  CA  HIS    85      12.547  -6.250   7.819  1.00 25.00           C
TER
END
