
#######################################################
#                                                     #
#                        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   77 (   77),  selected   77 , name T0303TS393_2-D2
# Molecule2: number of CA atoms   77 (  602),  selected   77 , name T0303_D2.pdb
# PARAMETERS: T0303TS393_2-D2.T0303_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      18      S      18          2.958
LGA    L      19      L      19          2.479
LGA    P      20      P      20          2.665
LGA    D      21      D      21          2.505
LGA    L      22      L      22          3.532
LGA    A      23      A      23          3.260
LGA    -       -      L      24           -
LGA    -       -      S      25           -
LGA    L      24      I      26          4.619
LGA    -       -      N      27           -
LGA    -       -      S      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      K      31           -
LGA    -       -      D      32           -
LGA    -       -      V      33           -
LGA    -       -      N      34           -
LGA    -       -      L      35           -
LGA    -       -      P      36           -
LGA    -       -      Q      37           -
LGA    -       -      A      38           -
LGA    -       -      S      39           -
LGA    -       -      E      40           -
LGA    -       -      N      41           -
LGA    -       -      L      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      T      45           -
LGA    S      25      W      46           #
LGA    I      26      I      47          4.538
LGA    N      27      G      48           -
LGA    -       -      N      49           -
LGA    -       -      G      50           -
LGA    S      28      A      51          3.245
LGA    A      29      D      52          3.059
LGA    L      30      V      53          3.138
LGA    K      31      L      54           #
LGA    D      32      -       -           -
LGA    V      33      -       -           -
LGA    N      34      -       -           -
LGA    L      35      -       -           -
LGA    P      36      S      55           #
LGA    Q      37      Q      56          4.468
LGA    A      38      R      57          2.146
LGA    S      39      -       -           -
LGA    E      40      A      58          1.622
LGA    N      41      V      59          5.445
LGA    L      42      D      60           -
LGA    V      43      W      61           -
LGA    M      44      A      62           #
LGA    T      45      C      63           -
LGA    W      46      T      64           -
LGA    I      47      Q      65           -
LGA    G      48      A      66           -
LGA    N      49      E      67           -
LGA    G      50      K      68           -
LGA    A      51      E      69           -
LGA    D      52      -       -           -
LGA    V      53      -       -           -
LGA    L      54      -       -           -
LGA    S      55      -       -           -
LGA    Q      56      -       -           -
LGA    R      57      -       -           -
LGA    A      58      -       -           -
LGA    V      59      -       -           -
LGA    D      60      -       -           -
LGA    W      61      -       -           -
LGA    A      62      -       -           -
LGA    C      63      -       -           -
LGA    T      64      -       -           -
LGA    Q      65      -       -           -
LGA    A      66      -       -           -
LGA    E      67      -       -           -
LGA    K      68      -       -           -
LGA    E      69      -       -           -
LGA    L      70      -       -           -
LGA    T      71      L      70          3.653
LGA    E      72      T      71          3.026
LGA    -       -      E      72           -
LGA    D      73      D      73          0.403
LGA    E      74      E      74          0.568
LGA    F      75      F      75          1.005
LGA    K      76      K      76          0.826
LGA    Y      77      Y      77          0.177
LGA    F      78      F      78          0.806
LGA    K      79      K      79          1.040
LGA    R      80      R      80          0.711
LGA    Q      81      Q      81          0.254
LGA    F      82      F      82          0.557
LGA    G      83      G      83          0.656
LGA    F      84      F      84          0.330
LGA    Y      85      Y      85          0.247
LGA    Y      86      Y      86          0.275
LGA    G      87      G      87          0.286
LGA    E      88      E      88          0.523
LGA    N      89      N      89          0.506
LGA    L      90      L      90          1.657
LGA    C      91      -       -           -
LGA    N      92      -       -           -
LGA    I      93      C      91          1.874
LGA    S      94      N      92          1.386
LGA    -       -      I      93           -
LGA    -       -      S      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77   77    5.0     37    2.42    70.27     34.280     1.468

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.469336 * X  +  -0.496665 * Y  +  -0.730101 * Z  + -14.293363
  Y_new =  -0.363467 * X  +   0.862191 * Y  +  -0.352872 * Z  +  89.731117
  Z_new =   0.804746 * X  +   0.099752 * Y  +  -0.585179 * Z  +  17.246363 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.972751   -0.168842  [ DEG:   170.3261     -9.6739 ]
  Theta =  -0.935247   -2.206346  [ DEG:   -53.5857   -126.4143 ]
  Phi   =  -2.482640    0.658953  [ DEG:  -142.2448     37.7552 ]
 
# 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: T0303TS393_2-D2                               
REMARK     2: T0303_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS393_2-D2.T0303_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   77   77   5.0   37   2.42   70.27  34.280
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS393_2-D2
PFRMAT TS
TARGET T0303
MODEL 2
PARENT N/A
ATOM     18  CA  SER    18     -13.968  86.205  19.836  1.00 25.00           C
ATOM     19  CA  LEU    19     -12.008  89.438  19.620  1.00 25.00           C
ATOM     20  CA  PRO    20     -10.321  90.276  22.955  1.00 25.00           C
ATOM     21  CA  ASP    21      -9.916  86.543  23.715  1.00 25.00           C
ATOM     22  CA  LEU    22      -8.377  85.981  20.254  1.00 25.00           C
ATOM     23  CA  ALA    23      -5.949  88.886  20.834  1.00 25.00           C
ATOM     24  CA  LEU    24      -4.966  87.418  24.231  1.00 25.00           C
ATOM     25  CA  SER    25      -4.368  84.001  22.610  1.00 25.00           C
ATOM     26  CA  ILE    26      -2.193  85.633  19.913  1.00 25.00           C
ATOM     27  CA  ASN    27      -0.180  87.462  22.610  1.00 25.00           C
ATOM     28  CA  SER    28       0.313  84.172  24.508  1.00 25.00           C
ATOM     29  CA  ALA    29       1.495  82.464  21.290  1.00 25.00           C
ATOM     30  CA  LEU    30       3.959  85.326  20.648  1.00 25.00           C
ATOM     31  CA  LYS    31       5.287  85.017  24.227  1.00 25.00           C
ATOM     32  CA  ASP    32       5.728  81.241  23.764  1.00 25.00           C
ATOM     33  CA  VAL    33       9.335  81.828  24.715  1.00 25.00           C
ATOM     34  CA  ASN    34       9.684  80.671  21.071  1.00 25.00           C
ATOM     35  CA  LEU    35       9.774  84.345  19.897  1.00 25.00           C
ATOM     36  CA  PRO    36      10.966  85.942  16.610  1.00 25.00           C
ATOM     37  CA  GLN    37       7.619  87.042  15.100  1.00 25.00           C
ATOM     38  CA  ALA    38       5.695  89.294  17.453  1.00 25.00           C
ATOM     39  CA  SER    39       5.656  92.763  15.879  1.00 25.00           C
ATOM     40  CA  GLU    40       2.285  93.176  17.646  1.00 25.00           C
ATOM     41  CA  ASN    41       1.594  96.904  18.185  1.00 25.00           C
ATOM     42  CA  LEU    42      -2.010  96.436  16.976  1.00 25.00           C
ATOM     43  CA  VAL    43      -2.456  93.480  19.369  1.00 25.00           C
ATOM     44  CA  MET    44      -1.086  95.585  22.262  1.00 25.00           C
ATOM     45  CA  THR    45      -3.504  98.420  21.377  1.00 25.00           C
ATOM     46  CA  TRP    46      -6.423  95.941  21.306  1.00 25.00           C
ATOM     47  CA  ILE    47      -5.380  94.577  24.729  1.00 25.00           C
ATOM     48  CA  GLY    48      -5.370  97.001  27.654  1.00 25.00           C
ATOM     49  CA  ASN    49      -4.943 100.684  28.656  1.00 25.00           C
ATOM     50  CA  GLY    50      -2.328 101.687  26.061  1.00 25.00           C
ATOM     51  CA  ALA    51       1.012  99.905  25.723  1.00 25.00           C
ATOM     52  CA  ASP    52       3.271 102.270  27.717  1.00 25.00           C
ATOM     53  CA  VAL    53       0.420 102.954  30.182  1.00 25.00           C
ATOM     54  CA  LEU    54      -0.166  99.191  30.585  1.00 25.00           C
ATOM     55  CA  SER    55       3.570  98.653  31.233  1.00 25.00           C
ATOM     56  CA  GLN    56       3.541 101.443  33.858  1.00 25.00           C
ATOM     57  CA  ARG    57       0.497  99.851  35.551  1.00 25.00           C
ATOM     58  CA  ALA    58       2.264  96.454  35.592  1.00 25.00           C
ATOM     59  CA  VAL    59       5.377  98.065  37.138  1.00 25.00           C
ATOM     60  CA  ASP    60       3.209  99.741  39.814  1.00 25.00           C
ATOM     61  CA  TRP    61       1.532  96.388  40.593  1.00 25.00           C
ATOM     62  CA  ALA    62       4.964  94.715  40.900  1.00 25.00           C
ATOM     63  CA  CYS    63       3.902  91.698  38.927  1.00 25.00           C
ATOM     64  CA  THR    64       6.630  90.063  40.945  1.00 25.00           C
ATOM     65  CA  GLN    65      10.357  90.825  40.849  1.00 25.00           C
ATOM     66  CA  ALA    66      11.412  90.005  37.286  1.00 25.00           C
ATOM     67  CA  GLU    67      15.102  90.201  36.613  1.00 25.00           C
ATOM     68  CA  LYS    68      15.474  93.258  34.308  1.00 25.00           C
ATOM     69  CA  GLU    69      14.138  96.263  32.346  1.00 25.00           C
ATOM     70  CA  LEU    70      16.650  95.005  29.717  1.00 25.00           C
ATOM     71  CA  THR    71      14.392  95.402  26.648  1.00 25.00           C
ATOM     72  CA  GLU    72      14.063  91.596  26.368  1.00 25.00           C
ATOM     73  CA  ASP    73      13.150  91.377  30.081  1.00 25.00           C
ATOM     74  CA  GLU    74      10.512  94.114  29.619  1.00 25.00           C
ATOM     75  CA  PHE    75       9.057  92.237  26.614  1.00 25.00           C
ATOM     76  CA  LYS    76       8.917  89.007  28.666  1.00 25.00           C
ATOM     77  CA  TYR    77       7.136  90.860  31.507  1.00 25.00           C
ATOM     78  CA  PHE    78       4.610  92.302  29.015  1.00 25.00           C
ATOM     79  CA  LYS    79       3.984  88.803  27.589  1.00 25.00           C
ATOM     80  CA  ARG    80       3.443  87.432  31.122  1.00 25.00           C
ATOM     81  CA  GLN    81       0.973  90.262  31.869  1.00 25.00           C
ATOM     82  CA  PHE    82      -0.912  89.505  28.623  1.00 25.00           C
ATOM     83  CA  GLY    83      -1.071  85.793  29.551  1.00 25.00           C
ATOM     84  CA  PHE    84      -2.415  86.693  33.022  1.00 25.00           C
ATOM     85  CA  TYR    85      -5.074  88.948  31.436  1.00 25.00           C
ATOM     86  CA  TYR    86      -6.091  86.119  29.063  1.00 25.00           C
ATOM     87  CA  GLY    87      -6.364  83.703  32.022  1.00 25.00           C
ATOM     88  CA  GLU    88      -8.536  86.225  33.915  1.00 25.00           C
ATOM     89  CA  ASN    89     -10.794  86.621  30.846  1.00 25.00           C
ATOM     90  CA  LEU    90     -11.122  82.816  30.566  1.00 25.00           C
ATOM     91  CA  CYS    91     -12.034  82.597  34.279  1.00 25.00           C
ATOM     92  CA  ASN    92     -15.563  83.864  33.837  1.00 25.00           C
ATOM     93  CA  ILE    93     -16.352  82.987  30.162  1.00 25.00           C
ATOM     94  CA  SER    94     -16.068  86.342  28.322  1.00 25.00           C
TER
END
