
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0352TS168_5
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS168_5.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    T       2      T       2           -
LGA    T       3      T       3           -
LGA    H       4      H       4           -
LGA    D       5      D       5           -
LGA    R       6      R       6           -
LGA    V       7      V       7           -
LGA    R       8      R       8           -
LGA    L       9      L       9           -
LGA    Q      10      Q      10           -
LGA    L      11      L      11           -
LGA    Q      12      Q      12           -
LGA    A      13      A      13           -
LGA    L      14      L      14           -
LGA    E      15      E      15           -
LGA    A      16      A      16           -
LGA    L      17      L      17           -
LGA    L      18      L      18           -
LGA    R      19      R      19           -
LGA    E      20      E      20           -
LGA    H      21      H      21           -
LGA    Q      22      Q      22           -
LGA    H      23      H      23           -
LGA    W      24      W      24           -
LGA    R      25      R      25           -
LGA    N      26      N      26           -
LGA    D      27      D      27           -
LGA    E      28      E      28           -
LGA    P      29      P      29           -
LGA    Q      30      -       -           -
LGA    P      31      -       -           -
LGA    H      32      -       -           -
LGA    Q      33      -       -           -
LGA    F      34      -       -           -
LGA    N      35      -       -           -
LGA    S      36      -       -           -
LGA    T      37      -       -           -
LGA    Q      38      Q      30           #
LGA    P      39      P      31          4.282
LGA    -       -      H      32           -
LGA    -       -      Q      33           -
LGA    F      40      F      34          3.708
LGA    F      41      N      35          3.871
LGA    M      42      S      36           #
LGA    D      43      T      37           -
LGA    T      44      -       -           -
LGA    M      45      -       -           -
LGA    E      46      -       -           -
LGA    P      47      -       -           -
LGA    L      48      -       -           -
LGA    E      49      Q      38          5.074
LGA    W      50      P      39          3.179
LGA    L      51      F      40          3.739
LGA    Q      52      F      41          3.937
LGA    W      53      M      42           -
LGA    V      54      D      43           -
LGA    -       -      T      44           -
LGA    -       -      M      45           -
LGA    -       -      E      46           -
LGA    -       -      P      47           -
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    -       -      W      50           -
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    L      55      W      53           #
LGA    I      56      V      54           #
LGA    P      57      L      55           #
LGA    -       -      I      56           -
LGA    R      58      P      57          1.850
LGA    M      59      R      58          3.784
LGA    H      60      M      59          2.312
LGA    D      61      H      60          3.595
LGA    -       -      D      61           -
LGA    L      62      L      62           #
LGA    L      63      L      63           -
LGA    -       -      D      64           -
LGA    D      64      N      65           #
LGA    N      65      K      66          1.609
LGA    K      66      Q      67          2.469
LGA    Q      67      -       -           -
LGA    P      68      -       -           -
LGA    L      69      P      68          4.526
LGA    P      70      L      69          4.211
LGA    G      71      P      70          2.362
LGA    A      72      G      71          1.560
LGA    F      73      A      72          2.895
LGA    A      74      -       -           -
LGA    V      75      -       -           -
LGA    A      76      -       -           -
LGA    P      77      F      73          1.833
LGA    Y      78      A      74          3.987
LGA    Y      79      -       -           -
LGA    E      80      -       -           -
LGA    M      81      -       -           -
LGA    A      82      V      75          1.286
LGA    L      83      A      76          0.890
LGA    A      84      P      77          0.830
LGA    T      85      Y      78          1.716
LGA    D      86      Y      79          3.081
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      A      82           -
LGA    -       -      L      83           -
LGA    -       -      A      84           -
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    -       -      H      87           -
LGA    -       -      P      88           -
LGA    -       -      Q      89           -
LGA    H      87      R      90          4.338
LGA    P      88      A      91          3.854
LGA    Q      89      L      92           #
LGA    R      90      I      93          4.821
LGA    A      91      L      94          0.769
LGA    L      92      A      95          3.134
LGA    -       -      E      96           -
LGA    I      93      L      97          1.352
LGA    L      94      E      98          1.228
LGA    A      95      K      99          2.437
LGA    E      96      L     100          3.201
LGA    L      97      D     101          2.868
LGA    E      98      A     102          2.573
LGA    K      99      L     103          3.002
LGA    L     100      F     104          3.557
LGA    D     101      A     105          3.068
LGA    A     102      D     106          2.952
LGA    L     103      D     107          3.564
LGA    F     104      -       -           -
LGA    A     105      -       -           -
LGA    D     106      A     108           #
LGA    D     107      S     109           -
LGA    A     108      -       -           -
LGA    S     109      -       -           -
LGA    L     110      -       -           -
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117  109    5.0     41    3.13     4.88     23.418     1.271

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.462633 * X  +  -0.722279 * Y  +  -0.514086 * Z  +  -7.645375
  Y_new =  -0.884794 * X  +   0.339678 * Y  +   0.318997 * Z  +   5.208315
  Z_new =  -0.055781 * X  +   0.602439 * Y  +  -0.796214 * Z  +   2.322693 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.493862   -0.647730  [ DEG:   142.8878    -37.1122 ]
  Theta =   0.055810    3.085782  [ DEG:     3.1977    176.8023 ]
  Phi   =  -2.052573    1.089020  [ DEG:  -117.6038     62.3963 ]
 
# 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: T0352TS168_5                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS168_5.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   41   3.13    4.88  23.418
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS168_5
PFRMAT TS
TARGET T0352
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1     -11.141 -12.136  18.329  1.00 25.00           C
ATOM      2  CA  THR     2      -8.533  -9.804  19.717  1.00 25.00           C
ATOM      3  CA  THR     3      -8.629  -6.250  18.362  1.00 25.00           C
ATOM      4  CA  HIS     4     -11.126  -3.369  18.725  1.00 25.00           C
ATOM      5  CA  ASP     5      -8.446  -1.229  20.430  1.00 25.00           C
ATOM      6  CA  ARG     6      -5.987  -2.010  17.600  1.00 25.00           C
ATOM      7  CA  VAL     7      -8.628  -1.036  15.003  1.00 25.00           C
ATOM      8  CA  ARG     8      -9.277   2.250  16.861  1.00 25.00           C
ATOM      9  CA  LEU     9      -5.518   2.978  16.937  1.00 25.00           C
ATOM     10  CA  GLN    10      -5.281   2.282  13.178  1.00 25.00           C
ATOM     11  CA  LEU    11      -8.230   4.640  12.531  1.00 25.00           C
ATOM     12  CA  GLN    12      -6.549   7.360  14.639  1.00 25.00           C
ATOM     13  CA  ALA    13      -3.291   6.901  12.679  1.00 25.00           C
ATOM     14  CA  LEU    14      -5.210   7.184   9.377  1.00 25.00           C
ATOM     15  CA  GLU    15      -6.909  10.387  10.609  1.00 25.00           C
ATOM     16  CA  ALA    16      -3.507  11.835  11.608  1.00 25.00           C
ATOM     17  CA  LEU    17      -2.097  10.972   8.153  1.00 25.00           C
ATOM     18  CA  LEU    18      -5.096  12.667   6.479  1.00 25.00           C
ATOM     19  CA  ARG    19      -4.571  15.785   8.640  1.00 25.00           C
ATOM     20  CA  GLU    20      -0.862  15.850   7.689  1.00 25.00           C
ATOM     21  CA  HIS    21      -1.782  15.553   3.983  1.00 25.00           C
ATOM     22  CA  GLN    22      -4.279  18.434   4.346  1.00 25.00           C
ATOM     23  CA  HIS    23      -1.599  20.574   6.051  1.00 25.00           C
ATOM     24  CA  TRP    24       0.860  19.793   3.221  1.00 25.00           C
ATOM     25  CA  ARG    25      -1.781  20.767   0.624  1.00 25.00           C
ATOM     26  CA  ASN    26      -1.748  24.119   2.298  1.00 25.00           C
ATOM     27  CA  ASP    27      -2.695  27.459   3.807  1.00 25.00           C
ATOM     28  CA  GLU    28       0.811  28.900   4.357  1.00 25.00           C
ATOM     29  CA  PRO    29       0.811  28.887   0.536  1.00 25.00           C
ATOM     30  CA  GLN    30      -1.363  29.717  -2.546  1.00 25.00           C
ATOM     31  CA  PRO    31       0.545  28.241  -5.497  1.00 25.00           C
ATOM     32  CA  HIS    32       3.136  25.463  -5.010  1.00 25.00           C
ATOM     33  CA  GLN    33       0.332  22.893  -4.560  1.00 25.00           C
ATOM     34  CA  PHE    34      -1.361  24.144  -7.761  1.00 25.00           C
ATOM     35  CA  ASN    35       1.956  23.859  -9.654  1.00 25.00           C
ATOM     36  CA  SER    36       3.468  20.830 -11.392  1.00 25.00           C
ATOM     37  CA  THR    37       1.205  20.370 -14.388  1.00 25.00           C
ATOM     38  CA  GLN    38      -1.451  18.018 -15.799  1.00 25.00           C
ATOM     39  CA  PRO    39      -3.702  21.064 -15.941  1.00 25.00           C
ATOM     40  CA  PHE    40      -6.134  18.937 -13.901  1.00 25.00           C
ATOM     41  CA  PHE    41      -8.577  15.974 -14.188  1.00 25.00           C
ATOM     42  CA  MET    42     -11.312  17.977 -12.387  1.00 25.00           C
ATOM     43  CA  ASP    43     -13.667  20.939 -12.859  1.00 25.00           C
ATOM     44  CA  THR    44     -15.177  23.165 -10.115  1.00 25.00           C
ATOM     45  CA  MET    45     -13.112  22.148  -7.087  1.00 25.00           C
ATOM     46  CA  GLU    46     -16.311  22.292  -5.021  1.00 25.00           C
ATOM     47  CA  PRO    47     -15.848  18.954  -3.321  1.00 25.00           C
ATOM     48  CA  LEU    48     -16.347  17.051  -0.034  1.00 25.00           C
ATOM     49  CA  GLU    49     -16.439  13.732  -1.943  1.00 25.00           C
ATOM     50  CA  TRP    50     -13.210  14.668  -3.776  1.00 25.00           C
ATOM     51  CA  LEU    51     -11.541  15.542  -0.441  1.00 25.00           C
ATOM     52  CA  GLN    52     -12.652  12.184   1.024  1.00 25.00           C
ATOM     53  CA  TRP    53     -11.236  10.355  -2.029  1.00 25.00           C
ATOM     54  CA  VAL    54      -7.919  12.230  -1.644  1.00 25.00           C
ATOM     55  CA  LEU    55      -7.789  11.287   2.065  1.00 25.00           C
ATOM     56  CA  ILE    56      -8.453   7.620   1.182  1.00 25.00           C
ATOM     57  CA  PRO    57      -5.655   7.718  -1.431  1.00 25.00           C
ATOM     58  CA  ARG    58      -3.263   9.231   1.150  1.00 25.00           C
ATOM     59  CA  MET    59      -4.194   6.489   3.657  1.00 25.00           C
ATOM     60  CA  HIS    60      -3.563   3.808   0.995  1.00 25.00           C
ATOM     61  CA  ASP    61      -0.154   5.361   0.203  1.00 25.00           C
ATOM     62  CA  LEU    62       0.730   5.383   3.929  1.00 25.00           C
ATOM     63  CA  LEU    63      -0.289   1.702   4.217  1.00 25.00           C
ATOM     64  CA  ASP    64       1.880   0.839   1.180  1.00 25.00           C
ATOM     65  CA  ASN    65       5.061   1.250   3.148  1.00 25.00           C
ATOM     66  CA  LYS    66       7.434  -0.771   5.305  1.00 25.00           C
ATOM     67  CA  GLN    67       7.639   2.023   7.829  1.00 25.00           C
ATOM     68  CA  PRO    68       6.620  -0.475  10.567  1.00 25.00           C
ATOM     69  CA  LEU    69       2.914  -0.543   9.569  1.00 25.00           C
ATOM     70  CA  PRO    70       1.712  -3.311   7.255  1.00 25.00           C
ATOM     71  CA  GLY    71      -1.812  -2.873   5.814  1.00 25.00           C
ATOM     72  CA  ALA    72      -5.173  -1.909   4.299  1.00 25.00           C
ATOM     73  CA  PHE    73      -6.733  -1.882   7.796  1.00 25.00           C
ATOM     74  CA  ALA    74      -6.508   1.940   7.894  1.00 25.00           C
ATOM     75  CA  VAL    75      -8.179   2.150   4.454  1.00 25.00           C
ATOM     76  CA  ALA    76     -10.976  -0.181   5.644  1.00 25.00           C
ATOM     77  CA  PRO    77     -11.487   1.983   8.762  1.00 25.00           C
ATOM     78  CA  TYR    78     -11.667   5.126   6.581  1.00 25.00           C
ATOM     79  CA  TYR    79     -14.247   3.435   4.312  1.00 25.00           C
ATOM     80  CA  GLU    80     -16.324   2.442   7.372  1.00 25.00           C
ATOM     81  CA  MET    81     -16.176   6.042   8.671  1.00 25.00           C
ATOM     82  CA  ALA    82     -17.303   7.348   5.252  1.00 25.00           C
ATOM     83  CA  LEU    83     -20.213   4.859   5.233  1.00 25.00           C
ATOM     84  CA  ALA    84     -21.229   5.981   8.750  1.00 25.00           C
ATOM     85  CA  THR    85     -24.514   7.065   7.237  1.00 25.00           C
ATOM     86  CA  ASP    86     -22.922   9.334   4.561  1.00 25.00           C
ATOM     87  CA  HIS    87     -24.419   6.970   1.993  1.00 25.00           C
ATOM     88  CA  PRO    88     -24.334   6.818  -1.810  1.00 25.00           C
ATOM     89  CA  GLN    89     -20.697   7.682  -2.641  1.00 25.00           C
ATOM     90  CA  ARG    90     -19.562   6.242   0.721  1.00 25.00           C
ATOM     91  CA  ALA    91     -21.544   3.036   0.044  1.00 25.00           C
ATOM     92  CA  LEU    92     -19.941   2.747  -3.422  1.00 25.00           C
ATOM     93  CA  ILE    93     -16.466   3.212  -1.881  1.00 25.00           C
ATOM     94  CA  LEU    94     -17.225   0.496   0.711  1.00 25.00           C
ATOM     95  CA  ALA    95     -18.387  -1.867  -2.071  1.00 25.00           C
ATOM     96  CA  GLU    96     -15.174  -1.174  -4.036  1.00 25.00           C
ATOM     97  CA  LEU    97     -13.078  -1.894  -0.912  1.00 25.00           C
ATOM     98  CA  GLU    98     -14.969  -5.180  -0.371  1.00 25.00           C
ATOM     99  CA  LYS    99     -14.358  -6.162  -4.022  1.00 25.00           C
ATOM    100  CA  LEU   100     -10.630  -5.377  -3.635  1.00 25.00           C
ATOM    101  CA  ASP   101     -10.486  -7.511  -0.458  1.00 25.00           C
ATOM    102  CA  ALA   102     -12.214 -10.396  -2.288  1.00 25.00           C
ATOM    103  CA  LEU   103      -9.709 -10.103  -5.170  1.00 25.00           C
ATOM    104  CA  PHE   104      -6.800 -10.162  -2.678  1.00 25.00           C
ATOM    105  CA  ALA   105      -8.267 -13.277  -1.002  1.00 25.00           C
ATOM    106  CA  ASP   106      -8.616 -14.979  -4.415  1.00 25.00           C
ATOM    107  CA  ASP   107      -4.979 -14.114  -5.245  1.00 25.00           C
ATOM    108  CA  ALA   108      -3.842 -15.556  -1.883  1.00 25.00           C
ATOM    109  CA  SER   109      -5.824 -18.762  -2.560  1.00 25.00           C
ATOM    110  CA  LEU   110      -8.940 -20.943  -1.931  1.00 25.00           C
ATOM    111  CA  GLU   111      -9.794 -19.890   1.631  1.00 25.00           C
ATOM    112  CA  HIS   112      -7.906 -22.095   4.061  1.00 25.00           C
ATOM    113  CA  HIS   113      -5.052 -24.218   2.752  1.00 25.00           C
ATOM    114  CA  HIS   114      -2.853 -23.170   5.658  1.00 25.00           C
ATOM    115  CA  HIS   115       0.902 -22.781   5.440  1.00 25.00           C
ATOM    116  CA  HIS   116       2.094 -19.524   7.028  1.00 25.00           C
ATOM    117  CA  HIS   117       0.407 -17.658   4.194  1.00 25.00           C
TER
END
