
#######################################################
#                                                     #
#                        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 T0353TS393_3
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS393_3.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    Q       2      -       -           -
LGA    I       3      -       -           -
LGA    H       4      -       -           -
LGA    V       5      -       -           -
LGA    Y       6      -       -           -
LGA    D       7      -       -           -
LGA    T       8      -       -           -
LGA    Y       9      -       -           -
LGA    V      10      -       -           -
LGA    K      11      -       -           -
LGA    A      12      -       -           -
LGA    K      13      -       -           -
LGA    D      14      M       1           #
LGA    G      15      Q       2          1.949
LGA    H      16      I       3          2.110
LGA    V      17      H       4          3.935
LGA    M      18      V       5          3.163
LGA    H      19      Y       6          2.193
LGA    F      20      D       7          2.458
LGA    D      21      T       8          5.084
LGA    V      22      Y       9          4.246
LGA    F      23      V      10          4.861
LGA    T      24      K      11           #
LGA    -       -      A      12           -
LGA    -       -      K      13           -
LGA    D      25      D      14           #
LGA    V      26      G      15          2.152
LGA    R      27      H      16          4.297
LGA    D      28      -       -           -
LGA    D      29      V      17          2.667
LGA    K      30      -       -           -
LGA    K      31      -       -           -
LGA    A      32      M      18          4.311
LGA    I      33      H      19          4.214
LGA    E      34      -       -           -
LGA    F      35      -       -           -
LGA    A      36      F      20           #
LGA    K      37      D      21           #
LGA    Q      38      V      22           -
LGA    W      39      F      23           -
LGA    L      40      T      24           -
LGA    S      41      D      25           -
LGA    S      42      V      26           -
LGA    I      43      R      27           -
LGA    G      44      -       -           -
LGA    E      45      -       -           -
LGA    E      46      -       -           -
LGA    G      47      D      28           #
LGA    A      48      D      29          1.735
LGA    T      49      K      30          2.305
LGA    V      50      K      31          1.924
LGA    -       -      A      32           -
LGA    -       -      I      33           -
LGA    T      51      E      34          1.787
LGA    S      52      F      35          3.384
LGA    -       -      A      36           -
LGA    -       -      K      37           -
LGA    -       -      Q      38           -
LGA    -       -      W      39           -
LGA    E      53      L      40           #
LGA    E      54      S      41          3.942
LGA    C      55      S      42          4.358
LGA    R      56      I      43          2.223
LGA    F      57      G      44          3.980
LGA    C      58      -       -           -
LGA    H      59      -       -           -
LGA    S      60      E      45           #
LGA    Q      61      E      46          3.424
LGA    K      62      G      47           -
LGA    A      63      A      48           #
LGA    P      64      T      49           #
LGA    D      65      V      50          2.400
LGA    E      66      T      51          3.651
LGA    V      67      -       -           -
LGA    I      68      S      52          2.169
LGA    E      69      E      53          3.219
LGA    A      70      E      54           #
LGA    I      71      C      55           #
LGA    K      72      -       -           -
LGA    Q      73      -       -           -
LGA    N      74      -       -           -
LGA    G      75      -       -           -
LGA    Y      76      R      56          3.199
LGA    F      77      F      57          2.279
LGA    I      78      C      58           -
LGA    Y      79      H      59           -
LGA    K      80      S      60           -
LGA    M      81      Q      61           -
LGA    E      82      K      62           -
LGA    G      83      A      63           -
LGA    C      84      P      64           -
LGA    N      85      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    -       -      I      78           -
LGA    -       -      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -
LGA    -       -      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   85    5.0     30    3.28     6.67     21.260     0.889

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.945210 * X  +  -0.292252 * Y  +   0.145489 * Z  +  -4.950321
  Y_new =  -0.065290 * X  +   0.605872 * Y  +   0.792878 * Z  +   4.678896
  Z_new =  -0.319868 * X  +   0.739937 * Y  +  -0.591758 * Z  +   3.075708 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.245379   -0.896214  [ DEG:   128.6507    -51.3493 ]
  Theta =   0.325590    2.816003  [ DEG:    18.6549    161.3451 ]
  Phi   =  -3.072628    0.068965  [ DEG:  -176.0486      3.9514 ]
 
# 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: T0353TS393_3                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS393_3.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   85   5.0   30   3.28    6.67  21.260
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS393_3
PFRMAT TS
TARGET T0353
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1     -20.157   9.412  11.015  1.00 25.00           C
ATOM      2  CA  GLN     2     -16.834   7.940   9.742  1.00 25.00           C
ATOM      3  CA  ILE     3     -13.651   6.513   8.151  1.00 25.00           C
ATOM      4  CA  HIS     4     -11.167   3.745   7.460  1.00 25.00           C
ATOM      5  CA  VAL     5      -7.463   2.947   7.067  1.00 25.00           C
ATOM      6  CA  TYR     6      -5.357   3.422   3.905  1.00 25.00           C
ATOM      7  CA  ASP     7      -1.850   3.279   2.451  1.00 25.00           C
ATOM      8  CA  THR     8      -1.675  -0.554   2.598  1.00 25.00           C
ATOM      9  CA  TYR     9      -2.238  -1.163  -1.129  1.00 25.00           C
ATOM     10  CA  VAL    10       0.579   1.104  -2.299  1.00 25.00           C
ATOM     11  CA  LYS    11       2.747  -0.881   0.040  1.00 25.00           C
ATOM     12  CA  ALA    12       6.467  -0.775   0.624  1.00 25.00           C
ATOM     13  CA  LYS    13      10.133  -0.733  -0.395  1.00 25.00           C
ATOM     14  CA  ASP    14      12.561   0.132  -3.195  1.00 25.00           C
ATOM     15  CA  GLY    15      11.486   0.792  -6.733  1.00 25.00           C
ATOM     16  CA  HIS    16       7.685   1.048  -6.208  1.00 25.00           C
ATOM     17  CA  VAL    17       4.051   2.150  -6.709  1.00 25.00           C
ATOM     18  CA  MET    18       4.780   4.031  -3.434  1.00 25.00           C
ATOM     19  CA  HIS    19       3.980   4.046   0.257  1.00 25.00           C
ATOM     20  CA  PHE    20       2.966   3.446   3.932  1.00 25.00           C
ATOM     21  CA  ASP    21       1.545   2.081   7.223  1.00 25.00           C
ATOM     22  CA  VAL    22      -2.122   1.308   7.277  1.00 25.00           C
ATOM     23  CA  PHE    23      -4.062  -1.306   9.327  1.00 25.00           C
ATOM     24  CA  THR    24      -7.079  -3.446  10.212  1.00 25.00           C
ATOM     25  CA  ASP    25     -10.150  -3.508  12.457  1.00 25.00           C
ATOM     26  CA  VAL    26     -10.266  -2.873  16.147  1.00 25.00           C
ATOM     27  CA  ARG    27      -9.395   0.181  18.288  1.00 25.00           C
ATOM     28  CA  ASP    28      -5.660  -0.543  17.845  1.00 25.00           C
ATOM     29  CA  ASP    29      -6.141  -0.834  14.056  1.00 25.00           C
ATOM     30  CA  LYS    30      -8.022   2.502  14.014  1.00 25.00           C
ATOM     31  CA  LYS    31      -5.202   4.147  16.016  1.00 25.00           C
ATOM     32  CA  ALA    32      -2.614   2.751  13.562  1.00 25.00           C
ATOM     33  CA  ILE    33      -4.646   4.103  10.611  1.00 25.00           C
ATOM     34  CA  GLU    34      -4.841   7.540  12.289  1.00 25.00           C
ATOM     35  CA  PHE    35      -1.054   7.506  12.856  1.00 25.00           C
ATOM     36  CA  ALA    36      -0.487   6.592   9.180  1.00 25.00           C
ATOM     37  CA  LYS    37      -2.785   9.455   8.088  1.00 25.00           C
ATOM     38  CA  GLN    38      -0.866  11.887  10.342  1.00 25.00           C
ATOM     39  CA  TRP    39       2.451  10.690   8.849  1.00 25.00           C
ATOM     40  CA  LEU    40       1.068  11.186   5.313  1.00 25.00           C
ATOM     41  CA  SER    41      -0.083  14.721   6.233  1.00 25.00           C
ATOM     42  CA  SER    42       3.387  15.509   7.649  1.00 25.00           C
ATOM     43  CA  ILE    43       4.545  14.806   4.114  1.00 25.00           C
ATOM     44  CA  GLY    44       3.568  16.149   0.661  1.00 25.00           C
ATOM     45  CA  GLU    45       2.222  16.798  -2.857  1.00 25.00           C
ATOM     46  CA  GLU    46      -0.676  15.718  -5.168  1.00 25.00           C
ATOM     47  CA  GLY    47      -2.606  12.579  -6.147  1.00 25.00           C
ATOM     48  CA  ALA    48      -3.060   8.822  -6.542  1.00 25.00           C
ATOM     49  CA  THR    49      -4.812   5.707  -7.785  1.00 25.00           C
ATOM     50  CA  VAL    50      -4.467   2.874  -5.246  1.00 25.00           C
ATOM     51  CA  THR    51      -6.662   0.486  -3.287  1.00 25.00           C
ATOM     52  CA  SER    52      -8.370  -2.930  -3.194  1.00 25.00           C
ATOM     53  CA  GLU    53      -9.880  -6.463  -2.924  1.00 25.00           C
ATOM     54  CA  GLU    54      -8.933  -9.308  -0.527  1.00 25.00           C
ATOM     55  CA  CYS    55      -6.214  -6.856   0.543  1.00 25.00           C
ATOM     56  CA  ARG    56      -6.780  -8.569   3.935  1.00 25.00           C
ATOM     57  CA  PHE    57      -8.655  -6.453   6.479  1.00 25.00           C
ATOM     58  CA  CYS    58      -7.654  -3.458   4.345  1.00 25.00           C
ATOM     59  CA  HIS    59     -10.056  -1.442   6.445  1.00 25.00           C
ATOM     60  CA  SER    60     -13.525  -1.002   5.053  1.00 25.00           C
ATOM     61  CA  GLN    61     -13.760  -3.340   2.079  1.00 25.00           C
ATOM     62  CA  LYS    62     -13.418  -0.200   0.019  1.00 25.00           C
ATOM     63  CA  ALA    63      -9.931   0.532   1.461  1.00 25.00           C
ATOM     64  CA  PRO    64      -9.902   4.300   0.738  1.00 25.00           C
ATOM     65  CA  ASP    65     -12.162   6.529   2.882  1.00 25.00           C
ATOM     66  CA  GLU    66      -9.140   7.644   4.953  1.00 25.00           C
ATOM     67  CA  VAL    67      -7.212   8.458   1.745  1.00 25.00           C
ATOM     68  CA  ILE    68     -10.187  10.490   0.444  1.00 25.00           C
ATOM     69  CA  GLU    69     -10.363  12.400   3.759  1.00 25.00           C
ATOM     70  CA  ALA    70      -6.610  13.135   3.565  1.00 25.00           C
ATOM     71  CA  ILE    71      -7.019  14.400  -0.028  1.00 25.00           C
ATOM     72  CA  LYS    72      -9.912  16.655   1.070  1.00 25.00           C
ATOM     73  CA  GLN    73      -7.781  18.037   3.936  1.00 25.00           C
ATOM     74  CA  ASN    74      -4.420  17.332   2.300  1.00 25.00           C
ATOM     75  CA  GLY    75      -1.535  15.661   0.411  1.00 25.00           C
ATOM     76  CA  TYR    76      -1.929  11.878   0.654  1.00 25.00           C
ATOM     77  CA  PHE    77       0.070   8.676   0.577  1.00 25.00           C
ATOM     78  CA  ILE    78      -2.999   7.159  -1.192  1.00 25.00           C
ATOM     79  CA  TYR    79      -6.283   7.135  -3.098  1.00 25.00           C
ATOM     80  CA  LYS    80      -9.033   4.848  -4.405  1.00 25.00           C
ATOM     81  CA  MET    81     -10.682   1.849  -6.179  1.00 25.00           C
ATOM     82  CA  GLU    82     -14.281   3.032  -5.763  1.00 25.00           C
ATOM     83  CA  GLY    83     -17.937   2.644  -4.854  1.00 25.00           C
ATOM     84  CA  CYS    84     -19.530   4.262  -1.820  1.00 25.00           C
ATOM     85  CA  ASN    85     -22.353   5.699  -3.988  1.00 25.00           C
TER
END
