
#######################################################
#                                                     #
#                        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   91 (   91),  selected   91 , name T0350TS168_2-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350TS168_2-D1.T0350_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    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    N       2      Q      10           #
LGA    I       3      -       -           -
LGA    E       4      P      11          4.259
LGA    R       5      V      12           #
LGA    L       6      W      13          4.180
LGA    T       7      D      14          4.275
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    T       8      D      17          3.954
LGA    L       9      T      18           #
LGA    Q      10      -       -           -
LGA    P      11      Q      19          4.912
LGA    V      12      I      20          1.351
LGA    W      13      H      21           -
LGA    D      14      -       -           -
LGA    R      15      -       -           -
LGA    Y      16      -       -           -
LGA    D      17      -       -           -
LGA    T      18      -       -           -
LGA    Q      19      -       -           -
LGA    I      20      -       -           -
LGA    H      21      -       -           -
LGA    S      36      -       -           -
LGA    Y      37      -       -           -
LGA    T      38      -       -           -
LGA    N      39      S      36          2.371
LGA    L      40      Y      37          2.269
LGA    A      41      T      38          1.855
LGA    E      42      N      39          1.782
LGA    M      43      L      40          1.836
LGA    V      44      A      41          1.273
LGA    G      45      E      42          1.354
LGA    E      46      M      43          1.403
LGA    M      47      V      44          1.326
LGA    N      48      G      45          0.969
LGA    K      49      E      46          0.989
LGA    L      50      M      47          1.383
LGA    L      51      N      48          1.665
LGA    E      52      K      49          1.836
LGA    P      53      L      50          1.158
LGA    S      54      L      51          2.387
LGA    -       -      E      52           -
LGA    Q      55      P      53          4.454
LGA    V      56      S      54          4.464
LGA    H      57      Q      55          2.954
LGA    L      58      V      56          5.118
LGA    K      59      H      57          3.085
LGA    F      60      L      58          3.194
LGA    E      61      K      59          3.152
LGA    L      62      F      60          2.475
LGA    H      63      E      61          4.202
LGA    D      64      L      62          1.144
LGA    K      65      H      63          2.616
LGA    L      66      D      64           -
LGA    N      67      K      65           -
LGA    E      68      L      66           -
LGA    Y      69      N      67           -
LGA    Y      70      E      68           -
LGA    V      71      Y      69           -
LGA    K      72      -       -           -
LGA    V      73      -       -           -
LGA    I      74      -       -           -
LGA    E      75      -       -           -
LGA    D      76      -       -           -
LGA    S      77      -       -           -
LGA    T      78      -       -           -
LGA    N      79      -       -           -
LGA    E      80      -       -           -
LGA    V      81      -       -           -
LGA    I      82      -       -           -
LGA    R      83      -       -           -
LGA    E      84      -       -           -
LGA    I      85      -       -           -
LGA    P      86      -       -           -
LGA    P      87      -       -           -
LGA    K      88      -       -           -
LGA    R      89      -       -           -
LGA    W      90      -       -           -
LGA    L      91      -       -           -
LGA    D      92      Y      70           #
LGA    F      93      -       -           -
LGA    Y      94      V      71           #
LGA    A      95      K      72          3.371
LGA    A      96      V      73           #
LGA    M      97      I      74          3.019
LGA    T      98      E      75           -
LGA    E      99      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    F     100      V      81          4.594
LGA    L     101      I      82          4.172
LGA    G     102      R      83           #
LGA    L     103      E      84           -
LGA    F     104      I      85           -
LGA    V     105      P      86           -
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    -       -      W      90           -
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    -       -      Y      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     37    3.01     0.00     26.614     1.189

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.237171 * X  +   0.681747 * Y  +   0.692077 * Z  +  10.940366
  Y_new =  -0.450601 * X  +   0.708334 * Y  +  -0.543343 * Z  +   1.432905
  Z_new =  -0.860644 * X  +  -0.182986 * Y  +   0.475192 * Z  + -23.008291 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.367576    2.774016  [ DEG:   -21.0606    158.9394 ]
  Theta =   1.036534    2.105059  [ DEG:    59.3890    120.6110 ]
  Phi   =  -1.086298    2.055295  [ DEG:   -62.2403    117.7597 ]
 
# 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: T0350TS168_2-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS168_2-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   91   91   5.0   37   3.01    0.00  26.614
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS168_2-D1
PFRMAT TS
TARGET T0350
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      10.001 -12.005  -2.977  1.00 25.00           C
ATOM      2  CA  ASN     2       9.981 -10.344  -6.360  1.00 25.00           C
ATOM      3  CA  ILE     3       6.901 -11.123  -8.348  1.00 25.00           C
ATOM      4  CA  GLU     4       3.647  -9.340  -7.332  1.00 25.00           C
ATOM      5  CA  ARG     5       2.065  -9.493 -10.787  1.00 25.00           C
ATOM      6  CA  LEU     6       5.116  -7.671 -12.145  1.00 25.00           C
ATOM      7  CA  THR     7       5.710  -6.687 -15.711  1.00 25.00           C
ATOM      8  CA  THR     8       4.556  -7.455 -19.234  1.00 25.00           C
ATOM      9  CA  LEU     9       1.964  -4.702 -18.612  1.00 25.00           C
ATOM     10  CA  GLN    10      -0.697  -7.287 -19.532  1.00 25.00           C
ATOM     11  CA  PRO    11       0.835  -6.839 -23.048  1.00 25.00           C
ATOM     12  CA  VAL    12       3.468  -9.396 -24.078  1.00 25.00           C
ATOM     13  CA  TRP    13       6.220  -6.768 -24.168  1.00 25.00           C
ATOM     14  CA  ASP    14       4.198  -3.883 -25.671  1.00 25.00           C
ATOM     15  CA  ARG    15       6.663  -3.645 -28.592  1.00 25.00           C
ATOM     16  CA  TYR    16       6.373  -7.419 -29.178  1.00 25.00           C
ATOM     17  CA  ASP    17       2.553  -7.153 -29.155  1.00 25.00           C
ATOM     18  CA  THR    18       2.714  -4.277 -31.681  1.00 25.00           C
ATOM     19  CA  GLN    19       5.022  -6.348 -33.928  1.00 25.00           C
ATOM     20  CA  ILE    20       2.603  -9.310 -33.726  1.00 25.00           C
ATOM     21  CA  HIS    21      -0.321  -7.017 -34.651  1.00 25.00           C
ATOM     36  CA  SER    36       2.252   8.490 -39.204  1.00 25.00           C
ATOM     37  CA  TYR    37       1.728   9.521 -35.538  1.00 25.00           C
ATOM     38  CA  THR    38      -1.225   8.707 -33.239  1.00 25.00           C
ATOM     39  CA  ASN    39       0.721   5.771 -31.737  1.00 25.00           C
ATOM     40  CA  LEU    40       3.745   8.047 -31.145  1.00 25.00           C
ATOM     41  CA  ALA    41       1.495  10.634 -29.440  1.00 25.00           C
ATOM     42  CA  GLU    42      -0.001   7.901 -27.212  1.00 25.00           C
ATOM     43  CA  MET    43       3.515   6.704 -26.278  1.00 25.00           C
ATOM     44  CA  VAL    44       4.536  10.294 -25.418  1.00 25.00           C
ATOM     45  CA  GLY    45       1.412  10.687 -23.238  1.00 25.00           C
ATOM     46  CA  GLU    46       2.223   7.403 -21.443  1.00 25.00           C
ATOM     47  CA  MET    47       5.812   8.592 -20.834  1.00 25.00           C
ATOM     48  CA  ASN    48       4.501  11.905 -19.428  1.00 25.00           C
ATOM     49  CA  LYS    49       2.114  10.006 -17.112  1.00 25.00           C
ATOM     50  CA  LEU    50       5.000   7.795 -15.910  1.00 25.00           C
ATOM     51  CA  LEU    51       7.131  10.903 -15.231  1.00 25.00           C
ATOM     52  CA  GLU    52       4.251  12.476 -13.257  1.00 25.00           C
ATOM     53  CA  PRO    53       3.867   9.263 -11.209  1.00 25.00           C
ATOM     54  CA  SER    54       7.569   9.558 -10.242  1.00 25.00           C
ATOM     55  CA  GLN    55       7.590   6.832  -7.589  1.00 25.00           C
ATOM     56  CA  VAL    56       9.832   4.926 -10.042  1.00 25.00           C
ATOM     57  CA  HIS    57      12.950   6.971  -9.255  1.00 25.00           C
ATOM     58  CA  LEU    58      15.449   8.110 -11.845  1.00 25.00           C
ATOM     59  CA  LYS    59      12.281   8.301 -14.031  1.00 25.00           C
ATOM     60  CA  PHE    60      14.443   8.119 -17.148  1.00 25.00           C
ATOM     61  CA  GLU    61      11.261   6.737 -18.717  1.00 25.00           C
ATOM     62  CA  LEU    62      10.045   5.455 -22.143  1.00 25.00           C
ATOM     63  CA  HIS    63       9.872   5.312 -25.947  1.00 25.00           C
ATOM     64  CA  ASP    64      12.085   6.830 -28.618  1.00 25.00           C
ATOM     65  CA  LYS    65      15.325   7.790 -30.333  1.00 25.00           C
ATOM     66  CA  LEU    66      16.858  11.236 -29.940  1.00 25.00           C
ATOM     67  CA  ASN    67      16.353  14.672 -28.445  1.00 25.00           C
ATOM     68  CA  GLU    68      15.201  17.752 -26.514  1.00 25.00           C
ATOM     69  CA  TYR    69      18.026  18.950 -24.311  1.00 25.00           C
ATOM     70  CA  TYR    70      16.704  17.479 -21.006  1.00 25.00           C
ATOM     71  CA  VAL    71      14.247  17.499 -18.119  1.00 25.00           C
ATOM     72  CA  LYS    72      12.471  18.859 -14.996  1.00 25.00           C
ATOM     73  CA  VAL    73      14.145  16.309 -12.658  1.00 25.00           C
ATOM     74  CA  ILE    74      11.969  15.861  -9.610  1.00 25.00           C
ATOM     75  CA  GLU    75      13.185  12.244  -9.265  1.00 25.00           C
ATOM     76  CA  ASP    76      12.916  11.242  -5.639  1.00 25.00           C
ATOM     77  CA  SER    77      15.440   8.594  -4.662  1.00 25.00           C
ATOM     78  CA  THR    78      18.778   7.423  -6.105  1.00 25.00           C
ATOM     79  CA  ASN    79      19.260  11.150  -6.871  1.00 25.00           C
ATOM     80  CA  GLU    80      18.625  13.209 -10.037  1.00 25.00           C
ATOM     81  CA  VAL    81      19.167  12.075 -13.632  1.00 25.00           C
ATOM     82  CA  ILE    82      16.456  13.377 -15.987  1.00 25.00           C
ATOM     83  CA  ARG    83      12.624  13.099 -16.370  1.00 25.00           C
ATOM     84  CA  GLU    84       9.566  12.597 -18.602  1.00 25.00           C
ATOM     85  CA  ILE    85       8.534  16.129 -17.569  1.00 25.00           C
ATOM     86  CA  PRO    86       9.375  17.607 -20.972  1.00 25.00           C
ATOM     87  CA  PRO    87       9.629  14.106 -22.436  1.00 25.00           C
ATOM     88  CA  LYS    88      11.629  13.503 -25.645  1.00 25.00           C
ATOM     89  CA  ARG    89      14.901  13.613 -23.657  1.00 25.00           C
ATOM     90  CA  TRP    90      13.481  11.103 -21.136  1.00 25.00           C
ATOM     91  CA  LEU    91      12.419   8.792 -24.000  1.00 25.00           C
ATOM     92  CA  ASP    92      15.924   9.030 -25.524  1.00 25.00           C
ATOM     93  CA  PHE    93      17.485   8.184 -22.131  1.00 25.00           C
ATOM     94  CA  TYR    94      15.154   5.164 -21.784  1.00 25.00           C
ATOM     95  CA  ALA    95      16.119   3.985 -25.297  1.00 25.00           C
ATOM     96  CA  ALA    96      19.831   4.339 -24.422  1.00 25.00           C
ATOM     97  CA  MET    97      19.293   2.322 -21.213  1.00 25.00           C
ATOM     98  CA  THR    98      17.485  -0.406 -23.200  1.00 25.00           C
ATOM     99  CA  GLU    99      20.367  -0.515 -25.720  1.00 25.00           C
ATOM    100  CA  PHE   100      22.891  -0.824 -22.856  1.00 25.00           C
ATOM    101  CA  LEU   101      20.849  -3.682 -21.330  1.00 25.00           C
ATOM    102  CA  GLY   102      20.751  -5.455 -24.723  1.00 25.00           C
ATOM    103  CA  LEU   103      24.544  -5.056 -25.069  1.00 25.00           C
ATOM    104  CA  PHE   104      25.041  -6.495 -21.555  1.00 25.00           C
ATOM    105  CA  VAL   105      24.563  -4.986 -18.129  1.00 25.00           C
TER
END
