
#######################################################
#                                                     #
#                        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_1-D2
# Molecule2: number of CA atoms   72 (  556),  selected   72 , name T0330_D2.pdb
# PARAMETERS: T0330TS393_1-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    V      17      S      19          3.669
LGA    E      18      M      20          2.595
LGA    S      19      N      21          5.114
LGA    M      20      R      22          1.204
LGA    N      21      R      23          4.262
LGA    R      22      V      24           #
LGA    R      23      -       -           -
LGA    V      24      L      25          3.362
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      A      26           #
LGA    S      45      D      27          5.176
LGA    G      46      A      28           -
LGA    K      47      -       -           -
LGA    M      48      L      29           #
LGA    D      49      I      30          2.519
LGA    -       -      E      31           -
LGA    -       -      V      32           -
LGA    G      50      Y      33           #
LGA    A      51      G      34          4.091
LGA    I      52      T      35          2.827
LGA    I      53      E      36          4.392
LGA    Y      54      G      37          2.145
LGA    E      55      S      38           -
LGA    V      56      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    L      57      I      53          4.870
LGA    -       -      Y      54           -
LGA    -       -      E      55           -
LGA    -       -      V      56           -
LGA    S      58      L      57          2.726
LGA    N      59      S      58          2.541
LGA    -       -      N      59           -
LGA    -       -      V      60           -
LGA    -       -      G      61           -
LGA    V      60      L      62           #
LGA    G      61      E      63          4.189
LGA    L      62      R      64          1.250
LGA    E      63      A      65          2.354
LGA    R      64      -       -           -
LGA    A      65      -       -           -
LGA    E      66      E      66           #
LGA    I      67      I      67          3.676
LGA    A      68      A      68          0.954
LGA    D      69      D      69          3.190
LGA    K      70      K      70          0.755
LGA    F      71      F      71          2.144
LGA    D      72      D      72          1.977
LGA    K      73      K      73          0.569
LGA    A      74      A      74          1.163
LGA    K      75      K      75          1.722
LGA    E      76      E      76          0.991
LGA    T      77      T      77          0.305
LGA    Y      78      Y      78          0.878
LGA    I      79      I      79          0.574
LGA    A      80      A      80          0.333
LGA    L      81      L      81          0.627
LGA    F      82      F      82          0.599
LGA    R      83      R      83          0.783
LGA    E      84      E      84          1.236
LGA    R      85      R      85          1.765
LGA    A      86      A      86          3.437
LGA    R      87      -       -           -
LGA    R      88      -       -           -
LGA    E      89      -       -           -
LGA    D      90      R      87          3.469
LGA    I      91      R      88          4.991
LGA    -       -      E      89           -
LGA    -       -      D      90           -
LGA    -       -      I      91           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   72    5.0     40    2.81    50.00     38.040     1.373

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.641646 * X  +   0.387494 * Y  +  -0.661921 * Z  +  19.944674
  Y_new =  -0.164336 * X  +  -0.912412 * Y  +  -0.374831 * Z  +  30.898172
  Z_new =  -0.749189 * X  +  -0.131731 * Y  +   0.649124 * Z  +  12.027393 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.200218    2.941375  [ DEG:   -11.4716    168.5284 ]
  Theta =   0.846837    2.294755  [ DEG:    48.5202    131.4798 ]
  Phi   =  -2.890866    0.250727  [ DEG:  -165.6344     14.3656 ]
 
# 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_1-D2                               
REMARK     2: T0330_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS393_1-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   2.81   50.00  38.040
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS393_1-D2
PFRMAT TS
TARGET T0330
MODEL 1
PARENT N/A
ATOM     17  CA  VAL    17      15.749  34.491   8.209  1.00 25.00           C
ATOM     18  CA  GLU    18      16.749  32.457   5.157  1.00 25.00           C
ATOM     19  CA  SER    19      20.489  33.269   5.292  1.00 25.00           C
ATOM     20  CA  MET    20      20.173  35.371   2.106  1.00 25.00           C
ATOM     21  CA  ASN    21      17.193  37.248   3.610  1.00 25.00           C
ATOM     22  CA  ARG    22      19.194  37.913   6.807  1.00 25.00           C
ATOM     23  CA  ARG    23      22.130  39.225   4.727  1.00 25.00           C
ATOM     24  CA  VAL    24      19.759  41.523   2.785  1.00 25.00           C
ATOM     25  CA  LEU    25      18.297  42.832   6.074  1.00 25.00           C
ATOM     26  CA  ALA    26      21.826  43.498   7.406  1.00 25.00           C
ATOM     27  CA  ASP    27      22.713  45.376   4.189  1.00 25.00           C
ATOM     28  CA  ALA    28      19.526  47.478   4.507  1.00 25.00           C
ATOM     29  CA  LEU    29      20.396  48.289   8.148  1.00 25.00           C
ATOM     30  CA  ILE    30      23.931  49.325   7.098  1.00 25.00           C
ATOM     31  CA  GLU    31      22.483  51.573   4.356  1.00 25.00           C
ATOM     32  CA  VAL    32      20.102  53.175   6.891  1.00 25.00           C
ATOM     33  CA  TYR    33      17.702  52.729   3.960  1.00 25.00           C
ATOM     34  CA  GLY    34      14.027  53.644   3.969  1.00 25.00           C
ATOM     35  CA  THR    35      11.442  53.060   1.242  1.00 25.00           C
ATOM     36  CA  GLU    36       8.549  52.035  -0.945  1.00 25.00           C
ATOM     37  CA  GLY    37      10.147  49.696  -3.458  1.00 25.00           C
ATOM     38  CA  SER    38       8.658  47.535  -6.172  1.00 25.00           C
ATOM     39  CA  THR    39       7.986  43.849  -7.009  1.00 25.00           C
ATOM     40  CA  GLY    40       9.573  41.467  -9.552  1.00 25.00           C
ATOM     41  CA  SER    41       8.910  38.500  -7.223  1.00 25.00           C
ATOM     42  CA  HIS    42       9.550  34.830  -6.212  1.00 25.00           C
ATOM     43  CA  ASP    43      12.660  32.736  -7.056  1.00 25.00           C
ATOM     44  CA  PHE    44      14.674  35.545  -5.398  1.00 25.00           C
ATOM     45  CA  SER    45      17.437  32.974  -5.131  1.00 25.00           C
ATOM     46  CA  GLY    46      19.286  33.404  -8.434  1.00 25.00           C
ATOM     47  CA  LYS    47      16.421  35.305 -10.117  1.00 25.00           C
ATOM     48  CA  MET    48      17.706  38.179 -12.244  1.00 25.00           C
ATOM     49  CA  ASP    49      18.321  41.014  -9.726  1.00 25.00           C
ATOM     50  CA  GLY    50      19.627  38.623  -7.034  1.00 25.00           C
ATOM     51  CA  ALA    51      22.381  37.416  -9.407  1.00 25.00           C
ATOM     52  CA  ILE    52      23.356  41.042 -10.159  1.00 25.00           C
ATOM     53  CA  ILE    53      23.502  41.807  -6.409  1.00 25.00           C
ATOM     54  CA  TYR    54      25.714  38.732  -5.843  1.00 25.00           C
ATOM     55  CA  GLU    55      28.038  39.852  -8.674  1.00 25.00           C
ATOM     56  CA  VAL    56      28.257  43.355  -7.141  1.00 25.00           C
ATOM     57  CA  LEU    57      29.095  41.835  -3.726  1.00 25.00           C
ATOM     58  CA  SER    58      31.822  39.677  -5.329  1.00 25.00           C
ATOM     59  CA  ASN    59      33.275  42.763  -7.071  1.00 25.00           C
ATOM     60  CA  VAL    60      35.539  42.521  -4.006  1.00 25.00           C
ATOM     61  CA  GLY    61      36.239  46.213  -4.572  1.00 25.00           C
ATOM     62  CA  LEU    62      34.003  48.527  -6.512  1.00 25.00           C
ATOM     63  CA  GLU    63      34.188  52.189  -5.649  1.00 25.00           C
ATOM     64  CA  ARG    64      32.615  53.431  -8.884  1.00 25.00           C
ATOM     65  CA  ALA    65      29.965  55.968  -7.785  1.00 25.00           C
ATOM     66  CA  GLU    66      27.436  54.410 -10.203  1.00 25.00           C
ATOM     67  CA  ILE    67      28.227  50.925  -8.824  1.00 25.00           C
ATOM     68  CA  ALA    68      27.743  52.205  -5.246  1.00 25.00           C
ATOM     69  CA  ASP    69      24.382  53.756  -6.229  1.00 25.00           C
ATOM     70  CA  LYS    70      23.295  50.449  -7.827  1.00 25.00           C
ATOM     71  CA  PHE    71      24.295  48.558  -4.650  1.00 25.00           C
ATOM     72  CA  ASP    72      22.297  51.032  -2.518  1.00 25.00           C
ATOM     73  CA  LYS    73      19.253  50.576  -4.796  1.00 25.00           C
ATOM     74  CA  ALA    74      19.571  46.772  -4.499  1.00 25.00           C
ATOM     75  CA  LYS    75      19.767  47.061  -0.686  1.00 25.00           C
ATOM     76  CA  GLU    76      16.643  49.277  -0.669  1.00 25.00           C
ATOM     77  CA  THR    77      14.794  46.729  -2.851  1.00 25.00           C
ATOM     78  CA  TYR    78      15.822  43.910  -0.471  1.00 25.00           C
ATOM     79  CA  ILE    79      14.576  45.947   2.522  1.00 25.00           C
ATOM     80  CA  ALA    80      11.243  46.571   0.742  1.00 25.00           C
ATOM     81  CA  LEU    81      10.908  42.827   0.005  1.00 25.00           C
ATOM     82  CA  PHE    82      11.619  42.016   3.680  1.00 25.00           C
ATOM     83  CA  ARG    83       8.969  44.552   4.779  1.00 25.00           C
ATOM     84  CA  GLU    84       6.441  42.994   2.361  1.00 25.00           C
ATOM     85  CA  ARG    85       7.231  39.510   3.740  1.00 25.00           C
ATOM     86  CA  ALA    86       6.747  40.789   7.317  1.00 25.00           C
ATOM     87  CA  ARG    87       3.386  42.341   6.334  1.00 25.00           C
ATOM     88  CA  ARG    88       1.538  40.613   3.492  1.00 25.00           C
ATOM     89  CA  GLU    89       0.677  36.987   3.956  1.00 25.00           C
ATOM     90  CA  ASP    90       3.074  36.671   6.949  1.00 25.00           C
ATOM     91  CA  ILE    91       6.477  35.092   7.718  1.00 25.00           C
TER
END
