
#######################################################
#                                                     #
#                        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   96 (   96),  selected   96 , name T0321TS393_4-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS393_4-D1.T0321_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    W       2      W       2           -
LGA    E       3      E       3           -
LGA    I       4      I       4           -
LGA    Y       5      Y       5           -
LGA    D       6      D       6           -
LGA    A       7      A       7           -
LGA    M       8      M       8           -
LGA    I       9      I       9           -
LGA    N      10      N      10           -
LGA    G      11      G      11           -
LGA    I      12      I      12           -
LGA    P      13      P      13           -
LGA    E      14      E      14           -
LGA    D      15      D      15           -
LGA    F      16      F      16           -
LGA    L      17      L      17           -
LGA    V      18      -       -           -
LGA    D      19      -       -           -
LGA    E      20      -       -           -
LGA    L      21      V      18           #
LGA    -       -      D      19           -
LGA    V      22      E      20          3.924
LGA    C      23      L      21          2.563
LGA    G      24      V      22          5.512
LGA    T      25      -       -           -
LGA    T      26      -       -           -
LGA    H      27      -       -           -
LGA    S      28      C      23           #
LGA    V      29      G      24          0.940
LGA    I      30      T      25          2.627
LGA    R      31      -       -           -
LGA    S      32      -       -           -
LGA    G      33      -       -           -
LGA    N      34      -       -           -
LGA    G      35      -       -           -
LGA    V      36      T      26          4.387
LGA    G      37      H      27          2.203
LGA    L      38      S      28          3.932
LGA    -       -      V      29           -
LGA    -       -      I      30           -
LGA    -       -      R      31           -
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    -       -      G      37           -
LGA    -       -      L      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      N      41           -
LGA    -       -      R      42           -
LGA    G      39      P      43           #
LGA    P      40      F      44           -
LGA    N      41      E      45           -
LGA    -       -      T      46           -
LGA    R      42      R      47          3.277
LGA    P      43      M      48          2.599
LGA    -       -      P      49           -
LGA    F      44      M      50          3.662
LGA    E      45      L      51          3.132
LGA    -       -      T      52           -
LGA    T      46      Q      53          2.154
LGA    R      47      N      54          2.803
LGA    M      48      L      55          2.228
LGA    P      49      L      56           #
LGA    M      50      G      57           -
LGA    L      51      L      58          3.014
LGA    T      52      P      59          4.144
LGA    Q      53      L      60           #
LGA    N      54      R      61          2.305
LGA    L      55      V      62          4.614
LGA    L      56      A      63           #
LGA    G      57      A      64           #
LGA    L      58      -       -           -
LGA    P      59      G      65          4.508
LGA    L      60      C      66           -
LGA    R      61      V      67           -
LGA    V      62      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    -       -      S      76           -
LGA    -       -      I      77           -
LGA    -       -      G      78           -
LGA    -       -      L      79           -
LGA    -       -      A      80           -
LGA    -       -      A      81           -
LGA    A      63      I      82          2.955
LGA    -       -      N      83           -
LGA    -       -      A      84           -
LGA    A      64      Y      85          3.327
LGA    G      65      Y      86          3.984
LGA    C      66      -       -           -
LGA    V      67      N      87          1.929
LGA    K      68      -       -           -
LGA    S      69      -       -           -
LGA    W      70      N      88          4.626
LGA    N      71      P      89          3.373
LGA    Y      72      Q      90          1.997
LGA    -       -      V      91           -
LGA    -       -      A      92           -
LGA    V      73      R      93          3.873
LGA    E      74      E      94           -
LGA    A      75      H      95           -
LGA    S      76      G      96           -
LGA    I      77      -       -           -
LGA    G      78      -       -           -
LGA    L      79      -       -           -
LGA    A      80      -       -           -
LGA    A      81      -       -           -
LGA    I      82      -       -           -
LGA    N      83      -       -           -
LGA    A      84      -       -           -
LGA    Y      85      -       -           -
LGA    Y      86      -       -           -
LGA    N      87      -       -           -
LGA    N      88      -       -           -
LGA    P      89      -       -           -
LGA    Q      90      -       -           -
LGA    V      91      -       -           -
LGA    A      92      -       -           -
LGA    R      93      -       -           -
LGA    E      94      -       -           -
LGA    H      95      -       -           -
LGA    G      96      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   96   96    5.0     28    3.39     7.14     16.315     0.802

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.681976 * X  +   0.723810 * Y  +   0.104919 * Z  +  -2.572608
  Y_new =   0.333979 * X  +  -0.435825 * Y  +   0.835772 * Z  +  58.092079
  Z_new =   0.650667 * X  +  -0.534935 * Y  +  -0.538959 * Z  +  67.670639 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.359942    0.781651  [ DEG:  -135.2147     44.7853 ]
  Theta =  -0.708462   -2.433131  [ DEG:   -40.5919   -139.4081 ]
  Phi   =   0.455392   -2.686200  [ DEG:    26.0921   -153.9079 ]
 
# 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: T0321TS393_4-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS393_4-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   96   96   5.0   28   3.39    7.14  16.315
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS393_4-D1
PFRMAT TS
TARGET T0321
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1     -18.578  73.026  70.877  1.00 25.00           C
ATOM      2  CA  TRP     2     -17.520  69.420  70.324  1.00 25.00           C
ATOM      3  CA  GLU     3     -21.257  68.602  70.117  1.00 25.00           C
ATOM      4  CA  ILE     4     -20.439  64.908  69.524  1.00 25.00           C
ATOM      5  CA  TYR     5     -18.088  64.918  72.548  1.00 25.00           C
ATOM      6  CA  ASP     6     -20.822  66.517  74.700  1.00 25.00           C
ATOM      7  CA  ALA     7     -23.325  63.860  73.540  1.00 25.00           C
ATOM      8  CA  MET     8     -20.822  61.092  74.400  1.00 25.00           C
ATOM      9  CA  ILE     9     -20.289  62.618  77.872  1.00 25.00           C
ATOM     10  CA  ASN    10     -24.077  62.764  78.415  1.00 25.00           C
ATOM     11  CA  GLY    11     -26.999  64.098  80.478  1.00 25.00           C
ATOM     12  CA  ILE    12     -24.349  65.074  83.023  1.00 25.00           C
ATOM     13  CA  PRO    13     -24.329  62.032  85.226  1.00 25.00           C
ATOM     14  CA  GLU    14     -22.349  58.860  84.774  1.00 25.00           C
ATOM     15  CA  ASP    15     -20.148  56.141  83.275  1.00 25.00           C
ATOM     16  CA  PHE    16     -17.242  55.860  80.834  1.00 25.00           C
ATOM     17  CA  LEU    17     -14.636  57.584  78.751  1.00 25.00           C
ATOM     18  CA  VAL    18     -11.903  59.514  76.854  1.00 25.00           C
ATOM     19  CA  ASP    19      -8.998  61.700  75.650  1.00 25.00           C
ATOM     20  CA  GLU    20     -10.492  61.518  72.108  1.00 25.00           C
ATOM     21  CA  LEU    21     -10.241  59.778  68.768  1.00 25.00           C
ATOM     22  CA  VAL    22      -9.647  63.093  66.883  1.00 25.00           C
ATOM     23  CA  CYS    23      -9.227  62.547  63.110  1.00 25.00           C
ATOM     24  CA  GLY    24     -11.180  61.540  60.074  1.00 25.00           C
ATOM     25  CA  THR    25      -8.131  61.403  57.732  1.00 25.00           C
ATOM     26  CA  THR    26      -8.491  65.184  57.914  1.00 25.00           C
ATOM     27  CA  HIS    27      -5.234  64.988  59.871  1.00 25.00           C
ATOM     28  CA  SER    28      -2.635  67.034  61.630  1.00 25.00           C
ATOM     29  CA  VAL    29      -0.478  63.924  61.586  1.00 25.00           C
ATOM     30  CA  ILE    30       3.281  64.306  62.215  1.00 25.00           C
ATOM     31  CA  ARG    31       7.006  65.068  62.600  1.00 25.00           C
ATOM     32  CA  SER    32       6.184  66.217  66.194  1.00 25.00           C
ATOM     33  CA  GLY    33       8.931  65.385  68.703  1.00 25.00           C
ATOM     34  CA  ASN    34      11.066  64.068  65.842  1.00 25.00           C
ATOM     35  CA  GLY    35       8.467  61.325  65.677  1.00 25.00           C
ATOM     36  CA  VAL    36       4.681  61.260  66.171  1.00 25.00           C
ATOM     37  CA  GLY    37       2.277  59.901  63.576  1.00 25.00           C
ATOM     38  CA  LEU    38       0.017  58.620  60.774  1.00 25.00           C
ATOM     39  CA  GLY    39       0.481  61.251  57.999  1.00 25.00           C
ATOM     40  CA  PRO    40      -3.324  60.832  57.708  1.00 25.00           C
ATOM     41  CA  ASN    41      -4.274  63.332  54.989  1.00 25.00           C
ATOM     42  CA  ARG    42      -5.939  61.014  52.416  1.00 25.00           C
ATOM     43  CA  PRO    43      -9.117  63.064  52.824  1.00 25.00           C
ATOM     44  CA  PHE    44     -10.792  59.749  53.682  1.00 25.00           C
ATOM     45  CA  GLU    45     -14.107  61.533  53.394  1.00 25.00           C
ATOM     46  CA  THR    46     -16.092  62.994  56.237  1.00 25.00           C
ATOM     47  CA  ARG    47     -17.015  60.773  59.166  1.00 25.00           C
ATOM     48  CA  MET    48     -14.876  58.351  57.221  1.00 25.00           C
ATOM     49  CA  PRO    49     -16.458  55.037  56.087  1.00 25.00           C
ATOM     50  CA  MET    50     -13.706  54.040  58.557  1.00 25.00           C
ATOM     51  CA  LEU    51     -16.176  54.340  61.468  1.00 25.00           C
ATOM     52  CA  THR    52     -18.698  52.159  59.585  1.00 25.00           C
ATOM     53  CA  GLN    53     -15.981  49.543  58.926  1.00 25.00           C
ATOM     54  CA  ASN    54     -15.030  49.559  62.636  1.00 25.00           C
ATOM     55  CA  LEU    55     -18.707  49.096  63.605  1.00 25.00           C
ATOM     56  CA  LEU    56     -19.008  46.166  61.157  1.00 25.00           C
ATOM     57  CA  GLY    57     -15.635  44.641  60.142  1.00 25.00           C
ATOM     58  CA  LEU    58     -11.984  43.607  59.885  1.00 25.00           C
ATOM     59  CA  PRO    59     -10.950  46.648  61.975  1.00 25.00           C
ATOM     60  CA  LEU    60     -12.869  45.176  64.920  1.00 25.00           C
ATOM     61  CA  ARG    61     -12.679  42.166  67.281  1.00 25.00           C
ATOM     62  CA  VAL    62      -8.902  41.917  66.701  1.00 25.00           C
ATOM     63  CA  ALA    63      -8.516  45.654  67.444  1.00 25.00           C
ATOM     64  CA  ALA    64     -10.541  45.245  70.669  1.00 25.00           C
ATOM     65  CA  GLY    65      -8.337  42.291  71.709  1.00 25.00           C
ATOM     66  CA  CYS    66      -5.191  44.367  71.025  1.00 25.00           C
ATOM     67  CA  VAL    67      -6.602  47.241  73.126  1.00 25.00           C
ATOM     68  CA  LYS    68      -7.371  44.808  75.983  1.00 25.00           C
ATOM     69  CA  SER    69     -10.548  44.785  78.023  1.00 25.00           C
ATOM     70  CA  TRP    70     -12.304  47.048  75.444  1.00 25.00           C
ATOM     71  CA  ASN    71     -10.597  49.998  77.120  1.00 25.00           C
ATOM     72  CA  TYR    72      -9.337  48.942  80.555  1.00 25.00           C
ATOM     73  CA  VAL    73      -6.117  47.804  82.288  1.00 25.00           C
ATOM     74  CA  GLU    74      -4.348  47.568  78.900  1.00 25.00           C
ATOM     75  CA  ALA    75      -5.544  51.094  78.001  1.00 25.00           C
ATOM     76  CA  SER    76      -4.260  52.413  81.359  1.00 25.00           C
ATOM     77  CA  ILE    77      -0.870  50.735  80.748  1.00 25.00           C
ATOM     78  CA  GLY    78      -0.694  52.305  77.260  1.00 25.00           C
ATOM     79  CA  LEU    79      -1.506  55.743  78.739  1.00 25.00           C
ATOM     80  CA  ALA    80       1.238  55.285  81.371  1.00 25.00           C
ATOM     81  CA  ALA    81       3.736  54.312  78.635  1.00 25.00           C
ATOM     82  CA  ILE    82       2.763  57.414  76.610  1.00 25.00           C
ATOM     83  CA  ASN    83       3.242  59.615  79.707  1.00 25.00           C
ATOM     84  CA  ALA    84       6.687  58.056  80.314  1.00 25.00           C
ATOM     85  CA  TYR    85       7.649  58.702  76.664  1.00 25.00           C
ATOM     86  CA  TYR    86      10.853  57.225  78.218  1.00 25.00           C
ATOM     87  CA  ASN    87      11.400  56.688  81.951  1.00 25.00           C
ATOM     88  CA  ASN    88      14.028  54.175  80.896  1.00 25.00           C
ATOM     89  CA  PRO    89      13.858  53.091  77.269  1.00 25.00           C
ATOM     90  CA  GLN    90      17.558  52.259  77.810  1.00 25.00           C
ATOM     91  CA  VAL    91      16.806  48.527  77.393  1.00 25.00           C
ATOM     92  CA  ALA    92      14.895  49.250  74.152  1.00 25.00           C
ATOM     93  CA  ARG    93      17.839  51.325  72.851  1.00 25.00           C
ATOM     94  CA  GLU    94      20.255  48.477  73.699  1.00 25.00           C
ATOM     95  CA  HIS    95      18.000  45.985  71.862  1.00 25.00           C
ATOM     96  CA  GLY    96      18.964  42.648  73.381  1.00 25.00           C
TER
END
