
#######################################################
#                                                     #
#                        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 T0347TS393_5-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS393_5-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      R      18           -
LGA    P      19      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      -       -           -
LGA    I      52      T      20           #
LGA    -       -      Q      21           -
LGA    V      53      I      22          1.547
LGA    P      54      A      23          2.099
LGA    V      55      V      24          3.216
LGA    V      56      G      25          4.449
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    A      57      K      32           #
LGA    G      58      R      33          3.437
LGA    -       -      K      34           -
LGA    P      59      E      35          3.779
LGA    K      60      W      36          1.709
LGA    D      61      R      37           #
LGA    R      62      H      51           #
LGA    A      63      I      52           #
LGA    Y      64      V      53           #
LGA    L      65      P      54           -
LGA    I      66      -       -           -
LGA    D      67      -       -           -
LGA    H      68      V      55           #
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    H      69      Y      64          4.507
LGA    H      70      -       -           -
LGA    L      71      L      65          2.482
LGA    V      72      I      66          1.691
LGA    L      73      -       -           -
LGA    A      74      -       -           -
LGA    L      75      D      67          3.968
LGA    S      76      -       -           -
LGA    K      77      -       -           -
LGA    E      78      -       -           -
LGA    G      79      -       -           -
LGA    V      80      -       -           -
LGA    E      81      -       -           -
LGA    H      82      -       -           -
LGA    V      83      H      68          2.720
LGA    L      84      H      69          5.018
LGA    T      85      H      70           -
LGA    S      86      L      71           -
LGA    E      87      V      72           -
LGA    V      88      L      73           -
LGA    A      89      A      74           -
LGA    K      90      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    F      91      G      95           #
LGA    S      92      -       -           -
LGA    H      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      K      96          5.144
LGA    K      96      D      97          1.181
LGA    D      97      E      98          1.716
LGA    E      98      F      99          1.535
LGA    F      99      W     100          0.910
LGA    W     100      S     101          1.276
LGA    S     101      V     102          2.003
LGA    V     102      M     103          1.643
LGA    M     103      D     104          0.758
LGA    D     104      H     105          1.742
LGA    H     105      R     106          2.622
LGA    R     106      N     107          2.582
LGA    N     107      L     108          3.938
LGA    L     108      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     26    2.90     7.69     19.619     0.867

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.932684 * X  +  -0.038362 * Y  +  -0.358648 * Z  +   6.615455
  Y_new =   0.025878 * X  +  -0.984649 * Y  +   0.172618 * Z  +  47.450104
  Z_new =  -0.359764 * X  +  -0.170279 * Y  +  -0.917374 * Z  +  -7.110698 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.958065    0.183527  [ DEG:  -169.4847     10.5153 ]
  Theta =   0.368015    2.773577  [ DEG:    21.0857    158.9143 ]
  Phi   =   0.027738   -3.113854  [ DEG:     1.5893   -178.4107 ]
 
# 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: T0347TS393_5-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS393_5-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   26   2.90    7.69  19.619
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS393_5-D1
PFRMAT TS
TARGET T0347
MODEL 5
PARENT N/A
ATOM      7  CA  PRO     7      30.399  73.328 -23.632  1.00 25.00           C
ATOM      8  CA  ARG     8      28.339  72.987 -20.408  1.00 25.00           C
ATOM      9  CA  LEU     9      26.990  69.902 -18.609  1.00 25.00           C
ATOM     10  CA  SER    10      24.479  69.227 -21.382  1.00 25.00           C
ATOM     11  CA  ARG    11      24.894  66.996 -24.376  1.00 25.00           C
ATOM     12  CA  ILE    12      24.076  63.773 -22.606  1.00 25.00           C
ATOM     13  CA  ALA    13      20.374  62.887 -22.604  1.00 25.00           C
ATOM     14  CA  ILE    14      18.897  63.849 -19.232  1.00 25.00           C
ATOM     15  CA  ASP    15      16.839  66.738 -20.677  1.00 25.00           C
ATOM     16  CA  LYS    16      14.151  66.193 -18.002  1.00 25.00           C
ATOM     17  CA  LEU    17      13.983  62.689 -19.341  1.00 25.00           C
ATOM     18  CA  ARG    18      13.855  59.396 -21.325  1.00 25.00           C
ATOM     19  CA  PRO    19      12.541  56.357 -19.400  1.00 25.00           C
ATOM     20  CA  THR    20       9.586  58.684 -18.673  1.00 25.00           C
ATOM     21  CA  GLN    21       8.180  56.155 -16.164  1.00 25.00           C
ATOM     22  CA  ILE    22      11.599  55.913 -14.455  1.00 25.00           C
ATOM     23  CA  ALA    23      11.794  59.733 -14.250  1.00 25.00           C
ATOM     24  CA  VAL    24       8.284  59.854 -12.723  1.00 25.00           C
ATOM     25  CA  GLY    25       9.284  57.199 -10.150  1.00 25.00           C
ATOM     26  CA  PHE    26      12.423  59.206  -9.263  1.00 25.00           C
ATOM     27  CA  ARG    27      10.310  62.371  -8.835  1.00 25.00           C
ATOM     28  CA  GLU    28       7.881  60.471  -6.564  1.00 25.00           C
ATOM     29  CA  VAL    29      10.815  59.173  -4.472  1.00 25.00           C
ATOM     30  CA  GLU    30      12.201  62.729  -4.163  1.00 25.00           C
ATOM     31  CA  LEU    31       8.761  63.999  -3.054  1.00 25.00           C
ATOM     32  CA  LYS    32       8.546  61.208  -0.440  1.00 25.00           C
ATOM     33  CA  ARG    33      12.036  62.115   0.850  1.00 25.00           C
ATOM     34  CA  LYS    34      11.015  65.797   1.096  1.00 25.00           C
ATOM     35  CA  GLU    35       7.856  64.819   3.028  1.00 25.00           C
ATOM     36  CA  TRP    36       9.950  62.681   5.419  1.00 25.00           C
ATOM     37  CA  ARG    37      12.358  65.609   5.965  1.00 25.00           C
ATOM     51  CA  HIS    51       4.131  48.011   5.782  1.00 25.00           C
ATOM     52  CA  ILE    52       1.542  46.849   3.248  1.00 25.00           C
ATOM     53  CA  VAL    53       1.174  46.811  -0.481  1.00 25.00           C
ATOM     54  CA  PRO    54       4.875  47.592  -0.648  1.00 25.00           C
ATOM     55  CA  VAL    55       5.569  47.262  -4.401  1.00 25.00           C
ATOM     56  CA  VAL    56       8.509  48.955  -6.161  1.00 25.00           C
ATOM     57  CA  ALA    57       8.570  48.534  -9.998  1.00 25.00           C
ATOM     58  CA  GLY    58       9.518  49.090 -13.649  1.00 25.00           C
ATOM     59  CA  PRO    59      11.757  48.629 -16.692  1.00 25.00           C
ATOM     60  CA  LYS    60      10.639  46.305 -19.459  1.00 25.00           C
ATOM     61  CA  ASP    61      11.685  42.638 -19.258  1.00 25.00           C
ATOM     62  CA  ARG    62      13.824  43.699 -16.316  1.00 25.00           C
ATOM     63  CA  ALA    63      13.467  44.411 -12.579  1.00 25.00           C
ATOM     64  CA  TYR    64      11.346  44.389  -9.364  1.00 25.00           C
ATOM     65  CA  LEU    65       8.336  43.963  -7.019  1.00 25.00           C
ATOM     66  CA  ILE    66       5.651  41.635  -5.639  1.00 25.00           C
ATOM     67  CA  ASP    67       2.009  40.897  -4.657  1.00 25.00           C
ATOM     68  CA  HIS    68       3.329  37.330  -4.594  1.00 25.00           C
ATOM     69  CA  HIS    69       4.125  38.608  -1.072  1.00 25.00           C
ATOM     70  CA  HIS    70       5.514  35.169  -0.113  1.00 25.00           C
ATOM     71  CA  LEU    71       7.686  35.140  -3.267  1.00 25.00           C
ATOM     72  CA  VAL    72       8.992  38.641  -2.431  1.00 25.00           C
ATOM     73  CA  LEU    73       9.817  37.508   1.134  1.00 25.00           C
ATOM     74  CA  ALA    74      11.674  34.453  -0.241  1.00 25.00           C
ATOM     75  CA  LEU    75      13.654  36.700  -2.627  1.00 25.00           C
ATOM     76  CA  SER    76      14.560  39.027   0.276  1.00 25.00           C
ATOM     77  CA  LYS    77      15.715  36.025   2.355  1.00 25.00           C
ATOM     78  CA  GLU    78      16.632  38.730   4.878  1.00 25.00           C
ATOM     79  CA  GLY    79      15.900  42.334   4.023  1.00 25.00           C
ATOM     80  CA  VAL    80      12.758  43.703   2.470  1.00 25.00           C
ATOM     81  CA  GLU    81      14.792  46.212   0.488  1.00 25.00           C
ATOM     82  CA  HIS    82      14.873  43.440  -2.067  1.00 25.00           C
ATOM     83  CA  VAL    83      11.624  42.691  -3.979  1.00 25.00           C
ATOM     84  CA  LEU    84       9.657  45.127  -1.759  1.00 25.00           C
ATOM     85  CA  THR    85       7.788  42.732   0.533  1.00 25.00           C
ATOM     86  CA  SER    86       3.958  42.789   0.597  1.00 25.00           C
ATOM     87  CA  GLU    87       0.388  41.869  -0.367  1.00 25.00           C
ATOM     88  CA  VAL    88      -1.028  38.739  -1.934  1.00 25.00           C
ATOM     89  CA  ALA    89      -4.789  38.798  -2.770  1.00 25.00           C
ATOM     90  CA  LYS    90      -4.593  35.274  -1.366  1.00 25.00           C
ATOM     91  CA  PHE    91      -4.636  33.952   2.204  1.00 25.00           C
ATOM     92  CA  SER    92      -7.220  36.519   3.470  1.00 25.00           C
ATOM     93  CA  HIS    93      -6.459  38.673   6.520  1.00 25.00           C
ATOM     94  CA  LEU    94      -3.304  38.386   8.596  1.00 25.00           C
ATOM     95  CA  GLY    95      -4.943  35.230   9.907  1.00 25.00           C
ATOM     96  CA  LYS    96      -3.295  31.850   9.432  1.00 25.00           C
ATOM     97  CA  ASP    97      -0.231  29.556   9.581  1.00 25.00           C
ATOM     98  CA  GLU    98       0.886  30.781   6.129  1.00 25.00           C
ATOM     99  CA  PHE    99       0.479  34.417   7.261  1.00 25.00           C
ATOM    100  CA  TRP   100       2.547  33.696  10.402  1.00 25.00           C
ATOM    101  CA  SER   101       5.280  32.078   8.262  1.00 25.00           C
ATOM    102  CA  VAL   102       5.307  35.129   5.947  1.00 25.00           C
ATOM    103  CA  MET   103       5.609  37.454   8.974  1.00 25.00           C
ATOM    104  CA  ASP   104       8.521  35.364  10.321  1.00 25.00           C
ATOM    105  CA  HIS   105      10.251  35.532   6.908  1.00 25.00           C
ATOM    106  CA  ARG   106       9.416  39.088   5.933  1.00 25.00           C
ATOM    107  CA  ASN   107       5.934  39.910   4.615  1.00 25.00           C
ATOM    108  CA  LEU   108       2.261  39.377   3.913  1.00 25.00           C
TER
END
