
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0359TS168_3
# Molecule2: number of CA atoms   93 (  690),  selected   93 , name T0359.pdb
# PARAMETERS: T0359TS168_3.T0359.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    S       3      S       3          4.427
LGA    E       4      E       4          2.237
LGA    T       5      T       5          1.155
LGA    F       6      F       6          1.141
LGA    D       7      D       7          0.962
LGA    V       8      V       8          1.586
LGA    E       9      E       9          2.303
LGA    L      10      L      10          1.219
LGA    T      11      T      11          2.177
LGA    K      12      K      12          0.244
LGA    N      13      N      13          1.590
LGA    V      14      V      14          2.946
LGA    Q      15      Q      15          2.857
LGA    G      16      G      16          2.248
LGA    L      17      L      17          1.759
LGA    G      18      G      18          1.320
LGA    I      19      I      19          0.744
LGA    T      20      T      20          1.039
LGA    I      21      I      21          2.030
LGA    A      22      A      22          1.473
LGA    G      23      G      23          2.155
LGA    Y      24      Y      24          2.961
LGA    I      25      -       -           -
LGA    G      26      I      25          3.863
LGA    D      27      G      26           #
LGA    K      28      D      27           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      P      32          0.981
LGA    P      32      S      33          1.516
LGA    S      33      G      34          2.821
LGA    G      34      -       -           -
LGA    I      35      I      35          2.387
LGA    F      36      F      36          1.149
LGA    V      37      V      37          1.161
LGA    K      38      K      38          1.302
LGA    S      39      S      39          0.999
LGA    I      40      I      40          1.925
LGA    T      41      T      41          1.529
LGA    K      42      K      42          1.862
LGA    S      43      S      43          2.273
LGA    S      44      S      44          0.863
LGA    A      45      A      45          1.118
LGA    V      46      V      46          0.773
LGA    E      47      E      47          0.704
LGA    H      48      H      48          1.610
LGA    D      49      D      49          1.363
LGA    G      50      G      50          1.059
LGA    R      51      R      51          1.692
LGA    I      52      I      52          1.705
LGA    Q      53      Q      53          0.534
LGA    I      54      I      54          0.812
LGA    G      55      G      55          1.406
LGA    D      56      D      56          0.841
LGA    Q      57      Q      57          1.174
LGA    I      58      I      58          1.274
LGA    I      59      I      59          1.983
LGA    A      60      A      60          3.665
LGA    V      61      V      61          1.956
LGA    D      62      D      62          0.628
LGA    G      63      G      63          0.561
LGA    T      64      T      64          0.996
LGA    N      65      N      65          1.095
LGA    L      66      L      66          1.470
LGA    Q      67      Q      67          1.431
LGA    G      68      G      68          0.639
LGA    F      69      F      69          1.002
LGA    T      70      T      70          1.167
LGA    N      71      N      71          1.890
LGA    Q      72      Q      72          1.911
LGA    Q      73      Q      73          2.251
LGA    A      74      A      74          1.962
LGA    V      75      V      75          1.861
LGA    E      76      E      76          2.029
LGA    V      77      V      77          1.892
LGA    L      78      L      78          1.415
LGA    R      79      R      79          2.003
LGA    H      80      H      80          2.093
LGA    T      81      T      81          1.889
LGA    G      82      G      82          2.777
LGA    Q      83      Q      83          1.634
LGA    T      84      T      84          1.354
LGA    V      85      V      85          1.444
LGA    L      86      L      86          1.239
LGA    L      87      L      87          0.736
LGA    T      88      T      88          1.521
LGA    L      89      L      89          2.299
LGA    M      90      M      90          1.158
LGA    R      91      R      91          0.383
LGA    R      92      R      92          1.244
LGA    G      93      G      93          1.334
LGA    E      94      E      94          2.267
LGA    T      95      T      95          6.801
LGA    S      96      -       -           -
LGA    V      97      S      96           #
LGA    -       -      V      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   93    5.0     87    1.91    95.40     84.078     4.322

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.284164 * X  +  -0.363044 * Y  +  -0.887384 * Z  +  -4.549843
  Y_new =  -0.663535 * X  +   0.593620 * Y  +  -0.455342 * Z  +  13.692562
  Z_new =   0.692078 * X  +   0.718202 * Y  +  -0.072207 * Z  +  -7.080239 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.670998   -1.470594  [ DEG:    95.7411    -84.2589 ]
  Theta =  -0.764363   -2.377229  [ DEG:   -43.7948   -136.2052 ]
  Phi   =  -1.166169    1.975423  [ DEG:   -66.8166    113.1834 ]
 
# 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: T0359TS168_3                                  
REMARK     2: T0359.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS168_3.T0359.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   93   5.0   87   1.91   95.40  84.078
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS168_3
PFRMAT TS
TARGET T0359
MODEL 3
PARENT N/A
ATOM      1  CA  SER     1       8.968  -0.352   1.541  1.00 25.00           C
ATOM      2  CA  MET     2       5.921   1.646   2.666  1.00 25.00           C
ATOM      3  CA  SER     3       7.031   3.986  -0.055  1.00 25.00           C
ATOM      4  CA  GLU     4       5.535   7.397   0.509  1.00 25.00           C
ATOM      5  CA  THR     5       1.784   7.372  -0.135  1.00 25.00           C
ATOM      6  CA  PHE     6       0.332  10.455   1.557  1.00 25.00           C
ATOM      7  CA  ASP     7      -2.583  12.362   2.963  1.00 25.00           C
ATOM      8  CA  VAL     8      -2.346  15.810   1.274  1.00 25.00           C
ATOM      9  CA  GLU     9      -5.023  18.429   2.074  1.00 25.00           C
ATOM     10  CA  LEU    10      -6.825  21.625   0.913  1.00 25.00           C
ATOM     11  CA  THR    11      -8.394  25.000   1.541  1.00 25.00           C
ATOM     12  CA  LYS    12     -11.078  25.038  -1.232  1.00 25.00           C
ATOM     13  CA  ASN    13     -11.751  28.685  -0.254  1.00 25.00           C
ATOM     14  CA  VAL    14     -14.460  30.180  -2.368  1.00 25.00           C
ATOM     15  CA  GLN    15     -12.830  28.664  -5.506  1.00 25.00           C
ATOM     16  CA  GLY    16     -12.373  25.601  -7.712  1.00 25.00           C
ATOM     17  CA  LEU    17      -9.391  23.812  -6.169  1.00 25.00           C
ATOM     18  CA  GLY    18      -7.043  25.104  -8.788  1.00 25.00           C
ATOM     19  CA  ILE    19      -5.583  21.611  -8.787  1.00 25.00           C
ATOM     20  CA  THR    20      -6.027  19.790 -12.127  1.00 25.00           C
ATOM     21  CA  ILE    21      -7.847  16.572 -13.094  1.00 25.00           C
ATOM     22  CA  ALA    22      -7.252  13.838 -15.755  1.00 25.00           C
ATOM     23  CA  GLY    23      -5.878  11.777 -18.652  1.00 25.00           C
ATOM     24  CA  TYR    24      -7.497   8.449 -17.764  1.00 25.00           C
ATOM     25  CA  ILE    25      -4.432   6.845 -19.297  1.00 25.00           C
ATOM     26  CA  GLY    26      -6.968   4.962 -21.444  1.00 25.00           C
ATOM     27  CA  ASP    27      -8.235   2.473 -18.884  1.00 25.00           C
ATOM     28  CA  LYS    28      -4.856   0.774 -18.339  1.00 25.00           C
ATOM     29  CA  LYS    29      -5.497  -2.196 -15.973  1.00 25.00           C
ATOM     30  CA  LEU    30      -3.626  -0.171 -13.303  1.00 25.00           C
ATOM     31  CA  GLU    31      -0.639   0.260 -15.635  1.00 25.00           C
ATOM     32  CA  PRO    32      -1.863   3.900 -15.762  1.00 25.00           C
ATOM     33  CA  SER    33      -5.427   4.660 -14.669  1.00 25.00           C
ATOM     34  CA  GLY    34      -4.347   6.852 -11.744  1.00 25.00           C
ATOM     35  CA  ILE    35      -3.800   9.458 -14.420  1.00 25.00           C
ATOM     36  CA  PHE    36      -3.108  12.779 -12.791  1.00 25.00           C
ATOM     37  CA  VAL    37      -2.539  15.886 -10.697  1.00 25.00           C
ATOM     38  CA  LYS    38      -1.957  17.546 -14.031  1.00 25.00           C
ATOM     39  CA  SER    39      -0.858  20.996 -12.739  1.00 25.00           C
ATOM     40  CA  ILE    40       0.589  23.388 -10.110  1.00 25.00           C
ATOM     41  CA  THR    41      -1.968  26.201 -10.259  1.00 25.00           C
ATOM     42  CA  LYS    42      -0.052  28.878  -8.299  1.00 25.00           C
ATOM     43  CA  SER    43      -2.961  31.097  -7.234  1.00 25.00           C
ATOM     44  CA  SER    44      -4.491  28.083  -5.552  1.00 25.00           C
ATOM     45  CA  ALA    45      -5.429  25.875  -2.535  1.00 25.00           C
ATOM     46  CA  VAL    46      -3.091  23.069  -3.575  1.00 25.00           C
ATOM     47  CA  GLU    47      -0.178  25.555  -3.558  1.00 25.00           C
ATOM     48  CA  HIS    48      -0.868  26.376   0.119  1.00 25.00           C
ATOM     49  CA  ASP    49       0.457  23.007   1.300  1.00 25.00           C
ATOM     50  CA  GLY    50       3.455  22.537  -1.078  1.00 25.00           C
ATOM     51  CA  ARG    51       2.296  19.024  -1.991  1.00 25.00           C
ATOM     52  CA  ILE    52       0.283  18.485  -5.153  1.00 25.00           C
ATOM     53  CA  GLN    53       3.267  18.867  -7.459  1.00 25.00           C
ATOM     54  CA  ILE    54       3.306  18.661 -11.245  1.00 25.00           C
ATOM     55  CA  GLY    55       2.319  15.168 -12.306  1.00 25.00           C
ATOM     56  CA  ASP    56       1.482  13.343  -9.064  1.00 25.00           C
ATOM     57  CA  GLN    57      -0.267  10.015  -9.425  1.00 25.00           C
ATOM     58  CA  ILE    58      -3.705  10.765  -7.859  1.00 25.00           C
ATOM     59  CA  ILE    59      -6.231   9.167  -5.526  1.00 25.00           C
ATOM     60  CA  ALA    60      -9.986   9.895  -5.173  1.00 25.00           C
ATOM     61  CA  VAL    61     -11.829  12.195  -2.703  1.00 25.00           C
ATOM     62  CA  ASP    62     -12.093  11.114   0.901  1.00 25.00           C
ATOM     63  CA  GLY    63     -11.944   7.451   2.015  1.00 25.00           C
ATOM     64  CA  THR    64     -11.583   6.424  -1.594  1.00 25.00           C
ATOM     65  CA  ASN    65      -8.687   4.705  -3.323  1.00 25.00           C
ATOM     66  CA  LEU    66      -8.246   4.813  -7.117  1.00 25.00           C
ATOM     67  CA  GLN    67      -5.882   2.023  -8.272  1.00 25.00           C
ATOM     68  CA  GLY    68      -9.059   0.314  -9.557  1.00 25.00           C
ATOM     69  CA  PHE    69     -10.784   3.163 -11.403  1.00 25.00           C
ATOM     70  CA  THR    70     -10.868   4.841 -14.833  1.00 25.00           C
ATOM     71  CA  ASN    71     -10.907   8.618 -14.033  1.00 25.00           C
ATOM     72  CA  GLN    72     -14.208  10.401 -14.804  1.00 25.00           C
ATOM     73  CA  GLN    73     -15.624   9.294 -11.422  1.00 25.00           C
ATOM     74  CA  ALA    74     -12.482  10.591  -9.655  1.00 25.00           C
ATOM     75  CA  VAL    75     -12.809  13.942 -11.481  1.00 25.00           C
ATOM     76  CA  GLU    76     -16.488  14.177 -10.443  1.00 25.00           C
ATOM     77  CA  VAL    77     -15.535  13.439  -6.808  1.00 25.00           C
ATOM     78  CA  LEU    78     -12.838  16.155  -6.938  1.00 25.00           C
ATOM     79  CA  ARG    79     -15.379  18.645  -8.357  1.00 25.00           C
ATOM     80  CA  HIS    80     -17.845  17.758  -5.564  1.00 25.00           C
ATOM     81  CA  THR    81     -16.024  18.145  -2.229  1.00 25.00           C
ATOM     82  CA  GLY    82     -16.207  21.956  -1.989  1.00 25.00           C
ATOM     83  CA  GLN    83     -15.015  21.526   1.598  1.00 25.00           C
ATOM     84  CA  THR    84     -11.954  19.472   2.533  1.00 25.00           C
ATOM     85  CA  VAL    85      -9.845  16.783   0.935  1.00 25.00           C
ATOM     86  CA  LEU    86      -8.046  13.846   2.445  1.00 25.00           C
ATOM     87  CA  LEU    87      -6.226  13.150  -0.878  1.00 25.00           C
ATOM     88  CA  THR    88      -3.222  11.173  -1.979  1.00 25.00           C
ATOM     89  CA  LEU    89      -0.182  13.097  -3.202  1.00 25.00           C
ATOM     90  CA  MET    90       1.507   9.955  -4.563  1.00 25.00           C
ATOM     91  CA  ARG    91       4.924   9.753  -6.060  1.00 25.00           C
ATOM     92  CA  ARG    92       7.920   7.727  -7.158  1.00 25.00           C
ATOM     93  CA  GLY    93      11.624   8.445  -6.892  1.00 25.00           C
ATOM     94  CA  GLU    94      13.029   4.883  -7.115  1.00 25.00           C
ATOM     95  CA  THR    95      16.136   4.862  -9.289  1.00 25.00           C
ATOM     96  CA  SER    96      16.287   3.449 -12.818  1.00 25.00           C
ATOM     97  CA  VAL    97      14.212   4.904 -15.631  1.00 25.00           C
TER
END
