
#######################################################
#                                                     #
#                        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   68 (   68),  selected   68 , name T0299TS677_1-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS677_1-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      T       2           -
LGA    -       -      R       3           -
LGA    -       -      Y       4           -
LGA    -       -      A       5           -
LGA    -       -      L       6           -
LGA    -       -      L       7           -
LGA    -       -      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    L       6      N      12          3.860
LGA    L       7      V      13          4.329
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    V       8      K      18          3.675
LGA    R       9      V      19          1.094
LGA    G      10      V      20           #
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    I      11      L      24          2.175
LGA    N      12      R      25          2.749
LGA    V      13      Q      26           #
LGA    -       -      E      27           -
LGA    -       -      L      28           -
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    -       -      L      31           -
LGA    -       -      G      32           -
LGA    -       -      L      33           -
LGA    G      14      E      34          2.870
LGA    G      15      K      35          1.688
LGA    -       -      V      36           -
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    -       -      G      43           -
LGA    -       -      N      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      F      47           -
LGA    -       -      T      48           -
LGA    K      16      S      49          1.105
LGA    -       -      I      50           -
LGA    N      17      D      51          3.124
LGA    K      18      S      52           -
LGA    V      19      K      53           #
LGA    -       -      A      54           -
LGA    -       -      Q      55           -
LGA    V      20      L      56          0.919
LGA    M      21      V      57          0.632
LGA    A      22      E      58          0.576
LGA    E      23      K      59          0.834
LGA    L      24      L      60          0.836
LGA    R      25      E      61          0.443
LGA    Q      26      T      62          0.636
LGA    E      27      F      63          1.304
LGA    L      28      F      64          1.507
LGA    T      29      A      65          0.814
LGA    N      30      V      66          1.011
LGA    L      31      H      67          1.021
LGA    G      32      Y      68          1.583
LGA    L      33      P      69          5.561
LGA    E      34      F      70          5.272
LGA    K      35      I      71           #
LGA    V      36      -       -           -
LGA    E      37      -       -           -
LGA    S      38      -       -           -
LGA    Y      39      -       -           -
LGA    I      40      -       -           -
LGA    N      41      -       -           -
LGA    S      42      -       -           -
LGA    G      43      -       -           -
LGA    N      44      -       -           -
LGA    S      49      -       -           -
LGA    I      50      -       -           -
LGA    D      51      -       -           -
LGA    S      52      -       -           -
LGA    K      53      -       -           -
LGA    A      54      -       -           -
LGA    Q      55      -       -           -
LGA    L      56      -       -           -
LGA    V      57      -       -           -
LGA    E      58      -       -           -
LGA    K      59      -       -           -
LGA    L      60      -       -           -
LGA    E      61      -       -           -
LGA    T      62      -       -           -
LGA    F      63      -       -           -
LGA    F      64      -       -           -
LGA    A      65      -       -           -
LGA    V      66      -       -           -
LGA    H      67      -       -           -
LGA    Y      68      -       -           -
LGA    P      69      -       -           -
LGA    F      70      Q      72          4.763
LGA    I      71      S      73          1.159
LGA    Q      72      F      74          3.767
LGA    S      73      S      75           #
LGA    F      74      L      76           #
LGA    S      75      L      77           -
LGA    -       -      S      78           -
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    L      76      I     174          4.206
LGA    L      77      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   68   91    5.0     29    2.69     3.45     23.124     1.039

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.706304 * X  +  -0.651721 * Y  +  -0.276394 * Z  +  18.570189
  Y_new =  -0.053251 * X  +  -0.438244 * Y  +   0.897277 * Z  +  16.460640
  Z_new =  -0.705903 * X  +  -0.619032 * Y  +  -0.344239 * Z  + -39.101540 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.078304    1.063288  [ DEG:  -119.0781     60.9219 ]
  Theta =   0.783697    2.357896  [ DEG:    44.9025    135.0975 ]
  Phi   =  -0.075252    3.066341  [ DEG:    -4.3116    175.6884 ]
 
# 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: T0299TS677_1-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS677_1-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   68   91   5.0   29   2.69    3.45  23.124
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS677_1-D1
PFRMAT     TS
TARGET     T0299
MODEL      1
PARENT     1lf1A
ATOM     27  CA  LEU     6       7.264  33.961  -3.948  1.00 99.00
ATOM     28  CA  LEU     7       3.589  32.935  -4.330  1.00 99.00
ATOM     29  CA  VAL     8       0.805  35.257  -3.066  1.00 99.00
ATOM     30  CA  ARG     9      -2.664  33.876  -2.222  1.00 99.00
ATOM     31  CA  GLY    10      -5.749  35.787  -1.086  1.00 84.00
ATOM     32  CA  ILE    11      -9.177  37.248  -1.735  1.00 69.00
ATOM     33  CA  ASN    12     -10.835  39.791  -4.020  1.00 51.00
ATOM     34  CA  VAL    13     -13.552  42.177  -2.923  1.00 51.00
ATOM     35  CA  GLY    14     -16.673  42.231  -5.071  1.00 75.00
ATOM     36  CA  GLY    15     -17.615  45.639  -6.667  1.00 77.00
ATOM     41  CA  LYS    16     -17.670  47.804   0.192  1.00 92.00
ATOM     42  CA  ASN    17     -18.840  47.069   3.735  1.00 94.00
ATOM     43  CA  LYS    18     -16.849  43.832   3.753  1.00 99.00
ATOM     44  CA  VAL    19     -13.649  45.753   3.123  1.00 99.00
ATOM     45  CA  VAL    20     -12.132  47.353   6.190  1.00 99.00
ATOM     46  CA  MET    21      -9.208  47.118   8.589  1.00 99.00
ATOM     47  CA  ALA    22     -10.849  44.513  10.856  1.00 99.00
ATOM     48  CA  GLU    23     -12.032  42.191   8.078  1.00 84.00
ATOM     49  CA  LEU    24      -8.639  42.315   6.330  1.00 61.00
ATOM     50  CA  ARG    25      -6.915  41.667   9.621  1.00 99.00
ATOM     51  CA  GLN    26      -9.234  38.721  10.221  1.00 94.00
ATOM     52  CA  GLU    27      -8.371  37.406   6.745  1.00 99.00
ATOM     53  CA  LEU    28      -4.659  37.865   7.474  1.00 99.00
ATOM     54  CA  THR    29      -4.711  36.110  10.883  1.00 99.00
ATOM     55  CA  ASN    30      -7.425  33.466  10.421  1.00 76.00
ATOM     56  CA  LEU    31      -7.136  32.549   6.739  1.00 76.00
ATOM     57  CA  GLY    32      -3.468  33.480   6.171  1.00 72.00
ATOM     58  CA  LEU    33      -4.023  35.662   3.107  1.00 78.00
ATOM     59  CA  GLU    34      -0.926  37.428   1.757  1.00 42.00
ATOM     60  CA  LYS    35      -2.678  39.625  -0.852  1.00 87.00
ATOM     61  CA  VAL    36      -5.953  41.586  -0.961  1.00 90.00
ATOM     62  CA  GLU    37      -7.563  42.753  -4.202  1.00 71.00
ATOM     63  CA  SER    38      -9.626  45.973  -4.317  1.00 54.00
ATOM     64  CA  TYR    39     -12.123  45.670  -7.184  1.00 57.00
ATOM     65  CA  ILE    40     -13.110  49.189  -8.157  1.00 31.00
ATOM     66  CA  ASN    41     -15.654  49.041 -11.014  1.00 21.00
ATOM     67  CA  SER    42     -15.486  51.896 -13.565  1.00 38.00
ATOM     68  CA  GLY    43     -19.028  51.569 -14.850  1.00 44.00
ATOM     69  CA  ASN    44     -22.150  49.900 -13.415  1.00 36.00
ATOM     71  CA  SER    49     -18.533  52.559 -10.251  1.00 29.00
ATOM     72  CA  ILE    50     -15.881  55.268 -10.357  1.00 44.00
ATOM     73  CA  ASP    51     -16.987  56.944 -13.598  1.00 43.00
ATOM     74  CA  SER    52     -20.546  57.145 -12.273  1.00 52.00
ATOM     75  CA  LYS    53     -19.519  58.128  -8.742  1.00 66.00
ATOM     76  CA  ALA    54     -15.890  58.892  -8.025  1.00 70.00
ATOM     77  CA  GLN    55     -16.435  58.867  -4.250  1.00 79.00
ATOM     78  CA  LEU    56     -15.481  55.175  -4.410  1.00 83.00
ATOM     79  CA  VAL    57     -11.838  56.335  -4.838  1.00 76.00
ATOM     80  CA  GLU    58     -11.776  57.063  -1.144  1.00 66.00
ATOM     81  CA  LYS    59     -12.636  53.427  -0.310  1.00 66.00
ATOM     82  CA  LEU    60      -9.661  52.295  -2.427  1.00 62.00
ATOM     83  CA  GLU    61      -7.439  54.575  -0.330  1.00 40.00
ATOM     84  CA  THR    62      -8.867  53.172   2.917  1.00 35.00
ATOM     85  CA  PHE    63      -8.092  49.665   1.710  1.00 48.00
ATOM     86  CA  PHE    64      -4.486  50.364   0.654  1.00 33.00
ATOM     87  CA  ALA    65      -3.786  52.155   3.930  1.00 47.00
ATOM     88  CA  VAL    66      -5.131  49.179   5.835  1.00 99.00
ATOM     89  CA  HIS    67      -2.911  46.844   3.860  1.00 99.00
ATOM     90  CA  TYR    68       0.116  49.004   4.610  1.00 87.00
ATOM     91  CA  PRO    69      -0.816  48.866   8.295  1.00 99.00
ATOM     92  CA  PHE    70      -1.345  45.090   8.276  1.00 99.00
ATOM     93  CA  ILE    71       1.751  44.269   6.265  1.00 80.00
ATOM     94  CA  GLN    72       0.143  42.600   3.269  1.00 72.00
ATOM     95  CA  SER    73       0.240  43.164  -0.510  1.00 81.00
ATOM     96  CA  PHE    74      -2.771  44.939  -2.092  1.00 41.00
ATOM     97  CA  SER    75      -4.011  45.035  -5.677  1.00 37.00
ATOM     98  CA  LEU    76      -5.602  48.238  -6.970  1.00 19.00
ATOM     99  CA  LEU    77      -7.919  46.963  -9.701  1.00 34.00
TER
END
