
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0300AL380_1
# Molecule2: number of CA atoms   89 (  695),  selected   89 , name T0300
# PARAMETERS: T0300AL380_1.T0300  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       7           -
LGA    -       -      K       8           -
LGA    -       -      T       9           -
LGA    -       -      Y      10           -
LGA    -       -      E      11           -
LGA    -       -      E      12           -
LGA    -       -      M      13           -
LGA    -       -      V      14           -
LGA    -       -      K      15           -
LGA    -       -      E      16           -
LGA    -       -      V      17           -
LGA    -       -      E      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      K      21           -
LGA    -       -      L      22           -
LGA    -       -      E      23           -
LGA    -       -      N      24           -
LGA    -       -      K      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      Q      29           -
LGA    -       -      K      30           -
LGA    -       -      V      31           -
LGA    -       -      S      39           -
LGA    -       -      D      40           -
LGA    -       -      D      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      L      44           -
LGA    -       -      T      45           -
LGA    T       9      A      46          0.893
LGA    Y      10      A      47          0.369
LGA    E      11      K      48          0.524
LGA    E      12      R      49          0.630
LGA    M      13      E      50          0.472
LGA    V      14      S      51          0.143
LGA    K      15      I      52          0.297
LGA    E      16      I      53          0.452
LGA    V      17      V      54          0.576
LGA    E      18      S      55          0.580
LGA    R      19      S      56          0.249
LGA    L      20      S      57          0.283
LGA    K      21      R      58          0.300
LGA    L      22      A      59          0.586
LGA    E      23      L      60          0.968
LGA    N      24      G      61          0.946
LGA    K      25      A      62          0.898
LGA    T      26      V      63          0.893
LGA    L      27      A      64          0.680
LGA    K      28      M      65          0.815
LGA    Q      29      R      66          0.533
LGA    K      30      K      67          0.745
LGA    V      31      I      68          0.713
LGA    K      32      E      69          0.338
LGA    S      33      A      70          0.555
LGA    S      34      K      71          0.285
LGA    G      35      V      72          0.942
LGA    A      36      R      73          1.441
LGA    V      37      S      74          1.093
LGA    -       -      R      75           -
LGA    -       -      A      76           -
LGA    -       -      A      77           -
LGA    -       -      K      78           -
LGA    -       -      A      79           -
LGA    -       -      V      80           -
LGA    -       -      T      81           -
LGA    -       -      E      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      S      87           -
LGA    -       -      L      88           -
LGA    -       -      L      89           -
LGA    -       -      Q      90           -
LGA    -       -      S      91           -
LGA    -       -      L      92           -
LGA    -       -      T      93           -
LGA    -       -      L      94           -
LGA    -       -      R      95           -
LGA    -       -      V      96           -
LGA    -       -      D      97           -
LGA    -       -      V      98           -
LGA    -       -      S      99           -
LGA    -       -      M     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29   89    5.0     29    0.69     6.90     32.407     3.653

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.114619 * X  +  -0.425618 * Y  +  -0.897615 * Z  +  32.738995
  Y_new =   0.978911 * X  +  -0.105420 * Y  +   0.174986 * Z  + -59.270512
  Z_new =  -0.169104 * X  +  -0.898741 * Y  +   0.404559 * Z  +  23.100239 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.147827    1.993766  [ DEG:   -65.7656    114.2344 ]
  Theta =   0.169920    2.971673  [ DEG:     9.7357    170.2643 ]
  Phi   =   1.454239   -1.687354  [ DEG:    83.3217    -96.6783 ]
 
# 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: T0300AL380_1                                  
REMARK     2: T0300                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0300AL380_1.T0300 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29   89   5.0   29   0.69    6.90  32.407
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL380_1
REMARK Aligment from pdb entry: 1debA
ATOM      1  N   THR     9      54.734 -16.173 -14.594  1.00  0.00              
ATOM      2  CA  THR     9      55.337 -14.937 -15.061  1.00  0.00              
ATOM      3  C   THR     9      54.924 -13.857 -14.062  1.00  0.00              
ATOM      4  O   THR     9      54.160 -14.111 -13.129  1.00  0.00              
ATOM      5  N   TYR    10      55.417 -12.647 -14.268  1.00  0.00              
ATOM      6  CA  TYR    10      55.070 -11.541 -13.394  1.00  0.00              
ATOM      7  C   TYR    10      53.573 -11.237 -13.545  1.00  0.00              
ATOM      8  O   TYR    10      52.904 -10.874 -12.578  1.00  0.00              
ATOM      9  N   GLU    11      53.055 -11.392 -14.761  1.00  0.00              
ATOM     10  CA  GLU    11      51.646 -11.120 -15.021  1.00  0.00              
ATOM     11  C   GLU    11      50.707 -12.191 -14.475  1.00  0.00              
ATOM     12  O   GLU    11      49.591 -11.898 -14.072  1.00  0.00              
ATOM     13  N   GLU    12      51.157 -13.433 -14.469  1.00  0.00              
ATOM     14  CA  GLU    12      50.331 -14.501 -13.945  1.00  0.00              
ATOM     15  C   GLU    12      50.201 -14.327 -12.437  1.00  0.00              
ATOM     16  O   GLU    12      49.138 -14.542 -11.863  1.00  0.00              
ATOM     17  N   MET    13      51.277 -13.889 -11.801  1.00  0.00              
ATOM     18  CA  MET    13      51.245 -13.670 -10.362  1.00  0.00              
ATOM     19  C   MET    13      50.292 -12.535 -10.059  1.00  0.00              
ATOM     20  O   MET    13      49.494 -12.602  -9.122  1.00  0.00              
ATOM     21  N   VAL    14      50.386 -11.485 -10.860  1.00  0.00              
ATOM     22  CA  VAL    14      49.532 -10.343 -10.640  1.00  0.00              
ATOM     23  C   VAL    14      48.087 -10.795 -10.661  1.00  0.00              
ATOM     24  O   VAL    14      47.279 -10.327  -9.869  1.00  0.00              
ATOM     25  N   LYS    15      47.754 -11.704 -11.565  1.00  0.00              
ATOM     26  CA  LYS    15      46.390 -12.194 -11.622  1.00  0.00              
ATOM     27  C   LYS    15      46.027 -12.999 -10.370  1.00  0.00              
ATOM     28  O   LYS    15      44.895 -12.933  -9.888  1.00  0.00              
ATOM     29  N   GLU    16      46.979 -13.767  -9.853  1.00  0.00              
ATOM     30  CA  GLU    16      46.716 -14.556  -8.659  1.00  0.00              
ATOM     31  C   GLU    16      46.420 -13.615  -7.503  1.00  0.00              
ATOM     32  O   GLU    16      45.466 -13.818  -6.749  1.00  0.00              
ATOM     33  N   VAL    17      47.236 -12.573  -7.381  1.00  0.00              
ATOM     34  CA  VAL    17      47.080 -11.609  -6.305  1.00  0.00              
ATOM     35  C   VAL    17      45.718 -10.946  -6.372  1.00  0.00              
ATOM     36  O   VAL    17      45.048 -10.792  -5.352  1.00  0.00              
ATOM     37  N   GLU    18      45.294 -10.568  -7.571  1.00  0.00              
ATOM     38  CA  GLU    18      43.992  -9.939  -7.734  1.00  0.00              
ATOM     39  C   GLU    18      42.854 -10.844  -7.251  1.00  0.00              
ATOM     40  O   GLU    18      41.941 -10.393  -6.566  1.00  0.00              
ATOM     41  N   ARG    19      42.906 -12.118  -7.610  1.00  0.00              
ATOM     42  CA  ARG    19      41.858 -13.049  -7.208  1.00  0.00              
ATOM     43  C   ARG    19      41.974 -13.369  -5.717  1.00  0.00              
ATOM     44  O   ARG    19      40.967 -13.533  -5.022  1.00  0.00              
ATOM     45  N   LEU    20      43.202 -13.444  -5.220  1.00  0.00              
ATOM     46  CA  LEU    20      43.419 -13.741  -3.802  1.00  0.00              
ATOM     47  C   LEU    20      42.887 -12.616  -2.913  1.00  0.00              
ATOM     48  O   LEU    20      42.248 -12.872  -1.896  1.00  0.00              
ATOM     49  N   LYS    21      43.150 -11.373  -3.314  1.00  0.00              
ATOM     50  CA  LYS    21      42.677 -10.201  -2.585  1.00  0.00              
ATOM     51  C   LYS    21      41.147 -10.149  -2.565  1.00  0.00              
ATOM     52  O   LYS    21      40.529  -9.748  -1.570  1.00  0.00              
ATOM     53  N   LEU    22      40.520 -10.511  -3.670  1.00  0.00              
ATOM     54  CA  LEU    22      39.063 -10.427  -3.687  1.00  0.00              
ATOM     55  C   LEU    22      38.511 -11.527  -2.786  1.00  0.00              
ATOM     56  O   LEU    22      37.608 -11.298  -1.984  1.00  0.00              
ATOM     57  N   GLU    23      39.090 -12.708  -2.890  1.00  0.00              
ATOM     58  CA  GLU    23      38.685 -13.816  -2.063  1.00  0.00              
ATOM     59  C   GLU    23      38.859 -13.404  -0.602  1.00  0.00              
ATOM     60  O   GLU    23      37.934 -13.572   0.196  1.00  0.00              
ATOM     61  N   ASN    24      40.023 -12.846  -0.255  1.00  0.00              
ATOM     62  CA  ASN    24      40.265 -12.402   1.116  1.00  0.00              
ATOM     63  C   ASN    24      39.224 -11.400   1.544  1.00  0.00              
ATOM     64  O   ASN    24      38.782 -11.440   2.675  1.00  0.00              
ATOM     65  N   LYS    25      38.840 -10.492   0.657  1.00  0.00              
ATOM     66  CA  LYS    25      37.820  -9.513   1.018  1.00  0.00              
ATOM     67  C   LYS    25      36.470 -10.198   1.247  1.00  0.00              
ATOM     68  O   LYS    25      35.710  -9.819   2.151  1.00  0.00              
ATOM     69  N   THR    26      36.177 -11.220   0.447  1.00  0.00              
ATOM     70  CA  THR    26      34.906 -11.912   0.591  1.00  0.00              
ATOM     71  C   THR    26      34.863 -12.753   1.867  1.00  0.00              
ATOM     72  O   THR    26      33.842 -12.766   2.561  1.00  0.00              
ATOM     73  N   LEU    27      35.968 -13.436   2.180  1.00  0.00              
ATOM     74  CA  LEU    27      36.036 -14.230   3.395  1.00  0.00              
ATOM     75  C   LEU    27      35.801 -13.324   4.617  1.00  0.00              
ATOM     76  O   LEU    27      35.039 -13.679   5.503  1.00  0.00              
ATOM     77  N   LYS    28      36.426 -12.148   4.647  1.00  0.00              
ATOM     78  CA  LYS    28      36.231 -11.210   5.756  1.00  0.00              
ATOM     79  C   LYS    28      34.772 -10.792   5.871  1.00  0.00              
ATOM     80  O   LYS    28      34.236 -10.660   6.963  1.00  0.00              
ATOM     81  N   GLN    29      34.135 -10.551   4.729  1.00  0.00              
ATOM     82  CA  GLN    29      32.728 -10.166   4.711  1.00  0.00              
ATOM     83  C   GLN    29      31.889 -11.291   5.352  1.00  0.00              
ATOM     84  O   GLN    29      30.981 -11.050   6.163  1.00  0.00              
ATOM     85  N   LYS    30      32.216 -12.524   4.996  1.00  0.00              
ATOM     86  CA  LYS    30      31.497 -13.673   5.516  1.00  0.00              
ATOM     87  C   LYS    30      31.644 -13.819   7.016  1.00  0.00              
ATOM     88  O   LYS    30      30.670 -14.033   7.715  1.00  0.00              
ATOM     89  N   VAL    31      32.875 -13.725   7.499  1.00  0.00              
ATOM     90  CA  VAL    31      33.156 -13.865   8.920  1.00  0.00              
ATOM     91  C   VAL    31      32.424 -12.761   9.684  1.00  0.00              
ATOM     92  O   VAL    31      31.844 -12.985  10.737  1.00  0.00              
ATOM     93  N   LYS    32      32.432 -11.574   9.106  1.00  0.00              
ATOM     94  CA  LYS    32      31.792 -10.405   9.671  1.00  0.00              
ATOM     95  C   LYS    32      30.286 -10.658   9.764  1.00  0.00              
ATOM     96  O   LYS    32      29.658 -10.378  10.782  1.00  0.00              
ATOM     97  N   SER    33      29.722 -11.202   8.691  1.00  0.00              
ATOM     98  CA  SER    33      28.294 -11.520   8.597  1.00  0.00              
ATOM     99  C   SER    33      27.946 -12.527   9.689  1.00  0.00              
ATOM    100  O   SER    33      27.065 -12.312  10.530  1.00  0.00              
ATOM    101  N   SER    34      28.674 -13.629   9.671  1.00  0.00              
ATOM    102  CA  SER    34      28.456 -14.711  10.598  1.00  0.00              
ATOM    103  C   SER    34      28.737 -14.351  12.029  1.00  0.00              
ATOM    104  O   SER    34      28.067 -14.845  12.941  1.00  0.00              
ATOM    105  N   GLY    35      29.712 -13.481  12.240  1.00  0.00              
ATOM    106  CA  GLY    35      30.019 -13.079  13.594  1.00  0.00              
ATOM    107  C   GLY    35      28.811 -12.287  14.093  1.00  0.00              
ATOM    108  O   GLY    35      28.328 -12.538  15.196  1.00  0.00              
ATOM    109  N   ALA    36      28.286 -11.379  13.275  1.00  0.00              
ATOM    110  CA  ALA    36      27.111 -10.590  13.665  1.00  0.00              
ATOM    111  C   ALA    36      25.893 -11.502  13.895  1.00  0.00              
ATOM    112  O   ALA    36      25.055 -11.278  14.804  1.00  0.00              
ATOM    113  N   VAL    37      25.787 -12.533  13.066  1.00  0.00              
ATOM    114  CA  VAL    37      24.696 -13.485  13.187  1.00  0.00              
ATOM    115  C   VAL    37      24.754 -14.245  14.526  1.00  0.00              
ATOM    116  O   VAL    37      23.719 -14.489  15.148  1.00  0.00              
END
