
#######################################################
#                                                     #
#                        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   75 (   75),  selected   75 , name T0330TS168_5-D2
# Molecule2: number of CA atoms   72 (  556),  selected   72 , name T0330_D2.pdb
# PARAMETERS: T0330TS168_5-D2.T0330_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      -       -           -
LGA    E      18      -       -           -
LGA    S      19      -       -           -
LGA    M      20      -       -           -
LGA    N      21      -       -           -
LGA    R      22      -       -           -
LGA    R      23      -       -           -
LGA    V      24      -       -           -
LGA    L      25      -       -           -
LGA    A      26      -       -           -
LGA    D      27      -       -           -
LGA    A      28      -       -           -
LGA    L      29      -       -           -
LGA    I      30      -       -           -
LGA    E      31      -       -           -
LGA    V      32      -       -           -
LGA    Y      33      -       -           -
LGA    G      34      -       -           -
LGA    T      35      -       -           -
LGA    E      36      -       -           -
LGA    G      37      -       -           -
LGA    S      38      -       -           -
LGA    T      39      -       -           -
LGA    G      40      -       -           -
LGA    S      41      -       -           -
LGA    H      42      -       -           -
LGA    D      43      -       -           -
LGA    F      44      V      17          4.000
LGA    S      45      E      18          4.232
LGA    -       -      S      19           -
LGA    G      46      M      20          1.384
LGA    K      47      N      21          4.764
LGA    -       -      R      22           -
LGA    M      48      R      23          3.841
LGA    D      49      V      24          1.901
LGA    G      50      L      25          4.381
LGA    A      51      A      26          2.056
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    I      52      L      29          4.008
LGA    I      53      I      30           -
LGA    -       -      E      31           -
LGA    -       -      V      32           -
LGA    -       -      Y      33           -
LGA    -       -      G      34           -
LGA    -       -      T      35           -
LGA    -       -      E      36           -
LGA    -       -      G      37           -
LGA    -       -      S      38           -
LGA    Y      54      T      39          3.009
LGA    -       -      D      43           -
LGA    -       -      F      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      K      47           -
LGA    -       -      M      48           -
LGA    -       -      D      49           -
LGA    -       -      G      50           -
LGA    -       -      A      51           -
LGA    E      55      I      52           #
LGA    V      56      I      53          1.874
LGA    L      57      Y      54           #
LGA    S      58      E      55          2.614
LGA    -       -      V      56           -
LGA    N      59      L      57          4.777
LGA    V      60      S      58          2.673
LGA    -       -      N      59           -
LGA    -       -      V      60           -
LGA    -       -      G      61           -
LGA    -       -      L      62           -
LGA    G      61      E      63          3.128
LGA    L      62      R      64          2.942
LGA    E      63      A      65          3.380
LGA    -       -      E      66           -
LGA    -       -      I      67           -
LGA    R      64      A      68          3.510
LGA    A      65      D      69          3.995
LGA    E      66      K      70          1.509
LGA    I      67      F      71          1.750
LGA    A      68      D      72          1.281
LGA    D      69      K      73          0.777
LGA    K      70      A      74          1.161
LGA    F      71      K      75          1.486
LGA    D      72      E      76          1.168
LGA    K      73      T      77          0.789
LGA    A      74      Y      78          1.238
LGA    K      75      I      79          1.519
LGA    E      76      A      80          1.337
LGA    T      77      L      81          1.704
LGA    Y      78      F      82          1.917
LGA    I      79      R      83          1.766
LGA    A      80      E      84          1.913
LGA    L      81      R      85          3.027
LGA    F      82      A      86          2.831
LGA    R      83      -       -           -
LGA    E      84      -       -           -
LGA    R      85      R      87          1.267
LGA    A      86      R      88          2.700
LGA    R      87      -       -           -
LGA    R      88      -       -           -
LGA    E      89      E      89          2.595
LGA    D      90      D      90           #
LGA    I      91      I      91          4.669

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   72    5.0     40    2.79    10.00     38.074     1.386

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.827112 * X  +  -0.039172 * Y  +  -0.560670 * Z  +   8.175969
  Y_new =  -0.201517 * X  +  -0.910572 * Y  +   0.360900 * Z  +  46.917843
  Z_new =  -0.524668 * X  +   0.411489 * Y  +   0.745252 * Z  +  20.701405 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.504491   -2.637102  [ DEG:    28.9052   -151.0948 ]
  Theta =   0.552325    2.589267  [ DEG:    31.6459    148.3541 ]
  Phi   =  -2.902609    0.238983  [ DEG:  -166.3073     13.6927 ]
 
# 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: T0330TS168_5-D2                               
REMARK     2: T0330_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS168_5-D2.T0330_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   75   72   5.0   40   2.79   10.00  38.074
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS168_5-D2
PFRMAT TS
TARGET T0330
MODEL 5
PARENT N/A
ATOM     17  CA  VAL    17      11.102  42.980  20.034  1.00 25.00           C
ATOM     18  CA  GLU    18      10.418  40.476  17.238  1.00 25.00           C
ATOM     19  CA  SER    19      11.036  39.301  13.647  1.00 25.00           C
ATOM     20  CA  MET    20      10.442  42.856  12.354  1.00 25.00           C
ATOM     21  CA  ASN    21      12.899  44.236  14.947  1.00 25.00           C
ATOM     22  CA  ARG    22      15.508  41.639  13.892  1.00 25.00           C
ATOM     23  CA  ARG    23      15.014  42.600  10.217  1.00 25.00           C
ATOM     24  CA  VAL    24      15.445  46.302  11.101  1.00 25.00           C
ATOM     25  CA  LEU    25      18.659  45.494  13.021  1.00 25.00           C
ATOM     26  CA  ALA    26      19.981  43.512  10.023  1.00 25.00           C
ATOM     27  CA  ASP    27      19.177  46.446   7.697  1.00 25.00           C
ATOM     28  CA  ALA    28      21.003  48.848  10.055  1.00 25.00           C
ATOM     29  CA  LEU    29      24.042  46.518  10.114  1.00 25.00           C
ATOM     30  CA  ILE    30      24.030  46.364   6.288  1.00 25.00           C
ATOM     31  CA  GLU    31      23.864  50.187   6.110  1.00 25.00           C
ATOM     32  CA  VAL    32      26.803  50.451   8.551  1.00 25.00           C
ATOM     33  CA  TYR    33      29.322  47.643   8.888  1.00 25.00           C
ATOM     34  CA  GLY    34      30.378  45.772  12.027  1.00 25.00           C
ATOM     35  CA  THR    35      28.923  43.092  14.240  1.00 25.00           C
ATOM     36  CA  GLU    36      29.277  39.412  15.055  1.00 25.00           C
ATOM     37  CA  GLY    37      26.280  38.210  13.098  1.00 25.00           C
ATOM     38  CA  SER    38      26.587  34.424  13.648  1.00 25.00           C
ATOM     39  CA  THR    39      25.163  33.156  10.294  1.00 25.00           C
ATOM     40  CA  GLY    40      22.265  30.683   9.904  1.00 25.00           C
ATOM     41  CA  SER    41      22.270  30.045  13.681  1.00 25.00           C
ATOM     42  CA  HIS    42      18.716  31.506  13.722  1.00 25.00           C
ATOM     43  CA  ASP    43      17.028  30.977  10.321  1.00 25.00           C
ATOM     44  CA  PHE    44      18.325  34.342   9.180  1.00 25.00           C
ATOM     45  CA  SER    45      15.269  36.209   7.879  1.00 25.00           C
ATOM     46  CA  GLY    46      15.167  33.344   5.342  1.00 25.00           C
ATOM     47  CA  LYS    47      14.781  34.010   1.621  1.00 25.00           C
ATOM     48  CA  MET    48      14.292  35.891  -1.691  1.00 25.00           C
ATOM     49  CA  ASP    49      17.258  38.107  -0.761  1.00 25.00           C
ATOM     50  CA  GLY    50      19.718  35.338   0.215  1.00 25.00           C
ATOM     51  CA  ALA    51      21.747  35.985  -2.969  1.00 25.00           C
ATOM     52  CA  ILE    52      21.827  39.733  -2.187  1.00 25.00           C
ATOM     53  CA  ILE    53      23.014  38.989   1.377  1.00 25.00           C
ATOM     54  CA  TYR    54      25.766  36.703   0.010  1.00 25.00           C
ATOM     55  CA  GLU    55      26.866  39.445  -2.427  1.00 25.00           C
ATOM     56  CA  VAL    56      26.976  41.982   0.439  1.00 25.00           C
ATOM     57  CA  LEU    57      29.081  39.563   2.533  1.00 25.00           C
ATOM     58  CA  SER    58      31.484  39.071  -0.408  1.00 25.00           C
ATOM     59  CA  ASN    59      31.788  42.865  -0.828  1.00 25.00           C
ATOM     60  CA  VAL    60      30.835  42.809  -4.507  1.00 25.00           C
ATOM     61  CA  GLY    61      32.778  45.298  -6.543  1.00 25.00           C
ATOM     62  CA  LEU    62      30.953  48.517  -5.836  1.00 25.00           C
ATOM     63  CA  GLU    63      29.949  52.188  -5.821  1.00 25.00           C
ATOM     64  CA  ARG    64      27.156  54.675  -6.522  1.00 25.00           C
ATOM     65  CA  ALA    65      23.530  55.243  -7.612  1.00 25.00           C
ATOM     66  CA  GLU    66      23.266  51.590  -8.726  1.00 25.00           C
ATOM     67  CA  ILE    67      24.668  50.435  -5.355  1.00 25.00           C
ATOM     68  CA  ALA    68      22.129  52.635  -3.517  1.00 25.00           C
ATOM     69  CA  ASP    69      19.291  51.170  -5.632  1.00 25.00           C
ATOM     70  CA  LYS    70      20.500  47.623  -4.841  1.00 25.00           C
ATOM     71  CA  PHE    71      20.601  48.464  -1.106  1.00 25.00           C
ATOM     72  CA  ASP    72      17.041  49.863  -1.300  1.00 25.00           C
ATOM     73  CA  LYS    73      15.860  46.681  -3.073  1.00 25.00           C
ATOM     74  CA  ALA    74      17.513  44.531  -0.369  1.00 25.00           C
ATOM     75  CA  LYS    75      15.803  46.604   2.359  1.00 25.00           C
ATOM     76  CA  GLU    76      12.428  46.178   0.602  1.00 25.00           C
ATOM     77  CA  THR    77      12.994  42.397   0.378  1.00 25.00           C
ATOM     78  CA  TYR    78      13.857  42.281   4.107  1.00 25.00           C
ATOM     79  CA  ILE    79      10.675  44.248   4.930  1.00 25.00           C
ATOM     80  CA  ALA    80       8.600  41.825   2.809  1.00 25.00           C
ATOM     81  CA  LEU    81      10.186  38.845   4.618  1.00 25.00           C
ATOM     82  CA  PHE    82       9.393  40.446   8.005  1.00 25.00           C
ATOM     83  CA  ARG    83       5.766  41.015   6.915  1.00 25.00           C
ATOM     84  CA  GLU    84       5.503  37.360   5.800  1.00 25.00           C
ATOM     85  CA  ARG    85       6.905  36.205   9.172  1.00 25.00           C
ATOM     86  CA  ALA    86       4.366  38.406  11.009  1.00 25.00           C
ATOM     87  CA  ARG    87       1.528  36.940   8.894  1.00 25.00           C
ATOM     88  CA  ARG    88       1.616  33.238   9.516  1.00 25.00           C
ATOM     89  CA  GLU    89       4.881  31.604  10.725  1.00 25.00           C
ATOM     90  CA  ASP    90       4.917  32.211  14.507  1.00 25.00           C
ATOM     91  CA  ILE    91       6.837  35.348  15.636  1.00 25.00           C
TER
END
