
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   92 (  716),  selected   92 , name T0329_D2.pdb
# PARAMETERS: T0329TS168_5-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      -       -           -
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      T      17          2.783
LGA    F      46      -       -           -
LGA    F      47      -       -           -
LGA    G      48      S      18          2.020
LGA    S      49      A      19          0.721
LGA    G      50      D      20          1.606
LGA    V      51      L      21          1.450
LGA    V      52      T      22          1.207
LGA    V      53      S      23          0.980
LGA    A      54      A      24          1.089
LGA    V      55      L      25          1.047
LGA    T      56      N      26          1.253
LGA    R      57      Y      27          1.271
LGA    A      58      A      28          0.955
LGA    L      59      F      29          1.065
LGA    A      60      E      30          1.740
LGA    Y      61      Q      31          4.229
LGA    E      62      T      32          3.512
LGA    A      63      G      33          3.349
LGA    G      64      -       -           -
LGA    S      65      -       -           -
LGA    S      66      -       -           -
LGA    R      67      H      34          2.275
LGA    E      68      R      35          3.046
LGA    S      69      -       -           -
LGA    L      70      H      36          3.016
LGA    V      71      D      37          3.388
LGA    A      72      F      38           #
LGA    -       -      T      39           -
LGA    -       -      V      40           -
LGA    -       -      E      41           -
LGA    F      73      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    G      74      R      57           #
LGA    T      75      A      58          3.150
LGA    K      76      L      59          1.946
LGA    D      77      A      60          2.955
LGA    E      78      -       -           -
LGA    Q      79      Y      61          4.534
LGA    I      80      E      62           #
LGA    P      81      A      63          4.859
LGA    -       -      G      64           -
LGA    E      82      S      65          3.552
LGA    A      83      S      66           #
LGA    V      84      R      67          1.214
LGA    T      85      E      68          2.728
LGA    Q      86      S      69          1.276
LGA    -       -      L      70           -
LGA    T      87      V      71          2.079
LGA    E      88      A      72          3.595
LGA    -       -      F      73           -
LGA    -       -      G      74           -
LGA    -       -      T      75           -
LGA    -       -      K      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    -       -      Q      79           -
LGA    V      89      I      80          5.728
LGA    N      90      P      81           -
LGA    R      91      E      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      T      85           -
LGA    V      92      Q      86           #
LGA    L      93      T      87           -
LGA    E      94      E      88           -
LGA    V      95      -       -           -
LGA    F      96      V      89          5.616
LGA    K      97      N      90           -
LGA    -       -      R      91           -
LGA    P      98      V      92           #
LGA    Y      99      L      93          3.162
LGA    -       -      E      94           -
LGA    Y     100      V      95          5.176
LGA    A     101      F      96          4.164
LGA    D     102      K      97          1.539
LGA    H     103      P      98          2.755
LGA    C     104      Y      99          1.038
LGA    -       -      Y     100           -
LGA    Q     105      A     101          2.827
LGA    I     106      D     102           -
LGA    K     107      H     103           -
LGA    T     108      C     104           -
LGA    -       -      Q     105           -
LGA    -       -      I     106           -
LGA    -       -      K     107           -
LGA    -       -      T     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   92   92    5.0     41    2.93     4.88     29.268     1.355

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.061117 * X  +   0.961547 * Y  +   0.267754 * Z  +  -3.263387
  Y_new =   0.748498 * X  +  -0.133313 * Y  +   0.649598 * Z  +  31.667206
  Z_new =   0.660314 * X  +   0.240115 * Y  +  -0.711568 * Z  +  34.735340 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.816146   -0.325447  [ DEG:   161.3533    -18.6467 ]
  Theta =  -0.721237   -2.420356  [ DEG:   -41.3238   -138.6762 ]
  Phi   =   1.652269   -1.489324  [ DEG:    94.6680    -85.3320 ]
 
# 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_5-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS168_5-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   41   2.93    4.88  29.268
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS168_5-D2
PFRMAT TS
TARGET T0329
MODEL 5
PARENT N/A
ATOM     17  CA  THR    17       1.251  26.521  43.395  1.00 25.00           C
ATOM     18  CA  SER    18       2.129  24.305  40.431  1.00 25.00           C
ATOM     19  CA  ALA    19       2.668  26.489  37.332  1.00 25.00           C
ATOM     20  CA  ASP    20       4.465  23.598  35.578  1.00 25.00           C
ATOM     21  CA  LEU    21       1.577  21.239  36.451  1.00 25.00           C
ATOM     22  CA  THR    22      -0.942  23.772  35.068  1.00 25.00           C
ATOM     23  CA  SER    23       1.096  24.072  31.840  1.00 25.00           C
ATOM     24  CA  ALA    24       1.182  20.258  31.510  1.00 25.00           C
ATOM     25  CA  LEU    25      -2.611  20.104  32.019  1.00 25.00           C
ATOM     26  CA  ASN    26      -3.104  22.793  29.338  1.00 25.00           C
ATOM     27  CA  TYR    27      -0.865  20.835  26.926  1.00 25.00           C
ATOM     28  CA  ALA    28      -2.875  17.647  27.610  1.00 25.00           C
ATOM     29  CA  PHE    29      -6.141  19.535  26.949  1.00 25.00           C
ATOM     30  CA  GLU    30      -4.722  20.890  23.660  1.00 25.00           C
ATOM     31  CA  GLN    31      -3.673  17.354  22.628  1.00 25.00           C
ATOM     32  CA  THR    32      -5.809  14.776  24.438  1.00 25.00           C
ATOM     33  CA  GLY    33      -4.307  11.377  23.964  1.00 25.00           C
ATOM     34  CA  HIS    34      -4.541  11.165  27.737  1.00 25.00           C
ATOM     35  CA  ARG    35      -1.919   8.373  27.679  1.00 25.00           C
ATOM     36  CA  HIS    36       0.554  11.275  27.414  1.00 25.00           C
ATOM     37  CA  ASP    37       1.973  10.260  30.858  1.00 25.00           C
ATOM     38  CA  PHE    38      -1.292  11.462  32.415  1.00 25.00           C
ATOM     39  CA  THR    39       0.836  11.820  35.550  1.00 25.00           C
ATOM     40  CA  VAL    40      -1.211   8.847  36.684  1.00 25.00           C
ATOM     41  CA  GLU    41      -0.819  10.533  40.101  1.00 25.00           C
ATOM     42  CA  ASP    42      -3.285  13.272  39.059  1.00 25.00           C
ATOM     43  CA  ILE    43      -5.786  10.614  37.901  1.00 25.00           C
ATOM     44  CA  LYS    44      -5.418   8.777  41.241  1.00 25.00           C
ATOM     45  CA  ASN    45      -6.012  12.052  43.135  1.00 25.00           C
ATOM     46  CA  PHE    46      -9.140  12.729  41.033  1.00 25.00           C
ATOM     47  CA  PHE    47     -10.427   9.198  41.765  1.00 25.00           C
ATOM     48  CA  GLY    48      -9.075   8.606  45.287  1.00 25.00           C
ATOM     49  CA  SER    49     -10.333  11.015  47.926  1.00 25.00           C
ATOM     50  CA  GLY    50      -7.587  13.655  47.618  1.00 25.00           C
ATOM     51  CA  VAL    51      -8.100  16.090  44.678  1.00 25.00           C
ATOM     52  CA  VAL    52     -11.776  15.040  44.918  1.00 25.00           C
ATOM     53  CA  VAL    53     -12.326  17.525  47.779  1.00 25.00           C
ATOM     54  CA  ALA    54     -10.693  20.304  45.713  1.00 25.00           C
ATOM     55  CA  VAL    55     -12.943  19.445  42.734  1.00 25.00           C
ATOM     56  CA  THR    56     -16.027  19.555  45.001  1.00 25.00           C
ATOM     57  CA  ARG    57     -14.939  22.968  46.357  1.00 25.00           C
ATOM     58  CA  ALA    58     -14.465  24.263  42.785  1.00 25.00           C
ATOM     59  CA  LEU    59     -17.951  22.992  41.836  1.00 25.00           C
ATOM     60  CA  ALA    60     -19.447  24.729  44.903  1.00 25.00           C
ATOM     61  CA  TYR    61     -22.922  26.343  45.145  1.00 25.00           C
ATOM     62  CA  GLU    62     -23.257  27.316  41.473  1.00 25.00           C
ATOM     63  CA  ALA    63     -25.824  27.426  38.615  1.00 25.00           C
ATOM     64  CA  GLY    64     -28.488  24.811  39.470  1.00 25.00           C
ATOM     65  CA  SER    65     -27.392  22.680  36.482  1.00 25.00           C
ATOM     66  CA  SER    66     -23.741  22.932  37.611  1.00 25.00           C
ATOM     67  CA  ARG    67     -24.738  21.871  41.154  1.00 25.00           C
ATOM     68  CA  GLU    68     -26.676  18.884  39.741  1.00 25.00           C
ATOM     69  CA  SER    69     -23.638  17.879  37.636  1.00 25.00           C
ATOM     70  CA  LEU    70     -21.389  18.111  40.726  1.00 25.00           C
ATOM     71  CA  VAL    71     -23.840  15.932  42.704  1.00 25.00           C
ATOM     72  CA  ALA    72     -23.871  13.353  39.873  1.00 25.00           C
ATOM     73  CA  PHE    73     -20.042  13.324  39.825  1.00 25.00           C
ATOM     74  CA  GLY    74     -18.072  14.892  36.974  1.00 25.00           C
ATOM     75  CA  THR    75     -18.522  18.441  35.660  1.00 25.00           C
ATOM     76  CA  LYS    76     -20.643  19.676  32.791  1.00 25.00           C
ATOM     77  CA  ASP    77     -22.474  17.728  30.143  1.00 25.00           C
ATOM     78  CA  GLU    78     -24.477  14.463  30.091  1.00 25.00           C
ATOM     79  CA  GLN    79     -21.353  12.535  29.000  1.00 25.00           C
ATOM     80  CA  ILE    80     -19.341  14.142  31.836  1.00 25.00           C
ATOM     81  CA  PRO    81     -22.069  13.184  34.347  1.00 25.00           C
ATOM     82  CA  GLU    82     -22.039   9.583  33.044  1.00 25.00           C
ATOM     83  CA  ALA    83     -18.227   9.464  33.390  1.00 25.00           C
ATOM     84  CA  VAL    84     -17.472   6.002  32.043  1.00 25.00           C
ATOM     85  CA  THR    85     -19.542   6.543  28.938  1.00 25.00           C
ATOM     86  CA  GLN    86     -17.089   8.152  26.453  1.00 25.00           C
ATOM     87  CA  THR    87     -13.292   8.610  26.268  1.00 25.00           C
ATOM     88  CA  GLU    88     -13.758  12.272  25.247  1.00 25.00           C
ATOM     89  CA  VAL    89     -16.161  12.810  28.182  1.00 25.00           C
ATOM     90  CA  ASN    90     -13.625  11.229  30.578  1.00 25.00           C
ATOM     91  CA  ARG    91     -10.870  13.507  29.206  1.00 25.00           C
ATOM     92  CA  VAL    92     -13.128  16.565  29.680  1.00 25.00           C
ATOM     93  CA  LEU    93     -13.865  15.492  33.282  1.00 25.00           C
ATOM     94  CA  GLU    94     -10.118  15.075  33.952  1.00 25.00           C
ATOM     95  CA  VAL    95      -9.449  18.560  32.511  1.00 25.00           C
ATOM     96  CA  PHE    96     -12.195  20.033  34.737  1.00 25.00           C
ATOM     97  CA  LYS    97     -10.676  18.304  37.798  1.00 25.00           C
ATOM     98  CA  PRO    98      -7.224  19.699  36.904  1.00 25.00           C
ATOM     99  CA  TYR    99      -8.707  23.211  36.547  1.00 25.00           C
ATOM    100  CA  TYR   100     -10.411  22.864  39.960  1.00 25.00           C
ATOM    101  CA  ALA   101      -7.102  21.740  41.526  1.00 25.00           C
ATOM    102  CA  ASP   102      -5.314  24.745  39.965  1.00 25.00           C
ATOM    103  CA  HIS   103      -8.011  27.093  41.336  1.00 25.00           C
ATOM    104  CA  CYS   104      -7.628  25.541  44.815  1.00 25.00           C
ATOM    105  CA  GLN   105      -3.831  25.998  44.630  1.00 25.00           C
ATOM    106  CA  ILE   106      -3.710  28.995  42.235  1.00 25.00           C
ATOM    107  CA  LYS   107      -1.143  29.154  39.431  1.00 25.00           C
ATOM    108  CA  THR   108       2.517  30.017  40.170  1.00 25.00           C
TER
END
