
#######################################################
#                                                     #
#                        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   92 (   92),  selected   92 , name T0329TS168_4-D2
# Molecule2: number of CA atoms   92 (  716),  selected   92 , name T0329_D2.pdb
# PARAMETERS: T0329TS168_4-D2.T0329_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T      17      -       -           -
LGA    S      18      -       -           -
LGA    A      19      T      17           #
LGA    D      20      -       -           -
LGA    L      21      -       -           -
LGA    T      22      -       -           -
LGA    S      23      -       -           -
LGA    A      24      -       -           -
LGA    L      25      -       -           -
LGA    N      26      -       -           -
LGA    Y      27      -       -           -
LGA    A      28      -       -           -
LGA    F      29      -       -           -
LGA    E      30      -       -           -
LGA    Q      31      -       -           -
LGA    T      32      -       -           -
LGA    G      33      -       -           -
LGA    H      34      -       -           -
LGA    R      35      -       -           -
LGA    H      36      -       -           -
LGA    D      37      -       -           -
LGA    F      38      -       -           -
LGA    T      39      -       -           -
LGA    V      40      -       -           -
LGA    E      41      -       -           -
LGA    D      42      -       -           -
LGA    I      43      -       -           -
LGA    K      44      -       -           -
LGA    N      45      -       -           -
LGA    F      46      -       -           -
LGA    F      47      -       -           -
LGA    G      48      -       -           -
LGA    S      49      -       -           -
LGA    G      50      -       -           -
LGA    V      51      S      18           #
LGA    V      52      A      19           -
LGA    -       -      D      20           -
LGA    V      53      L      21           #
LGA    A      54      T      22          3.091
LGA    V      55      -       -           -
LGA    T      56      S      23           #
LGA    R      57      A      24          3.576
LGA    A      58      L      25          4.528
LGA    -       -      N      26           -
LGA    -       -      Y      27           -
LGA    L      59      A      28          1.444
LGA    A      60      F      29           #
LGA    Y      61      E      30          4.351
LGA    E      62      Q      31          5.300
LGA    A      63      T      32          3.822
LGA    G      64      G      33          3.286
LGA    S      65      H      34          2.185
LGA    S      66      -       -           -
LGA    R      67      R      35          2.912
LGA    E      68      H      36           #
LGA    S      69      -       -           -
LGA    L      70      D      37           #
LGA    V      71      F      38          5.417
LGA    -       -      T      39           -
LGA    -       -      V      40           -
LGA    -       -      E      41           -
LGA    -       -      D      42           -
LGA    -       -      I      43           -
LGA    -       -      K      44           -
LGA    -       -      N      45           -
LGA    -       -      F      46           -
LGA    -       -      F      47           -
LGA    -       -      G      48           -
LGA    -       -      S      49           -
LGA    -       -      G      50           -
LGA    -       -      V      51           -
LGA    -       -      V      52           -
LGA    -       -      V      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      T      56           -
LGA    -       -      R      57           -
LGA    A      72      A      58          4.521
LGA    F      73      L      59          3.848
LGA    G      74      A      60          4.368
LGA    T      75      Y      61           #
LGA    -       -      E      62           -
LGA    -       -      A      63           -
LGA    -       -      G      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      R      67           -
LGA    -       -      E      68           -
LGA    K      76      S      69          3.833
LGA    -       -      L      70           -
LGA    -       -      V      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      G      74           -
LGA    -       -      T      75           -
LGA    -       -      K      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    -       -      Q      79           -
LGA    D      77      I      80          3.569
LGA    E      78      P      81          2.035
LGA    Q      79      E      82          3.943
LGA    I      80      A      83           #
LGA    P      81      V      84          3.671
LGA    E      82      T      85          0.733
LGA    A      83      -       -           -
LGA    V      84      -       -           -
LGA    T      85      -       -           -
LGA    Q      86      Q      86           #
LGA    T      87      T      87          2.740
LGA    E      88      E      88           #
LGA    V      89      -       -           -
LGA    N      90      V      89          3.053
LGA    R      91      N      90          1.848
LGA    V      92      R      91          3.717
LGA    L      93      V      92          2.405
LGA    E      94      L      93          1.627
LGA    V      95      E      94          3.428
LGA    F      96      V      95          2.275
LGA    K      97      F      96          0.998
LGA    P      98      K      97          1.537
LGA    Y      99      P      98          1.341
LGA    Y     100      Y      99          1.180
LGA    A     101      Y     100          1.040
LGA    D     102      A     101          0.954
LGA    H     103      D     102          1.258
LGA    C     104      H     103          1.005
LGA    Q     105      C     104          1.140
LGA    I     106      Q     105          2.403
LGA    -       -      I     106           -
LGA    K     107      K     107          2.295
LGA    T     108      T     108          2.806

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   92   92    5.0     40    3.03    17.50     28.284     1.280

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.203040 * X  +  -0.097033 * Y  +   0.974351 * Z  +   6.285202
  Y_new =   0.832338 * X  +   0.507015 * Y  +   0.223939 * Z  +  20.818581
  Z_new =  -0.515740 * X  +   0.856458 * Y  +  -0.022180 * Z  +  43.224827 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.596688   -1.544904  [ DEG:    91.4835    -88.5165 ]
  Theta =   0.541871    2.599722  [ DEG:    31.0469    148.9531 ]
  Phi   =   1.810063   -1.331529  [ DEG:   103.7090    -76.2910 ]
 
# 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: T0329TS168_4-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS168_4-D2.T0329_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   92   92   5.0   40   3.03   17.50  28.284
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS168_4-D2
PFRMAT TS
TARGET T0329
MODEL 4
PARENT N/A
ATOM     17  CA  THR    17       5.618  11.651  43.389  1.00 25.00           C
ATOM     18  CA  SER    18       4.660  12.082  39.772  1.00 25.00           C
ATOM     19  CA  ALA    19       1.308  13.301  41.165  1.00 25.00           C
ATOM     20  CA  ASP    20       2.941  16.574  42.298  1.00 25.00           C
ATOM     21  CA  LEU    21       4.475  17.042  38.821  1.00 25.00           C
ATOM     22  CA  THR    22       1.057  16.430  37.204  1.00 25.00           C
ATOM     23  CA  SER    23      -0.541  18.998  39.552  1.00 25.00           C
ATOM     24  CA  ALA    24       2.181  21.542  38.663  1.00 25.00           C
ATOM     25  CA  LEU    25       1.582  20.914  34.932  1.00 25.00           C
ATOM     26  CA  ASN    26      -2.183  21.412  35.427  1.00 25.00           C
ATOM     27  CA  TYR    27      -1.528  24.691  37.294  1.00 25.00           C
ATOM     28  CA  ALA    28       0.758  25.877  34.461  1.00 25.00           C
ATOM     29  CA  PHE    29      -1.942  25.009  31.886  1.00 25.00           C
ATOM     30  CA  GLU    30      -4.541  26.948  33.923  1.00 25.00           C
ATOM     31  CA  GLN    31      -2.190  29.966  34.099  1.00 25.00           C
ATOM     32  CA  THR    32      -5.235  32.246  34.222  1.00 25.00           C
ATOM     33  CA  GLY    33      -3.753  33.623  30.999  1.00 25.00           C
ATOM     34  CA  HIS    34      -4.242  30.231  29.460  1.00 25.00           C
ATOM     35  CA  ARG    35      -2.381  31.566  26.370  1.00 25.00           C
ATOM     36  CA  HIS    36      -2.663  28.096  24.776  1.00 25.00           C
ATOM     37  CA  ASP    37      -3.280  24.467  23.656  1.00 25.00           C
ATOM     38  CA  PHE    38      -3.896  23.430  27.234  1.00 25.00           C
ATOM     39  CA  THR    39      -2.152  20.149  26.192  1.00 25.00           C
ATOM     40  CA  VAL    40      -5.417  18.309  25.373  1.00 25.00           C
ATOM     41  CA  GLU    41      -4.352  14.632  25.294  1.00 25.00           C
ATOM     42  CA  ASP    42      -2.033  15.213  28.287  1.00 25.00           C
ATOM     43  CA  ILE    43      -4.887  16.905  30.199  1.00 25.00           C
ATOM     44  CA  LYS    44      -7.198  13.954  29.415  1.00 25.00           C
ATOM     45  CA  ASN    45      -4.524  11.503  30.647  1.00 25.00           C
ATOM     46  CA  PHE    46      -4.125  13.523  33.876  1.00 25.00           C
ATOM     47  CA  PHE    47      -7.920  13.489  34.395  1.00 25.00           C
ATOM     48  CA  GLY    48      -9.031  10.244  32.886  1.00 25.00           C
ATOM     49  CA  SER    49     -12.714  10.572  33.942  1.00 25.00           C
ATOM     50  CA  GLY    50     -11.282  11.215  37.405  1.00 25.00           C
ATOM     51  CA  VAL    51      -9.924  14.603  38.479  1.00 25.00           C
ATOM     52  CA  VAL    52     -13.411  15.973  37.684  1.00 25.00           C
ATOM     53  CA  VAL    53     -14.682  14.787  41.096  1.00 25.00           C
ATOM     54  CA  ALA    54     -11.709  16.478  42.819  1.00 25.00           C
ATOM     55  CA  VAL    55     -12.426  19.726  40.921  1.00 25.00           C
ATOM     56  CA  THR    56     -16.105  19.557  41.970  1.00 25.00           C
ATOM     57  CA  ARG    57     -15.066  19.017  45.617  1.00 25.00           C
ATOM     58  CA  ALA    58     -12.703  22.024  45.414  1.00 25.00           C
ATOM     59  CA  LEU    59     -15.519  24.169  43.951  1.00 25.00           C
ATOM     60  CA  ALA    60     -17.860  23.066  46.774  1.00 25.00           C
ATOM     61  CA  TYR    61     -21.239  22.615  48.329  1.00 25.00           C
ATOM     62  CA  GLU    62     -23.072  25.608  46.911  1.00 25.00           C
ATOM     63  CA  ALA    63     -21.990  26.086  43.266  1.00 25.00           C
ATOM     64  CA  GLY    64     -24.862  23.675  42.490  1.00 25.00           C
ATOM     65  CA  SER    65     -24.256  24.126  38.734  1.00 25.00           C
ATOM     66  CA  SER    66     -20.523  23.426  39.228  1.00 25.00           C
ATOM     67  CA  ARG    67     -21.355  20.264  41.223  1.00 25.00           C
ATOM     68  CA  GLU    68     -23.727  19.108  38.449  1.00 25.00           C
ATOM     69  CA  SER    69     -21.001  19.717  35.829  1.00 25.00           C
ATOM     70  CA  LEU    70     -18.504  17.707  37.925  1.00 25.00           C
ATOM     71  CA  VAL    71     -21.027  14.842  38.229  1.00 25.00           C
ATOM     72  CA  ALA    72     -21.577  14.892  34.439  1.00 25.00           C
ATOM     73  CA  PHE    73     -17.792  14.786  33.863  1.00 25.00           C
ATOM     74  CA  GLY    74     -18.542  11.785  31.618  1.00 25.00           C
ATOM     75  CA  THR    75     -16.285  12.642  28.605  1.00 25.00           C
ATOM     76  CA  LYS    76     -19.077  11.353  26.351  1.00 25.00           C
ATOM     77  CA  ASP    77     -20.340  14.923  26.732  1.00 25.00           C
ATOM     78  CA  GLU    78     -20.686  17.939  24.396  1.00 25.00           C
ATOM     79  CA  GLN    79     -22.462  19.907  27.161  1.00 25.00           C
ATOM     80  CA  ILE    80     -19.671  19.012  29.625  1.00 25.00           C
ATOM     81  CA  PRO    81     -17.035  20.160  27.094  1.00 25.00           C
ATOM     82  CA  GLU    82     -18.912  23.460  26.598  1.00 25.00           C
ATOM     83  CA  ALA    83     -19.067  23.971  30.390  1.00 25.00           C
ATOM     84  CA  VAL    84     -20.344  27.495  30.900  1.00 25.00           C
ATOM     85  CA  THR    85     -21.165  28.101  27.220  1.00 25.00           C
ATOM     86  CA  GLN    86     -18.138  30.337  26.775  1.00 25.00           C
ATOM     87  CA  THR    87     -14.816  28.543  26.126  1.00 25.00           C
ATOM     88  CA  GLU    88     -12.944  31.250  28.083  1.00 25.00           C
ATOM     89  CA  VAL    89     -15.407  30.886  30.993  1.00 25.00           C
ATOM     90  CA  ASN    90     -14.917  27.087  30.964  1.00 25.00           C
ATOM     91  CA  ARG    91     -11.116  27.553  31.005  1.00 25.00           C
ATOM     92  CA  VAL    92     -11.419  29.972  33.959  1.00 25.00           C
ATOM     93  CA  LEU    93     -13.608  27.448  35.832  1.00 25.00           C
ATOM     94  CA  GLU    94     -11.037  24.689  35.167  1.00 25.00           C
ATOM     95  CA  VAL    95      -8.235  26.952  36.465  1.00 25.00           C
ATOM     96  CA  PHE    96     -10.271  27.709  39.618  1.00 25.00           C
ATOM     97  CA  LYS    97     -10.860  23.964  40.166  1.00 25.00           C
ATOM     98  CA  PRO    98      -7.112  23.291  39.761  1.00 25.00           C
ATOM     99  CA  TYR    99      -6.317  26.051  42.294  1.00 25.00           C
ATOM    100  CA  TYR   100      -8.834  24.548  44.759  1.00 25.00           C
ATOM    101  CA  ALA   101      -7.247  21.092  44.310  1.00 25.00           C
ATOM    102  CA  ASP   102      -3.774  22.577  44.941  1.00 25.00           C
ATOM    103  CA  HIS   103      -5.060  24.301  48.111  1.00 25.00           C
ATOM    104  CA  CYS   104      -6.579  20.999  49.319  1.00 25.00           C
ATOM    105  CA  GLN   105      -3.259  19.205  48.669  1.00 25.00           C
ATOM    106  CA  ILE   106      -4.419  17.083  51.627  1.00 25.00           C
ATOM    107  CA  LYS   107      -3.730  13.311  51.991  1.00 25.00           C
ATOM    108  CA  THR   108      -0.804  14.017  49.608  1.00 25.00           C
TER
END
