
#######################################################
#                                                     #
#                        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 T0359TS393_2
# Molecule2: number of CA atoms   93 (  690),  selected   93 , name T0359.pdb
# PARAMETERS: T0359TS393_2.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      -       -           -
LGA    S       3      M       2          5.866
LGA    -       -      S       3           -
LGA    E       4      E       4          3.902
LGA    T       5      T       5          0.232
LGA    F       6      F       6          0.407
LGA    D       7      D       7          0.647
LGA    V       8      V       8          0.970
LGA    E       9      E       9          1.384
LGA    L      10      L      10          1.444
LGA    T      11      T      11          1.691
LGA    K      12      K      12          1.509
LGA    N      13      N      13          1.979
LGA    V      14      V      14          3.654
LGA    Q      15      Q      15          2.781
LGA    G      16      G      16          0.798
LGA    L      17      L      17          1.383
LGA    G      18      G      18          0.643
LGA    I      19      I      19          0.628
LGA    T      20      T      20          1.619
LGA    I      21      I      21          1.674
LGA    A      22      A      22          1.047
LGA    G      23      G      23          1.470
LGA    Y      24      Y      24          2.722
LGA    I      25      -       -           -
LGA    G      26      I      25          2.996
LGA    D      27      G      26          6.836
LGA    K      28      D      27           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      P      32          4.251
LGA    P      32      S      33          0.819
LGA    S      33      G      34          2.074
LGA    G      34      -       -           -
LGA    I      35      I      35          1.849
LGA    F      36      F      36          2.616
LGA    V      37      V      37          0.959
LGA    K      38      K      38          0.624
LGA    S      39      S      39          1.365
LGA    I      40      I      40          1.095
LGA    T      41      T      41          1.179
LGA    K      42      K      42          1.066
LGA    S      43      S      43          1.975
LGA    S      44      S      44          0.949
LGA    A      45      A      45          1.700
LGA    V      46      V      46          1.807
LGA    E      47      E      47          1.015
LGA    H      48      H      48          0.878
LGA    D      49      D      49          1.400
LGA    G      50      G      50          1.411
LGA    R      51      R      51          1.428
LGA    I      52      I      52          0.617
LGA    Q      53      Q      53          1.515
LGA    I      54      I      54          0.693
LGA    G      55      G      55          2.044
LGA    D      56      D      56          2.261
LGA    Q      57      Q      57          2.062
LGA    I      58      I      58          2.268
LGA    I      59      I      59          1.938
LGA    A      60      A      60          2.686
LGA    V      61      V      61          1.078
LGA    D      62      D      62          0.897
LGA    G      63      G      63          2.092
LGA    T      64      T      64          1.793
LGA    N      65      N      65          4.145
LGA    L      66      L      66          1.144
LGA    Q      67      Q      67          1.289
LGA    G      68      G      68          2.381
LGA    F      69      F      69          1.116
LGA    T      70      T      70          1.681
LGA    N      71      N      71          2.009
LGA    Q      72      Q      72          1.839
LGA    Q      73      Q      73          1.749
LGA    A      74      A      74          1.719
LGA    V      75      V      75          1.887
LGA    E      76      E      76          1.715
LGA    V      77      V      77          1.314
LGA    L      78      L      78          1.291
LGA    R      79      R      79          2.103
LGA    H      80      H      80          2.192
LGA    T      81      T      81          2.113
LGA    G      82      G      82          1.650
LGA    Q      83      Q      83          2.381
LGA    T      84      T      84          1.788
LGA    V      85      V      85          1.842
LGA    L      86      L      86          1.602
LGA    L      87      L      87          1.509
LGA    T      88      T      88          1.334
LGA    L      89      L      89          0.713
LGA    M      90      M      90          1.228
LGA    R      91      R      91          1.260
LGA    R      92      R      92          1.528
LGA    G      93      G      93          3.138
LGA    E      94      E      94          3.214
LGA    T      95      T      95           #
LGA    S      96      S      96           -
LGA    V      97      V      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   93    5.0     87    2.08    93.10     82.545     3.991

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.689377 * X  +  -0.710090 * Y  +   0.143288 * Z  +  -4.398713
  Y_new =  -0.113205 * X  +   0.300975 * Y  +   0.946889 * Z  +  13.809962
  Z_new =  -0.715502 * X  +   0.636543 * Y  +  -0.287871 * Z  +  -7.275079 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.995513   -1.146079  [ DEG:   114.3345    -65.6655 ]
  Theta =   0.797343    2.344250  [ DEG:    45.6844    134.3156 ]
  Phi   =  -2.978831    0.162761  [ DEG:  -170.6745      9.3255 ]
 
# 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: T0359TS393_2                                  
REMARK     2: T0359.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS393_2.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   2.08   93.10  82.545
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS393_2
PFRMAT TS
TARGET T0359
MODEL 2
PARENT N/A
ATOM      1  CA  SER     1       9.272  -0.739   0.815  1.00 25.00           C
ATOM      2  CA  MET     2       6.227   1.469   1.079  1.00 25.00           C
ATOM      3  CA  SER     3       6.341   4.829  -0.713  1.00 25.00           C
ATOM      4  CA  GLU     4       5.141   7.104   2.123  1.00 25.00           C
ATOM      5  CA  THR     5       2.459   8.432  -0.215  1.00 25.00           C
ATOM      6  CA  PHE     6       1.294  11.611   1.600  1.00 25.00           C
ATOM      7  CA  ASP     7      -2.052  13.414   1.954  1.00 25.00           C
ATOM      8  CA  VAL     8      -2.713  17.150   1.723  1.00 25.00           C
ATOM      9  CA  GLU     9      -5.064  18.946   4.039  1.00 25.00           C
ATOM     10  CA  LEU    10      -6.667  20.309   0.913  1.00 25.00           C
ATOM     11  CA  THR    11      -9.290  23.061   0.742  1.00 25.00           C
ATOM     12  CA  LYS    12     -12.399  24.953  -0.369  1.00 25.00           C
ATOM     13  CA  ASN    13     -12.273  28.689  -0.012  1.00 25.00           C
ATOM     14  CA  VAL    14     -15.053  28.762  -2.668  1.00 25.00           C
ATOM     15  CA  GLN    15     -12.971  29.195  -5.855  1.00 25.00           C
ATOM     16  CA  GLY    16     -11.939  25.511  -6.260  1.00 25.00           C
ATOM     17  CA  LEU    17      -9.401  22.848  -5.413  1.00 25.00           C
ATOM     18  CA  GLY    18      -6.823  24.495  -7.765  1.00 25.00           C
ATOM     19  CA  ILE    19      -5.148  21.291  -9.049  1.00 25.00           C
ATOM     20  CA  THR    20      -7.103  20.099 -12.015  1.00 25.00           C
ATOM     21  CA  ILE    21      -7.185  16.252 -12.013  1.00 25.00           C
ATOM     22  CA  ALA    22      -6.504  14.951 -15.519  1.00 25.00           C
ATOM     23  CA  GLY    23      -5.449  11.891 -17.520  1.00 25.00           C
ATOM     24  CA  TYR    24      -3.883   8.559 -18.209  1.00 25.00           C
ATOM     25  CA  ILE    25      -6.020   8.648 -21.332  1.00 25.00           C
ATOM     26  CA  GLY    26      -8.222   6.279 -19.278  1.00 25.00           C
ATOM     27  CA  ASP    27      -7.345   2.560 -19.379  1.00 25.00           C
ATOM     28  CA  LYS    28      -4.216   3.946 -21.166  1.00 25.00           C
ATOM     29  CA  LYS    29      -1.290   1.546 -20.703  1.00 25.00           C
ATOM     30  CA  LEU    30      -2.140  -0.989 -17.994  1.00 25.00           C
ATOM     31  CA  GLU    31      -4.649   0.043 -15.358  1.00 25.00           C
ATOM     32  CA  PRO    32      -2.720   3.334 -15.548  1.00 25.00           C
ATOM     33  CA  SER    33      -5.511   5.578 -14.310  1.00 25.00           C
ATOM     34  CA  GLY    34      -3.708   6.811 -11.176  1.00 25.00           C
ATOM     35  CA  ILE    35      -3.427   9.978 -13.350  1.00 25.00           C
ATOM     36  CA  PHE    36      -1.503  13.076 -14.549  1.00 25.00           C
ATOM     37  CA  VAL    37      -1.764  15.768 -11.859  1.00 25.00           C
ATOM     38  CA  LYS    38      -1.454  18.187 -14.829  1.00 25.00           C
ATOM     39  CA  SER    39      -1.976  21.798 -13.752  1.00 25.00           C
ATOM     40  CA  ILE    40      -1.113  24.311 -11.019  1.00 25.00           C
ATOM     41  CA  THR    41      -3.088  27.523 -11.218  1.00 25.00           C
ATOM     42  CA  LYS    42      -1.607  29.631  -8.475  1.00 25.00           C
ATOM     43  CA  SER    43      -3.866  31.270  -5.912  1.00 25.00           C
ATOM     44  CA  SER    44      -5.048  27.954  -4.560  1.00 25.00           C
ATOM     45  CA  ALA    45      -4.339  24.977  -2.235  1.00 25.00           C
ATOM     46  CA  VAL    46      -1.580  23.493  -4.451  1.00 25.00           C
ATOM     47  CA  GLU    47       0.167  26.900  -4.555  1.00 25.00           C
ATOM     48  CA  HIS    48       0.305  26.972  -0.728  1.00 25.00           C
ATOM     49  CA  ASP    49       0.719  23.359   0.388  1.00 25.00           C
ATOM     50  CA  GLY    50       4.408  23.597  -0.621  1.00 25.00           C
ATOM     51  CA  ARG    51       4.017  20.006  -1.833  1.00 25.00           C
ATOM     52  CA  ILE    52       0.952  18.837  -3.702  1.00 25.00           C
ATOM     53  CA  GLN    53       2.059  18.382  -7.365  1.00 25.00           C
ATOM     54  CA  ILE    54       3.304  18.644 -10.943  1.00 25.00           C
ATOM     55  CA  GLY    55       3.467  15.568 -13.181  1.00 25.00           C
ATOM     56  CA  ASP    56       3.210  13.521  -9.924  1.00 25.00           C
ATOM     57  CA  GLN    57       0.326  11.039 -10.134  1.00 25.00           C
ATOM     58  CA  ILE    58      -3.088  11.628  -8.606  1.00 25.00           C
ATOM     59  CA  ILE    59      -4.942   9.151  -6.417  1.00 25.00           C
ATOM     60  CA  ALA    60      -8.189  10.127  -4.720  1.00 25.00           C
ATOM     61  CA  VAL    61     -10.563  12.114  -2.549  1.00 25.00           C
ATOM     62  CA  ASP    62     -11.746  10.969   0.891  1.00 25.00           C
ATOM     63  CA  GLY    63     -11.228   7.261   0.389  1.00 25.00           C
ATOM     64  CA  THR    64     -13.339   6.766  -2.795  1.00 25.00           C
ATOM     65  CA  ASN    65     -12.227   4.946  -5.929  1.00 25.00           C
ATOM     66  CA  LEU    66      -8.680   5.520  -7.292  1.00 25.00           C
ATOM     67  CA  GLN    67      -7.652   1.903  -8.088  1.00 25.00           C
ATOM     68  CA  GLY    68      -8.648   0.154 -11.277  1.00 25.00           C
ATOM     69  CA  PHE    69     -11.351   2.809 -11.846  1.00 25.00           C
ATOM     70  CA  THR    70     -11.039   5.623 -14.337  1.00 25.00           C
ATOM     71  CA  ASN    71     -10.185   9.298 -14.657  1.00 25.00           C
ATOM     72  CA  GLN    72     -13.706  10.754 -15.051  1.00 25.00           C
ATOM     73  CA  GLN    73     -14.770   9.138 -11.747  1.00 25.00           C
ATOM     74  CA  ALA    74     -11.685  10.599 -10.010  1.00 25.00           C
ATOM     75  CA  VAL    75     -12.497  14.062 -11.428  1.00 25.00           C
ATOM     76  CA  GLU    76     -16.105  13.754 -10.181  1.00 25.00           C
ATOM     77  CA  VAL    77     -14.846  12.752  -6.707  1.00 25.00           C
ATOM     78  CA  LEU    78     -12.480  15.764  -6.670  1.00 25.00           C
ATOM     79  CA  ARG    79     -15.367  18.075  -7.668  1.00 25.00           C
ATOM     80  CA  HIS    80     -17.535  16.616  -4.868  1.00 25.00           C
ATOM     81  CA  THR    81     -15.261  17.158  -1.847  1.00 25.00           C
ATOM     82  CA  GLY    82     -16.246  20.819  -1.264  1.00 25.00           C
ATOM     83  CA  GLN    83     -14.926  21.259   2.304  1.00 25.00           C
ATOM     84  CA  THR    84     -11.853  19.011   2.237  1.00 25.00           C
ATOM     85  CA  VAL    85     -10.263  17.203  -0.729  1.00 25.00           C
ATOM     86  CA  LEU    86      -7.575  14.957   0.895  1.00 25.00           C
ATOM     87  CA  LEU    87      -5.431  13.237  -1.758  1.00 25.00           C
ATOM     88  CA  THR    88      -3.771   9.813  -1.389  1.00 25.00           C
ATOM     89  CA  LEU    89      -0.658  10.714  -3.383  1.00 25.00           C
ATOM     90  CA  MET    90       1.674   8.892  -5.771  1.00 25.00           C
ATOM     91  CA  ARG    91       5.219   9.856  -4.905  1.00 25.00           C
ATOM     92  CA  ARG    92       6.825   6.852  -6.495  1.00 25.00           C
ATOM     93  CA  GLY    93      10.397   6.038  -5.302  1.00 25.00           C
ATOM     94  CA  GLU    94      13.833   5.148  -6.546  1.00 25.00           C
ATOM     95  CA  THR    95      16.338   3.484  -8.868  1.00 25.00           C
ATOM     96  CA  SER    96      17.455   3.612 -12.516  1.00 25.00           C
ATOM     97  CA  VAL    97      13.796   4.514 -13.264  1.00 25.00           C
TER
END
