
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS393_4.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    Q       2      Q       2           -
LGA    I       3      I       3           -
LGA    H       4      H       4           -
LGA    V       5      V       5           #
LGA    Y       6      Y       6          3.297
LGA    D       7      D       7          4.346
LGA    T       8      T       8          1.370
LGA    Y       9      Y       9          1.922
LGA    V      10      V      10          1.618
LGA    K      11      K      11           #
LGA    A      12      A      12           #
LGA    K      13      K      13           #
LGA    D      14      D      14          4.342
LGA    G      15      G      15          2.366
LGA    H      16      H      16          1.946
LGA    V      17      V      17          2.353
LGA    M      18      M      18          2.388
LGA    H      19      H      19          1.904
LGA    F      20      F      20          2.939
LGA    -       -      D      21           -
LGA    D      21      V      22          3.967
LGA    V      22      F      23           -
LGA    F      23      -       -           -
LGA    T      24      -       -           -
LGA    D      25      -       -           -
LGA    V      26      -       -           -
LGA    R      27      -       -           -
LGA    D      28      -       -           -
LGA    D      29      T      24           #
LGA    K      30      D      25           #
LGA    -       -      V      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    -       -      D      29           -
LGA    K      31      K      30           #
LGA    A      32      K      31          5.034
LGA    I      33      A      32          4.278
LGA    E      34      I      33          2.907
LGA    F      35      E      34          0.998
LGA    -       -      F      35           -
LGA    A      36      A      36          3.194
LGA    K      37      K      37          4.994
LGA    Q      38      Q      38           -
LGA    W      39      W      39           -
LGA    -       -      L      40           -
LGA    -       -      S      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      E      45           -
LGA    -       -      E      46           -
LGA    -       -      G      47           -
LGA    L      40      A      48          4.558
LGA    S      41      T      49          3.548
LGA    S      42      V      50          4.385
LGA    I      43      T      51          3.751
LGA    G      44      -       -           -
LGA    E      45      -       -           -
LGA    E      46      -       -           -
LGA    G      47      -       -           -
LGA    A      48      -       -           -
LGA    T      49      -       -           -
LGA    V      50      -       -           -
LGA    T      51      -       -           -
LGA    S      52      -       -           -
LGA    E      53      -       -           -
LGA    E      54      -       -           -
LGA    C      55      -       -           -
LGA    R      56      -       -           -
LGA    F      57      -       -           -
LGA    C      58      -       -           -
LGA    H      59      -       -           -
LGA    S      60      -       -           -
LGA    Q      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      -       -           -
LGA    P      64      -       -           -
LGA    D      65      -       -           -
LGA    E      66      -       -           -
LGA    V      67      -       -           -
LGA    I      68      -       -           -
LGA    E      69      -       -           -
LGA    A      70      S      52          2.551
LGA    I      71      -       -           -
LGA    K      72      -       -           -
LGA    Q      73      -       -           -
LGA    N      74      -       -           -
LGA    G      75      -       -           -
LGA    Y      76      E      53          2.480
LGA    F      77      E      54          1.444
LGA    I      78      C      55          4.205
LGA    Y      79      R      56          1.320
LGA    K      80      F      57          3.052
LGA    M      81      C      58          2.850
LGA    E      82      H      59          4.133
LGA    G      83      S      60           #
LGA    C      84      Q      61           -
LGA    N      85      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      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     31    3.26    45.16     21.104     0.923

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.557089 * X  +   0.830387 * Y  +  -0.010491 * Z  +  -1.379206
  Y_new =  -0.415193 * X  +  -0.267559 * Y  +   0.869498 * Z  +   5.260781
  Z_new =   0.719213 * X  +   0.488743 * Y  +   0.493825 * Z  +   1.781044 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.780227   -2.361366  [ DEG:    44.7037   -135.2963 ]
  Theta =  -0.802669   -2.338924  [ DEG:   -45.9895   -134.0105 ]
  Phi   =  -2.501113    0.640480  [ DEG:  -143.3032     36.6968 ]
 
# 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_4                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS393_4.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   31   3.26   45.16  21.104
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS393_4
PFRMAT TS
TARGET T0353
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      13.116  10.251  13.056  1.00 25.00           C
ATOM      2  CA  GLN     2      10.514   9.872  10.268  1.00 25.00           C
ATOM      3  CA  ILE     3       7.357   7.999   9.517  1.00 25.00           C
ATOM      4  CA  HIS     4       4.643   5.613   8.393  1.00 25.00           C
ATOM      5  CA  VAL     5       2.497   5.180   5.248  1.00 25.00           C
ATOM      6  CA  TYR     6       2.416   2.501   2.524  1.00 25.00           C
ATOM      7  CA  ASP     7      -1.235   2.911   1.339  1.00 25.00           C
ATOM      8  CA  THR     8      -2.093   2.840   5.052  1.00 25.00           C
ATOM      9  CA  TYR     9      -5.461   3.327   6.753  1.00 25.00           C
ATOM     10  CA  VAL    10      -7.817   0.783   8.265  1.00 25.00           C
ATOM     11  CA  LYS    11      -6.345  -2.057   6.179  1.00 25.00           C
ATOM     12  CA  ALA    12      -8.462  -4.209   8.471  1.00 25.00           C
ATOM     13  CA  LYS    13      -9.174  -4.241  12.225  1.00 25.00           C
ATOM     14  CA  ASP    14      -9.405  -4.622  16.051  1.00 25.00           C
ATOM     15  CA  GLY    15      -6.465  -3.065  17.966  1.00 25.00           C
ATOM     16  CA  HIS    16      -4.227  -0.333  16.523  1.00 25.00           C
ATOM     17  CA  VAL    17      -4.839   3.264  15.320  1.00 25.00           C
ATOM     18  CA  MET    18      -4.387   1.961  11.775  1.00 25.00           C
ATOM     19  CA  HIS    19      -1.791   0.295   9.536  1.00 25.00           C
ATOM     20  CA  PHE    20      -1.263  -2.028   6.608  1.00 25.00           C
ATOM     21  CA  ASP    21       0.532  -2.465   3.329  1.00 25.00           C
ATOM     22  CA  VAL    22      -2.864  -1.806   1.778  1.00 25.00           C
ATOM     23  CA  PHE    23      -1.185  -4.244  -0.559  1.00 25.00           C
ATOM     24  CA  THR    24       1.663  -3.954  -3.125  1.00 25.00           C
ATOM     25  CA  ASP    25       3.697  -4.855  -6.253  1.00 25.00           C
ATOM     26  CA  VAL    26       3.777  -4.434 -10.033  1.00 25.00           C
ATOM     27  CA  ARG    27       1.995  -1.298 -11.320  1.00 25.00           C
ATOM     28  CA  ASP    28      -1.343  -3.175 -11.347  1.00 25.00           C
ATOM     29  CA  ASP    29      -0.734  -4.358  -7.756  1.00 25.00           C
ATOM     30  CA  LYS    30       0.061  -0.769  -6.681  1.00 25.00           C
ATOM     31  CA  LYS    31      -3.156   0.469  -8.351  1.00 25.00           C
ATOM     32  CA  ALA    32      -5.166  -2.249  -6.551  1.00 25.00           C
ATOM     33  CA  ILE    33      -3.584  -1.241  -3.212  1.00 25.00           C
ATOM     34  CA  GLU    34      -4.455   2.428  -3.878  1.00 25.00           C
ATOM     35  CA  PHE    35      -8.067   1.447  -4.691  1.00 25.00           C
ATOM     36  CA  ALA    36      -8.273  -0.580  -1.448  1.00 25.00           C
ATOM     37  CA  LYS    37      -6.922   2.405   0.533  1.00 25.00           C
ATOM     38  CA  GLN    38      -9.517   4.697  -1.104  1.00 25.00           C
ATOM     39  CA  TRP    39     -12.300   2.217  -0.222  1.00 25.00           C
ATOM     40  CA  LEU    40     -11.069   2.088   3.403  1.00 25.00           C
ATOM     41  CA  SER    41     -11.047   5.915   3.557  1.00 25.00           C
ATOM     42  CA  SER    42     -14.617   6.016   2.173  1.00 25.00           C
ATOM     43  CA  ILE    43     -14.037   9.802   2.274  1.00 25.00           C
ATOM     44  CA  GLY    44     -13.252  11.924   5.341  1.00 25.00           C
ATOM     45  CA  GLU    45     -11.684  13.931   8.127  1.00 25.00           C
ATOM     46  CA  GLU    46      -8.412  14.548  10.068  1.00 25.00           C
ATOM     47  CA  GLY    47      -6.199  16.493   7.671  1.00 25.00           C
ATOM     48  CA  ALA    48      -3.505  13.953   6.787  1.00 25.00           C
ATOM     49  CA  THR    49      -0.968  11.684   8.598  1.00 25.00           C
ATOM     50  CA  VAL    50       2.366  10.741   7.013  1.00 25.00           C
ATOM     51  CA  THR    51       5.699  10.220   5.294  1.00 25.00           C
ATOM     52  CA  SER    52       7.719   7.341   3.881  1.00 25.00           C
ATOM     53  CA  GLU    53      10.144   4.520   4.616  1.00 25.00           C
ATOM     54  CA  GLU    54      11.521   2.007   2.149  1.00 25.00           C
ATOM     55  CA  CYS    55       8.240   0.222   1.381  1.00 25.00           C
ATOM     56  CA  ARG    56       9.476  -0.022  -2.179  1.00 25.00           C
ATOM     57  CA  PHE    57       6.531  -2.435  -2.760  1.00 25.00           C
ATOM     58  CA  CYS    58       4.179   0.473  -2.141  1.00 25.00           C
ATOM     59  CA  HIS    59       4.583   2.721  -5.230  1.00 25.00           C
ATOM     60  CA  SER    60       5.910   6.260  -5.933  1.00 25.00           C
ATOM     61  CA  GLN    61       8.988   5.216  -4.021  1.00 25.00           C
ATOM     62  CA  LYS    62       6.593   4.813  -1.056  1.00 25.00           C
ATOM     63  CA  ALA    63       3.208   6.473  -1.125  1.00 25.00           C
ATOM     64  CA  PRO    64       0.292   5.402  -3.290  1.00 25.00           C
ATOM     65  CA  ASP    65      -0.155   8.288  -5.768  1.00 25.00           C
ATOM     66  CA  GLU    66      -3.961   7.970  -5.489  1.00 25.00           C
ATOM     67  CA  VAL    67      -3.712   8.024  -1.668  1.00 25.00           C
ATOM     68  CA  ILE    68      -1.511  11.155  -1.832  1.00 25.00           C
ATOM     69  CA  GLU    69      -4.044  12.844  -4.155  1.00 25.00           C
ATOM     70  CA  ALA    70      -6.884  11.957  -1.743  1.00 25.00           C
ATOM     71  CA  ILE    71      -4.883  13.407   1.184  1.00 25.00           C
ATOM     72  CA  LYS    72      -4.258  16.620  -0.803  1.00 25.00           C
ATOM     73  CA  GLN    73      -7.996  16.885  -1.598  1.00 25.00           C
ATOM     74  CA  ASN    74     -10.369  14.934   0.672  1.00 25.00           C
ATOM     75  CA  GLY    75      -8.738  13.971   4.008  1.00 25.00           C
ATOM     76  CA  TYR    76      -7.561  11.061   6.201  1.00 25.00           C
ATOM     77  CA  PHE    77      -6.167   8.753   3.513  1.00 25.00           C
ATOM     78  CA  ILE    78      -3.064   7.937   5.586  1.00 25.00           C
ATOM     79  CA  TYR    79      -0.570   9.534   3.109  1.00 25.00           C
ATOM     80  CA  LYS    80       2.352  11.576   1.735  1.00 25.00           C
ATOM     81  CA  MET    81       5.710  11.489  -0.090  1.00 25.00           C
ATOM     82  CA  GLU    82       8.504  12.959  -2.211  1.00 25.00           C
ATOM     83  CA  GLY    83       9.126  14.311  -5.712  1.00 25.00           C
ATOM     84  CA  CYS    84       8.007  17.692  -4.463  1.00 25.00           C
ATOM     85  CA  ASN    85      10.213  20.738  -3.988  1.00 25.00           C
TER
END
