
#######################################################
#                                                     #
#                        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   87 (   87),  selected   87 , name T0358TS393_4
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS393_4.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    Q       3      -       -           -
LGA    S       4      -       -           -
LGA    V       5      -       -           -
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    P       8      -       -           -
LGA    P       9      -       -           -
LGA    G      10      -       -           -
LGA    P      11      -       -           -
LGA    F      12      -       -           -
LGA    T      13      -       -           -
LGA    R      14      G      10          3.609
LGA    R      15      -       -           -
LGA    Q      16      P      11           #
LGA    A      17      F      12          4.020
LGA    Q      18      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    A      19      Q      16           #
LGA    V      20      A      17          4.090
LGA    -       -      Q      18           -
LGA    T      21      A      19          4.646
LGA    T      22      V      20          0.716
LGA    T      23      T      21          2.481
LGA    Y      24      T      22           #
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    S      25      I      27           #
LGA    N      26      T      28          1.705
LGA    I      27      L      29          2.105
LGA    T      28      E      30          3.182
LGA    L      29      D      31          2.171
LGA    E      30      D      32          4.279
LGA    D      31      Q      33          3.938
LGA    D      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      -       -           -
LGA    S      35      G      34          3.269
LGA    H      36      S      35          3.514
LGA    F      37      H      36          0.932
LGA    R      38      F      37          2.432
LGA    L      39      R      38          1.542
LGA    V      40      L      39          3.269
LGA    V      41      V      40          1.877
LGA    R      42      V      41          1.331
LGA    D      43      R      42          1.847
LGA    T      44      D      43          1.866
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    E      45      R      47          1.768
LGA    G      46      M      48          1.581
LGA    R      47      V      49          1.809
LGA    M      48      W      50          1.621
LGA    V      49      R      51          2.803
LGA    W      50      A      52          3.286
LGA    R      51      W      53          3.675
LGA    A      52      N      54          4.528
LGA    W      53      -       -           -
LGA    N      54      -       -           -
LGA    F      55      -       -           -
LGA    E      56      -       -           -
LGA    P      57      -       -           -
LGA    D      58      -       -           -
LGA    A      59      -       -           -
LGA    G      60      -       -           -
LGA    E      61      -       -           -
LGA    G      62      -       -           -
LGA    L      63      -       -           -
LGA    N      64      -       -           -
LGA    R      65      -       -           -
LGA    Y      66      -       -           -
LGA    I      67      -       -           -
LGA    R      68      F      55           #
LGA    T      69      E      56           -
LGA    S      70      P      57           -
LGA    G      71      D      58           -
LGA    I      72      A      59           -
LGA    R      73      G      60           -
LGA    T      74      E      61           -
LGA    D      75      G      62           -
LGA    T      76      L      63           -
LGA    A      77      N      64           -
LGA    T      78      R      65           -
LGA    R      79      Y      66           -
LGA    L      80      I      67           -
LGA    E      81      R      68           -
LGA    H      82      T      69           -
LGA    H      83      S      70           -
LGA    H      84      G      71           -
LGA    H      85      I      72           -
LGA    H      86      R      73           -
LGA    H      87      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   87   66    5.0     30    2.88     6.67     29.008     1.006

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.597884 * X  +   0.799192 * Y  +  -0.061862 * Z  +   5.401733
  Y_new =   0.716838 * X  +   0.567617 * Y  +   0.404912 * Z  +   8.517715
  Z_new =   0.358717 * X  +   0.197745 * Y  +  -0.912261 * Z  +   1.686929 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.928131   -0.213461  [ DEG:   167.7696    -12.2304 ]
  Theta =  -0.366893   -2.774700  [ DEG:   -21.0214   -158.9786 ]
  Phi   =   2.265961   -0.875631  [ DEG:   129.8300    -50.1700 ]
 
# 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: T0358TS393_4                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_4.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   87   66   5.0   30   2.88    6.67  29.008
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_4
PFRMAT TS
TARGET T0358
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      -0.799  21.917   9.765  1.00 25.00           C
ATOM      2  CA  THR     2       0.073  18.658   7.940  1.00 25.00           C
ATOM      3  CA  GLN     3      -1.858  15.787   6.364  1.00 25.00           C
ATOM      4  CA  SER     4      -2.872  12.141   6.762  1.00 25.00           C
ATOM      5  CA  VAL     5      -0.663  10.064   4.562  1.00 25.00           C
ATOM      6  CA  LEU     6       1.938   7.319   4.726  1.00 25.00           C
ATOM      7  CA  LEU     7       4.701   6.150   7.107  1.00 25.00           C
ATOM      8  CA  PRO     8       6.184   6.388  10.621  1.00 25.00           C
ATOM      9  CA  PRO     9       4.494   5.217  13.890  1.00 25.00           C
ATOM     10  CA  GLY    10       4.558   1.480  14.638  1.00 25.00           C
ATOM     11  CA  PRO    11       7.803  -0.107  13.438  1.00 25.00           C
ATOM     12  CA  PHE    12       8.100   1.757  10.160  1.00 25.00           C
ATOM     13  CA  THR    13      11.493   0.251   9.263  1.00 25.00           C
ATOM     14  CA  ARG    14      10.701   0.830   5.603  1.00 25.00           C
ATOM     15  CA  ARG    15       7.875  -1.672   6.255  1.00 25.00           C
ATOM     16  CA  GLN    16       5.295   0.891   5.057  1.00 25.00           C
ATOM     17  CA  ALA    17       7.347   1.512   1.884  1.00 25.00           C
ATOM     18  CA  GLN    18       7.546  -2.258   1.246  1.00 25.00           C
ATOM     19  CA  ALA    19       3.756  -2.561   1.703  1.00 25.00           C
ATOM     20  CA  VAL    20       3.204   0.323  -0.754  1.00 25.00           C
ATOM     21  CA  THR    21       5.518  -1.368  -3.296  1.00 25.00           C
ATOM     22  CA  THR    22       3.597  -4.656  -2.892  1.00 25.00           C
ATOM     23  CA  THR    23       0.282  -2.815  -3.429  1.00 25.00           C
ATOM     24  CA  TYR    24       1.685  -1.158  -6.583  1.00 25.00           C
ATOM     25  CA  SER    25      -1.666  -1.813  -8.298  1.00 25.00           C
ATOM     26  CA  ASN    26      -3.638  -0.195  -5.413  1.00 25.00           C
ATOM     27  CA  ILE    27      -1.170   2.516  -4.276  1.00 25.00           C
ATOM     28  CA  THR    28      -2.406   5.921  -5.468  1.00 25.00           C
ATOM     29  CA  LEU    29      -3.639   9.560  -5.404  1.00 25.00           C
ATOM     30  CA  GLU    30      -3.375  13.228  -6.377  1.00 25.00           C
ATOM     31  CA  ASP    31      -5.821  13.038  -9.294  1.00 25.00           C
ATOM     32  CA  ASP    32      -6.680  16.644 -10.004  1.00 25.00           C
ATOM     33  CA  GLN    33      -4.967  16.206 -13.326  1.00 25.00           C
ATOM     34  CA  GLY    34      -3.739  12.675 -13.950  1.00 25.00           C
ATOM     35  CA  SER    35      -1.407  11.380 -11.285  1.00 25.00           C
ATOM     36  CA  HIS    36       1.059  10.331  -8.530  1.00 25.00           C
ATOM     37  CA  PHE    37       1.445  11.697  -4.964  1.00 25.00           C
ATOM     38  CA  ARG    38      -0.123  10.099  -1.889  1.00 25.00           C
ATOM     39  CA  LEU    39      -2.383   7.393  -0.386  1.00 25.00           C
ATOM     40  CA  VAL    40      -4.271   4.175   0.389  1.00 25.00           C
ATOM     41  CA  VAL    41      -3.228   0.570  -0.014  1.00 25.00           C
ATOM     42  CA  ARG    42      -3.208  -2.679   2.059  1.00 25.00           C
ATOM     43  CA  ASP    43      -6.044  -5.138   1.477  1.00 25.00           C
ATOM     44  CA  THR    44      -8.511  -5.877   4.281  1.00 25.00           C
ATOM     45  CA  GLU    45     -11.768  -5.474   2.258  1.00 25.00           C
ATOM     46  CA  GLY    46     -11.555  -1.878   3.499  1.00 25.00           C
ATOM     47  CA  ARG    47      -8.400  -0.742   5.257  1.00 25.00           C
ATOM     48  CA  MET    48      -5.574   1.771   4.995  1.00 25.00           C
ATOM     49  CA  VAL    49      -1.879   2.510   4.569  1.00 25.00           C
ATOM     50  CA  TRP    50       0.776   3.182   1.961  1.00 25.00           C
ATOM     51  CA  ARG    51       2.274   5.560  -0.617  1.00 25.00           C
ATOM     52  CA  ALA    52       2.457   6.200  -4.335  1.00 25.00           C
ATOM     53  CA  TRP    53       3.914   3.500  -6.665  1.00 25.00           C
ATOM     54  CA  ASN    54       3.834   6.155  -9.369  1.00 25.00           C
ATOM     55  CA  PHE    55       4.688   6.492 -13.099  1.00 25.00           C
ATOM     56  CA  GLU    56       8.304   5.737 -12.033  1.00 25.00           C
ATOM     57  CA  PRO    57       7.487   2.228 -13.147  1.00 25.00           C
ATOM     58  CA  ASP    58      10.724   0.711 -11.769  1.00 25.00           C
ATOM     59  CA  ALA    59       9.175   1.481  -8.417  1.00 25.00           C
ATOM     60  CA  GLY    60      11.691   4.300  -8.187  1.00 25.00           C
ATOM     61  CA  GLU    61       9.345   6.983  -6.815  1.00 25.00           C
ATOM     62  CA  GLY    62       8.771  10.745  -6.378  1.00 25.00           C
ATOM     63  CA  LEU    63       6.101  10.053  -3.721  1.00 25.00           C
ATOM     64  CA  ASN    64       8.502   7.703  -1.884  1.00 25.00           C
ATOM     65  CA  ARG    65      11.238  10.380  -1.983  1.00 25.00           C
ATOM     66  CA  TYR    66       8.786  12.972  -0.589  1.00 25.00           C
ATOM     67  CA  ILE    67       7.803  10.564   2.222  1.00 25.00           C
ATOM     68  CA  ARG    68      11.496   9.979   3.048  1.00 25.00           C
ATOM     69  CA  THR    69      12.098  13.760   3.147  1.00 25.00           C
ATOM     70  CA  SER    70      13.844  14.357  -0.216  1.00 25.00           C
ATOM     71  CA  GLY    71      14.359  18.012  -1.236  1.00 25.00           C
ATOM     72  CA  ILE    72      11.800  19.860   0.892  1.00 25.00           C
ATOM     73  CA  ARG    73      13.587  22.857   2.447  1.00 25.00           C
ATOM     74  CA  THR    74      17.261  22.888   1.261  1.00 25.00           C
ATOM     75  CA  ASP    75      20.996  22.946   2.057  1.00 25.00           C
ATOM     76  CA  THR    76      22.389  22.865   5.616  1.00 25.00           C
ATOM     77  CA  ALA    77      20.115  24.880   7.906  1.00 25.00           C
ATOM     78  CA  THR    78      17.761  26.360  10.501  1.00 25.00           C
ATOM     79  CA  ARG    79      18.786  27.558  13.930  1.00 25.00           C
ATOM     80  CA  LEU    80      17.548  28.272  17.408  1.00 25.00           C
ATOM     81  CA  GLU    81      15.714  25.577  19.460  1.00 25.00           C
ATOM     82  CA  HIS    82      17.795  22.715  20.736  1.00 25.00           C
ATOM     83  CA  HIS    83      21.578  22.836  20.403  1.00 25.00           C
ATOM     84  CA  HIS    84      22.041  19.045  20.454  1.00 25.00           C
ATOM     85  CA  HIS    85      21.111  15.758  18.944  1.00 25.00           C
ATOM     86  CA  HIS    86      19.507  12.590  20.237  1.00 25.00           C
ATOM     87  CA  HIS    87      16.766  13.249  22.829  1.00 25.00           C
TER
END
