
#######################################################
#                                                     #
#                        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 T0330TS393_2-D2
# Molecule2: number of CA atoms   72 (  556),  selected   72 , name T0330_D2.pdb
# PARAMETERS: T0330TS393_2-D2.T0330_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17           #
LGA    E      18      E      18          3.894
LGA    S      19      S      19          2.348
LGA    M      20      M      20          1.835
LGA    N      21      -       -           -
LGA    R      22      N      21          4.488
LGA    R      23      R      22          1.724
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      -       -           -
LGA    S      45      R      23          2.510
LGA    G      46      V      24          3.753
LGA    -       -      L      25           -
LGA    -       -      A      26           -
LGA    K      47      D      27          1.421
LGA    M      48      A      28          4.405
LGA    D      49      L      29          4.978
LGA    G      50      I      30          4.478
LGA    A      51      E      31           -
LGA    -       -      V      32           -
LGA    -       -      Y      33           -
LGA    -       -      G      34           -
LGA    I      52      T      35          2.518
LGA    I      53      E      36          2.336
LGA    Y      54      G      37          0.681
LGA    E      55      S      38           #
LGA    -       -      T      39           -
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    -       -      I      52           -
LGA    -       -      I      53           -
LGA    V      56      Y      54          4.610
LGA    -       -      E      55           -
LGA    L      57      V      56          1.386
LGA    S      58      L      57          3.164
LGA    N      59      S      58          3.065
LGA    -       -      N      59           -
LGA    -       -      V      60           -
LGA    -       -      G      61           -
LGA    -       -      L      62           -
LGA    V      60      E      63           #
LGA    G      61      R      64          0.427
LGA    L      62      A      65          5.140
LGA    E      63      E      66          1.949
LGA    R      64      I      67           #
LGA    A      65      A      68          2.985
LGA    E      66      D      69          4.314
LGA    I      67      K      70          1.207
LGA    A      68      F      71          0.656
LGA    D      69      D      72          0.978
LGA    K      70      K      73          1.085
LGA    F      71      A      74          0.816
LGA    D      72      K      75          0.633
LGA    K      73      E      76          0.829
LGA    A      74      T      77          0.811
LGA    K      75      Y      78          0.631
LGA    E      76      I      79          0.638
LGA    T      77      A      80          0.706
LGA    Y      78      L      81          0.562
LGA    I      79      F      82          0.705
LGA    A      80      R      83          0.977
LGA    L      81      E      84          0.728
LGA    F      82      R      85          1.214
LGA    R      83      A      86          3.010
LGA    E      84      -       -           -
LGA    R      85      -       -           -
LGA    A      86      -       -           -
LGA    R      87      -       -           -
LGA    R      88      R      87          4.084
LGA    E      89      R      88          1.262
LGA    D      90      E      89          3.644
LGA    I      91      D      90          4.228
LGA    -       -      I      91           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   72    5.0     44    2.68    20.45     42.523     1.581

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.553764 * X  +  -0.787669 * Y  +  -0.270042 * Z  +  10.148209
  Y_new =   0.048870 * X  +   0.354492 * Y  +  -0.933781 * Z  +  23.407261
  Z_new =   0.831238 * X  +   0.503898 * Y  +   0.234798 * Z  +   4.479899 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.134746   -2.006847  [ DEG:    65.0162   -114.9838 ]
  Theta =  -0.981331   -2.160261  [ DEG:   -56.2261   -123.7739 ]
  Phi   =   0.088023   -3.053570  [ DEG:     5.0433   -174.9567 ]
 
# 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: T0330TS393_2-D2                               
REMARK     2: T0330_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS393_2-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   44   2.68   20.45  42.523
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS393_2-D2
PFRMAT TS
TARGET T0330
MODEL 2
PARENT N/A
ATOM     17  CA  VAL    17      12.334  30.175   9.452  1.00 25.00           C
ATOM     18  CA  GLU    18      15.729  28.716   8.544  1.00 25.00           C
ATOM     19  CA  SER    19      18.290  29.686   5.867  1.00 25.00           C
ATOM     20  CA  MET    20      15.738  32.036   4.242  1.00 25.00           C
ATOM     21  CA  ASN    21      15.012  33.637   7.645  1.00 25.00           C
ATOM     22  CA  ARG    22      18.764  34.118   8.247  1.00 25.00           C
ATOM     23  CA  ARG    23      19.135  35.737   4.796  1.00 25.00           C
ATOM     24  CA  VAL    24      16.202  38.081   5.553  1.00 25.00           C
ATOM     25  CA  LEU    25      17.797  39.035   8.902  1.00 25.00           C
ATOM     26  CA  ALA    26      21.124  39.747   7.143  1.00 25.00           C
ATOM     27  CA  ASP    27      19.323  41.933   4.566  1.00 25.00           C
ATOM     28  CA  ALA    28      17.569  43.849   7.380  1.00 25.00           C
ATOM     29  CA  LEU    29      20.928  44.385   9.141  1.00 25.00           C
ATOM     30  CA  ILE    30      22.463  45.670   5.875  1.00 25.00           C
ATOM     31  CA  GLU    31      19.519  48.075   5.409  1.00 25.00           C
ATOM     32  CA  VAL    32      19.955  49.342   8.997  1.00 25.00           C
ATOM     33  CA  TYR    33      22.960  48.810  11.270  1.00 25.00           C
ATOM     34  CA  GLY    34      23.866  46.777  14.295  1.00 25.00           C
ATOM     35  CA  THR    35      25.521  43.377  13.590  1.00 25.00           C
ATOM     36  CA  GLU    36      27.182  40.464  11.741  1.00 25.00           C
ATOM     37  CA  GLY    37      26.249  38.286   8.709  1.00 25.00           C
ATOM     38  CA  SER    38      28.141  35.225   9.856  1.00 25.00           C
ATOM     39  CA  THR    39      25.499  32.467   9.301  1.00 25.00           C
ATOM     40  CA  GLY    40      27.396  29.858   7.234  1.00 25.00           C
ATOM     41  CA  SER    41      25.858  31.255   4.017  1.00 25.00           C
ATOM     42  CA  HIS    42      25.644  28.128   1.805  1.00 25.00           C
ATOM     43  CA  ASP    43      24.998  30.197  -1.253  1.00 25.00           C
ATOM     44  CA  PHE    44      22.236  32.341   0.350  1.00 25.00           C
ATOM     45  CA  SER    45      19.605  34.750  -0.968  1.00 25.00           C
ATOM     46  CA  GLY    46      15.885  34.984  -1.732  1.00 25.00           C
ATOM     47  CA  LYS    47      16.191  38.252  -3.538  1.00 25.00           C
ATOM     48  CA  MET    48      15.757  39.106  -7.201  1.00 25.00           C
ATOM     49  CA  ASP    49      19.227  38.293  -8.605  1.00 25.00           C
ATOM     50  CA  GLY    50      21.541  35.642  -7.093  1.00 25.00           C
ATOM     51  CA  ALA    51      24.436  36.895  -9.265  1.00 25.00           C
ATOM     52  CA  ILE    52      23.753  40.492  -8.142  1.00 25.00           C
ATOM     53  CA  ILE    53      23.731  39.371  -4.480  1.00 25.00           C
ATOM     54  CA  TYR    54      27.059  37.545  -4.994  1.00 25.00           C
ATOM     55  CA  GLU    55      28.562  40.682  -6.598  1.00 25.00           C
ATOM     56  CA  VAL    56      27.349  42.800  -3.647  1.00 25.00           C
ATOM     57  CA  LEU    57      28.904  40.310  -1.188  1.00 25.00           C
ATOM     58  CA  SER    58      32.213  40.438  -3.112  1.00 25.00           C
ATOM     59  CA  ASN    59      32.146  44.267  -3.023  1.00 25.00           C
ATOM     60  CA  VAL    60      32.885  47.903  -2.110  1.00 25.00           C
ATOM     61  CA  GLY    61      34.158  48.917  -5.612  1.00 25.00           C
ATOM     62  CA  LEU    62      31.587  46.896  -7.571  1.00 25.00           C
ATOM     63  CA  GLU    63      28.963  49.533  -8.373  1.00 25.00           C
ATOM     64  CA  ARG    64      28.581  53.281  -8.036  1.00 25.00           C
ATOM     65  CA  ALA    65      27.576  54.626  -4.594  1.00 25.00           C
ATOM     66  CA  GLU    66      24.143  55.629  -5.962  1.00 25.00           C
ATOM     67  CA  ILE    67      23.693  52.137  -7.464  1.00 25.00           C
ATOM     68  CA  ALA    68      24.634  50.545  -4.111  1.00 25.00           C
ATOM     69  CA  ASP    69      22.109  52.790  -2.308  1.00 25.00           C
ATOM     70  CA  LYS    70      19.397  51.801  -4.825  1.00 25.00           C
ATOM     71  CA  PHE    71      20.216  48.099  -4.290  1.00 25.00           C
ATOM     72  CA  ASP    72      19.996  48.573  -0.496  1.00 25.00           C
ATOM     73  CA  LYS    73      16.605  50.311  -0.885  1.00 25.00           C
ATOM     74  CA  ALA    74      15.354  47.432  -3.080  1.00 25.00           C
ATOM     75  CA  LYS    75      16.531  44.894  -0.464  1.00 25.00           C
ATOM     76  CA  GLU    76      14.725  46.854   2.286  1.00 25.00           C
ATOM     77  CA  THR    77      11.528  46.910   0.180  1.00 25.00           C
ATOM     78  CA  TYR    78      11.796  43.130  -0.376  1.00 25.00           C
ATOM     79  CA  ILE    79      12.252  42.586   3.388  1.00 25.00           C
ATOM     80  CA  ALA    80       9.177  44.755   4.099  1.00 25.00           C
ATOM     81  CA  LEU    81       7.141  42.746   1.553  1.00 25.00           C
ATOM     82  CA  PHE    82       8.275  39.474   3.189  1.00 25.00           C
ATOM     83  CA  ARG    83       7.269  40.819   6.631  1.00 25.00           C
ATOM     84  CA  GLU    84       3.836  41.822   5.264  1.00 25.00           C
ATOM     85  CA  ARG    85       3.386  38.329   3.760  1.00 25.00           C
ATOM     86  CA  ALA    86       4.327  36.737   7.115  1.00 25.00           C
ATOM     87  CA  ARG    87       1.802  38.983   8.916  1.00 25.00           C
ATOM     88  CA  ARG    88       4.772  39.951  11.113  1.00 25.00           C
ATOM     89  CA  GLU    89       6.907  37.322  12.810  1.00 25.00           C
ATOM     90  CA  ASP    90       8.615  35.315  10.043  1.00 25.00           C
ATOM     91  CA  ILE    91       8.599  33.561   6.614  1.00 25.00           C
TER
END
