
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0347TS168_3-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS168_3-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P       7      P       7           -
LGA    R       8      R       8           -
LGA    L       9      L       9           -
LGA    S      10      S      10           -
LGA    R      11      R      11           -
LGA    I      12      I      12           -
LGA    A      13      A      13           -
LGA    I      14      I      14           -
LGA    D      15      D      15           -
LGA    K      16      K      16           -
LGA    L      17      L      17           -
LGA    R      18      -       -           -
LGA    P      19      -       -           -
LGA    T      20      -       -           -
LGA    Q      21      -       -           -
LGA    I      22      -       -           -
LGA    A      23      -       -           -
LGA    V      24      -       -           -
LGA    G      25      -       -           -
LGA    F      26      -       -           -
LGA    R      27      -       -           -
LGA    E      28      -       -           -
LGA    V      29      -       -           -
LGA    E      30      -       -           -
LGA    L      31      -       -           -
LGA    K      32      -       -           -
LGA    R      33      -       -           -
LGA    K      34      -       -           -
LGA    E      35      -       -           -
LGA    W      36      -       -           -
LGA    R      37      -       -           -
LGA    H      51      R      18          4.489
LGA    I      52      P      19          3.218
LGA    V      53      T      20           -
LGA    P      54      Q      21           -
LGA    V      55      I      22           -
LGA    V      56      A      23           -
LGA    A      57      V      24           -
LGA    G      58      G      25           -
LGA    P      59      F      26           -
LGA    K      60      R      27           -
LGA    D      61      E      28           -
LGA    R      62      V      29           -
LGA    A      63      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    Y      64      H      51          2.867
LGA    L      65      I      52          1.574
LGA    I      66      V      53          1.447
LGA    D      67      P      54          3.714
LGA    H      68      V      55          3.087
LGA    H      69      V      56          4.564
LGA    H      70      A      57           -
LGA    L      71      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    V      72      L      65          2.517
LGA    L      73      I      66          2.433
LGA    A      74      D      67          1.684
LGA    L      75      H      68          2.772
LGA    S      76      H      69          4.062
LGA    K      77      -       -           -
LGA    E      78      -       -           -
LGA    G      79      -       -           -
LGA    V      80      -       -           -
LGA    E      81      H      70          1.992
LGA    H      82      L      71          3.895
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    V      83      L      75          4.338
LGA    L      84      S      76          5.076
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    T      85      V      83          5.194
LGA    S      86      L      84           -
LGA    E      87      T      85           -
LGA    V      88      S      86           #
LGA    A      89      E      87          2.879
LGA    K      90      V      88          2.296
LGA    F      91      A      89          0.602
LGA    S      92      K      90          1.081
LGA    H      93      F      91          3.326
LGA    L      94      S      92          1.300
LGA    -       -      H      93           -
LGA    G      95      L      94          3.052
LGA    K      96      G      95           #
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    D      97      E      98          3.361
LGA    E      98      F      99          2.539
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    F      99      V     102           #
LGA    W     100      M     103          1.803
LGA    S     101      D     104          3.344
LGA    V     102      H     105           -
LGA    M     103      R     106           #
LGA    D     104      N     107          2.655
LGA    H     105      L     108          3.202
LGA    R     106      -       -           -
LGA    N     107      -       -           -
LGA    L     108      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     31    3.13     0.00     20.563     0.959

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.052289 * X  +  -0.892357 * Y  +   0.448290 * Z  +   8.063288
  Y_new =   0.235426 * X  +  -0.425236 * Y  +  -0.873927 * Z  +  39.897701
  Z_new =   0.970485 * X  +   0.151236 * Y  +   0.187849 * Z  + -12.530882 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.677840   -2.463753  [ DEG:    38.8374   -141.1626 ]
  Theta =  -1.327232   -1.814360  [ DEG:   -76.0448   -103.9552 ]
  Phi   =   1.352239   -1.789353  [ DEG:    77.4776   -102.5224 ]
 
# 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: T0347TS168_3-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS168_3-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89   89   5.0   31   3.13    0.00  20.563
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS168_3-D1
PFRMAT TS
TARGET T0347
MODEL 3
PARENT N/A
ATOM      7  CA  PRO     7      14.423  75.965  -8.677  1.00 25.00           C
ATOM      8  CA  ARG     8      16.872  74.092 -10.867  1.00 25.00           C
ATOM      9  CA  LEU     9      17.348  72.829 -14.430  1.00 25.00           C
ATOM     10  CA  SER    10      20.272  72.027 -16.765  1.00 25.00           C
ATOM     11  CA  ARG    11      23.286  70.436 -15.086  1.00 25.00           C
ATOM     12  CA  ILE    12      21.149  67.323 -14.385  1.00 25.00           C
ATOM     13  CA  ALA    13      23.317  65.306 -11.975  1.00 25.00           C
ATOM     14  CA  ILE    14      22.096  62.417 -14.121  1.00 25.00           C
ATOM     15  CA  ASP    15      22.948  60.276 -11.062  1.00 25.00           C
ATOM     16  CA  LYS    16      19.927  61.703  -9.191  1.00 25.00           C
ATOM     17  CA  LEU    17      18.433  58.391  -8.236  1.00 25.00           C
ATOM     18  CA  ARG    18      20.515  55.843 -10.071  1.00 25.00           C
ATOM     19  CA  PRO    19      19.374  53.230 -12.591  1.00 25.00           C
ATOM     20  CA  THR    20      18.028  56.194 -14.607  1.00 25.00           C
ATOM     21  CA  GLN    21      17.199  53.863 -17.530  1.00 25.00           C
ATOM     22  CA  ILE    22      15.378  51.482 -15.146  1.00 25.00           C
ATOM     23  CA  ALA    23      13.386  54.415 -13.698  1.00 25.00           C
ATOM     24  CA  VAL    24      12.445  55.552 -17.232  1.00 25.00           C
ATOM     25  CA  GLY    25      11.310  51.998 -18.099  1.00 25.00           C
ATOM     26  CA  PHE    26       9.192  51.870 -14.911  1.00 25.00           C
ATOM     27  CA  ARG    27       7.609  55.242 -15.798  1.00 25.00           C
ATOM     28  CA  GLU    28       6.823  53.973 -19.325  1.00 25.00           C
ATOM     29  CA  VAL    29       5.226  50.816 -17.860  1.00 25.00           C
ATOM     30  CA  GLU    30       3.112  52.956 -15.489  1.00 25.00           C
ATOM     31  CA  LEU    31       1.990  55.144 -18.424  1.00 25.00           C
ATOM     32  CA  LYS    32       1.039  52.019 -20.423  1.00 25.00           C
ATOM     33  CA  ARG    33      -0.962  50.689 -17.440  1.00 25.00           C
ATOM     34  CA  LYS    34      -2.770  54.051 -17.124  1.00 25.00           C
ATOM     35  CA  GLU    35      -3.594  53.987 -20.863  1.00 25.00           C
ATOM     36  CA  TRP    36      -4.954  50.422 -20.528  1.00 25.00           C
ATOM     37  CA  ARG    37      -7.111  51.499 -17.552  1.00 25.00           C
ATOM     51  CA  HIS    51      -1.245  41.451  -4.778  1.00 25.00           C
ATOM     52  CA  ILE    52       1.805  39.368  -5.816  1.00 25.00           C
ATOM     53  CA  VAL    53       3.987  40.581  -8.609  1.00 25.00           C
ATOM     54  CA  PRO    54       7.067  38.276  -8.620  1.00 25.00           C
ATOM     55  CA  VAL    55      10.647  39.234  -9.477  1.00 25.00           C
ATOM     56  CA  VAL    56      14.167  40.454  -8.709  1.00 25.00           C
ATOM     57  CA  ALA    57      17.070  38.121  -9.110  1.00 25.00           C
ATOM     58  CA  GLY    58      17.664  35.459  -6.484  1.00 25.00           C
ATOM     59  CA  PRO    59      20.577  36.565  -4.256  1.00 25.00           C
ATOM     60  CA  LYS    60      23.481  35.505  -6.503  1.00 25.00           C
ATOM     61  CA  ASP    61      22.604  36.799 -10.034  1.00 25.00           C
ATOM     62  CA  ARG    62      20.800  36.654 -13.389  1.00 25.00           C
ATOM     63  CA  ALA    63      18.631  36.310 -16.497  1.00 25.00           C
ATOM     64  CA  TYR    64      15.837  35.822 -13.993  1.00 25.00           C
ATOM     65  CA  LEU    65      13.831  34.188 -11.185  1.00 25.00           C
ATOM     66  CA  ILE    66      10.373  34.365  -9.642  1.00 25.00           C
ATOM     67  CA  ASP    67       7.916  32.760  -7.196  1.00 25.00           C
ATOM     68  CA  HIS    68      10.710  31.264  -5.008  1.00 25.00           C
ATOM     69  CA  HIS    69      10.457  32.798  -1.507  1.00 25.00           C
ATOM     70  CA  HIS    70      13.362  35.163  -2.307  1.00 25.00           C
ATOM     71  CA  LEU    71      11.653  36.196  -5.575  1.00 25.00           C
ATOM     72  CA  VAL    72       8.389  36.861  -3.686  1.00 25.00           C
ATOM     73  CA  LEU    73      10.279  38.987  -1.120  1.00 25.00           C
ATOM     74  CA  ALA    74      11.934  40.972  -3.946  1.00 25.00           C
ATOM     75  CA  LEU    75       8.516  41.547  -5.576  1.00 25.00           C
ATOM     76  CA  SER    76       7.095  42.751  -2.229  1.00 25.00           C
ATOM     77  CA  LYS    77      10.053  45.147  -1.807  1.00 25.00           C
ATOM     78  CA  GLU    78       8.380  46.471   1.384  1.00 25.00           C
ATOM     79  CA  GLY    79       4.980  47.227  -0.170  1.00 25.00           C
ATOM     80  CA  VAL    80       5.142  47.143  -4.009  1.00 25.00           C
ATOM     81  CA  GLU    81       8.068  46.573  -6.371  1.00 25.00           C
ATOM     82  CA  HIS    82       6.509  44.506  -9.167  1.00 25.00           C
ATOM     83  CA  VAL    83       6.962  42.002 -11.957  1.00 25.00           C
ATOM     84  CA  LEU    84       4.634  39.484 -13.505  1.00 25.00           C
ATOM     85  CA  THR    85       3.166  36.748 -11.331  1.00 25.00           C
ATOM     86  CA  SER    86       2.831  34.731  -8.163  1.00 25.00           C
ATOM     87  CA  GLU    87       3.845  32.738  -5.038  1.00 25.00           C
ATOM     88  CA  VAL    88       6.059  30.073  -3.383  1.00 25.00           C
ATOM     89  CA  ALA    89       7.099  26.446  -3.857  1.00 25.00           C
ATOM     90  CA  LYS    90      10.880  26.365  -3.241  1.00 25.00           C
ATOM     91  CA  PHE    91      10.018  27.178   0.381  1.00 25.00           C
ATOM     92  CA  SER    92       6.983  25.501   1.876  1.00 25.00           C
ATOM     93  CA  HIS    93       3.361  24.731   0.809  1.00 25.00           C
ATOM     94  CA  LEU    94       0.525  24.981   3.322  1.00 25.00           C
ATOM     95  CA  GLY    95      -0.672  28.087   5.170  1.00 25.00           C
ATOM     96  CA  LYS    96       1.912  28.136   8.030  1.00 25.00           C
ATOM     97  CA  ASP    97       1.899  31.601   9.660  1.00 25.00           C
ATOM     98  CA  GLU    98       0.784  33.179   6.353  1.00 25.00           C
ATOM     99  CA  PHE    99       3.590  31.343   4.503  1.00 25.00           C
ATOM    100  CA  TRP   100       6.135  32.580   7.084  1.00 25.00           C
ATOM    101  CA  SER   101       4.850  36.164   6.669  1.00 25.00           C
ATOM    102  CA  VAL   102       5.156  35.859   2.863  1.00 25.00           C
ATOM    103  CA  MET   103       8.739  34.558   3.231  1.00 25.00           C
ATOM    104  CA  ASP   104       9.593  37.492   5.541  1.00 25.00           C
ATOM    105  CA  HIS   105       8.117  39.952   3.002  1.00 25.00           C
ATOM    106  CA  ARG   106       4.553  40.768   1.933  1.00 25.00           C
ATOM    107  CA  ASN   107       3.161  38.583  -0.830  1.00 25.00           C
ATOM    108  CA  LEU   108       1.137  35.432  -1.406  1.00 25.00           C
TER
END
