
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms   89 (  695),  selected   89 , name T0300
# PARAMETERS: T0300AL380_2.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          1.713
LGA    Y      10      A      47          0.965
LGA    E      11      K      48          0.580
LGA    E      12      R      49          0.620
LGA    M      13      E      50          0.210
LGA    V      14      S      51          0.333
LGA    K      15      I      52          0.477
LGA    E      16      I      53          0.507
LGA    V      17      V      54          0.559
LGA    E      18      S      55          0.312
LGA    R      19      S      56          0.393
LGA    L      20      S      57          0.445
LGA    K      21      R      58          0.407
LGA    L      22      A      59          0.520
LGA    E      23      L      60          0.978
LGA    N      24      G      61          0.990
LGA    K      25      A      62          0.930
LGA    T      26      V      63          0.829
LGA    L      27      A      64          0.633
LGA    K      28      M      65          0.737
LGA    Q      29      R      66          0.414
LGA    K      30      K      67          0.726
LGA    V      31      I      68          0.728
LGA    K      32      E      69          0.617
LGA    S      33      A      70          0.700
LGA    S      34      K      71          0.262
LGA    G      35      V      72          1.391
LGA    A      36      R      73          2.036
LGA    V      37      S      74          1.281
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    0.85     6.90     32.146     3.066

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.401396 * X  +   0.815394 * Y  +  -0.417149 * Z  +  10.713005
  Y_new =  -0.852401 * X  +   0.165934 * Y  +  -0.495861 * Z  +  20.517380
  Z_new =  -0.335103 * X  +   0.554615 * Y  +   0.761648 * Z  +  18.809471 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.629388   -2.512205  [ DEG:    36.0613   -143.9388 ]
  Theta =   0.341714    2.799878  [ DEG:    19.5788    160.4212 ]
  Phi   =  -1.130698    2.010894  [ DEG:   -64.7842    115.2158 ]
 
# 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_2                                  
REMARK     2: T0300                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0300AL380_2.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   0.85    6.90  32.146
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL380_2
REMARK Aligment from pdb entry: 1debB
ATOM      1  N   THR     9      54.296 -16.911 -14.676  1.00  0.00              
ATOM      2  CA  THR     9      54.655 -15.647 -15.305  1.00  0.00              
ATOM      3  C   THR     9      54.434 -14.453 -14.379  1.00  0.00              
ATOM      4  O   THR     9      53.788 -14.563 -13.332  1.00  0.00              
ATOM      5  N   TYR    10      54.956 -13.301 -14.784  1.00  0.00              
ATOM      6  CA  TYR    10      54.808 -12.098 -13.993  1.00  0.00              
ATOM      7  C   TYR    10      53.373 -11.608 -13.983  1.00  0.00              
ATOM      8  O   TYR    10      52.814 -11.373 -12.919  1.00  0.00              
ATOM      9  N   GLU    11      52.754 -11.461 -15.150  1.00  0.00              
ATOM     10  CA  GLU    11      51.378 -10.983 -15.144  1.00  0.00              
ATOM     11  C   GLU    11      50.506 -12.017 -14.442  1.00  0.00              
ATOM     12  O   GLU    11      49.413 -11.710 -13.961  1.00  0.00              
ATOM     13  N   GLU    12      51.009 -13.243 -14.354  1.00  0.00              
ATOM     14  CA  GLU    12      50.275 -14.305 -13.696  1.00  0.00              
ATOM     15  C   GLU    12      50.344 -14.210 -12.185  1.00  0.00              
ATOM     16  O   GLU    12      49.359 -14.482 -11.506  1.00  0.00              
ATOM     17  N   MET    13      51.496 -13.837 -11.642  1.00  0.00              
ATOM     18  CA  MET    13      51.585 -13.688 -10.197  1.00  0.00              
ATOM     19  C   MET    13      50.653 -12.512  -9.931  1.00  0.00              
ATOM     20  O   MET    13      49.953 -12.447  -8.924  1.00  0.00              
ATOM     21  N   VAL    14      50.626 -11.608 -10.901  1.00  0.00              
ATOM     22  CA  VAL    14      49.826 -10.401 -10.860  1.00  0.00              
ATOM     23  C   VAL    14      48.308 -10.676 -10.820  1.00  0.00              
ATOM     24  O   VAL    14      47.583 -10.044 -10.042  1.00  0.00              
ATOM     25  N   LYS    15      47.827 -11.607 -11.653  1.00  0.00              
ATOM     26  CA  LYS    15      46.402 -11.980 -11.686  1.00  0.00              
ATOM     27  C   LYS    15      46.155 -12.723 -10.377  1.00  0.00              
ATOM     28  O   LYS    15      45.058 -12.682  -9.825  1.00  0.00              
ATOM     29  N   GLU    16      47.207 -13.357  -9.856  1.00  0.00              
ATOM     30  CA  GLU    16      47.097 -14.095  -8.596  1.00  0.00              
ATOM     31  C   GLU    16      46.966 -13.176  -7.381  1.00  0.00              
ATOM     32  O   GLU    16      46.241 -13.497  -6.449  1.00  0.00              
ATOM     33  N   VAL    17      47.651 -12.036  -7.373  1.00  0.00              
ATOM     34  CA  VAL    17      47.504 -11.140  -6.237  1.00  0.00              
ATOM     35  C   VAL    17      46.037 -10.723  -6.180  1.00  0.00              
ATOM     36  O   VAL    17      45.352 -10.953  -5.170  1.00  0.00              
ATOM     37  N   GLU    18      45.555 -10.167  -7.303  1.00  0.00              
ATOM     38  CA  GLU    18      44.157  -9.684  -7.442  1.00  0.00              
ATOM     39  C   GLU    18      43.133 -10.745  -7.028  1.00  0.00              
ATOM     40  O   GLU    18      42.157 -10.431  -6.341  1.00  0.00              
ATOM     41  N   ARG    19      43.315 -11.982  -7.480  1.00  0.00              
ATOM     42  CA  ARG    19      42.348 -13.045  -7.178  1.00  0.00              
ATOM     43  C   ARG    19      42.288 -13.310  -5.676  1.00  0.00              
ATOM     44  O   ARG    19      41.206 -13.366  -5.068  1.00  0.00              
ATOM     45  N   LEU    20      43.462 -13.501  -5.088  1.00  0.00              
ATOM     46  CA  LEU    20      43.562 -13.742  -3.663  1.00  0.00              
ATOM     47  C   LEU    20      43.019 -12.563  -2.864  1.00  0.00              
ATOM     48  O   LEU    20      42.353 -12.761  -1.851  1.00  0.00              
ATOM     49  N   LYS    21      43.297 -11.335  -3.302  1.00  0.00              
ATOM     50  CA  LYS    21      42.786 -10.183  -2.568  1.00  0.00              
ATOM     51  C   LYS    21      41.265 -10.167  -2.613  1.00  0.00              
ATOM     52  O   LYS    21      40.608  -9.887  -1.613  1.00  0.00              
ATOM     53  N   LEU    22      40.697 -10.486  -3.764  1.00  0.00              
ATOM     54  CA  LEU    22      39.241 -10.510  -3.884  1.00  0.00              
ATOM     55  C   LEU    22      38.678 -11.573  -2.938  1.00  0.00              
ATOM     56  O   LEU    22      37.754 -11.306  -2.162  1.00  0.00              
ATOM     57  N   GLU    23      39.242 -12.774  -2.986  1.00  0.00              
ATOM     58  CA  GLU    23      38.755 -13.833  -2.119  1.00  0.00              
ATOM     59  C   GLU    23      38.903 -13.496  -0.631  1.00  0.00              
ATOM     60  O   GLU    23      38.009 -13.763   0.141  1.00  0.00              
ATOM     61  N   ASN    24      40.024 -12.906  -0.230  1.00  0.00              
ATOM     62  CA  ASN    24      40.225 -12.564   1.186  1.00  0.00              
ATOM     63  C   ASN    24      39.179 -11.570   1.623  1.00  0.00              
ATOM     64  O   ASN    24      38.654 -11.634   2.732  1.00  0.00              
ATOM     65  N   LYS    25      38.874 -10.652   0.719  1.00  0.00              
ATOM     66  CA  LYS    25      37.870  -9.640   0.974  1.00  0.00              
ATOM     67  C   LYS    25      36.486 -10.277   1.222  1.00  0.00              
ATOM     68  O   LYS    25      35.778  -9.866   2.128  1.00  0.00              
ATOM     69  N   THR    26      36.115 -11.292   0.439  1.00  0.00              
ATOM     70  CA  THR    26      34.817 -11.944   0.600  1.00  0.00              
ATOM     71  C   THR    26      34.776 -12.750   1.879  1.00  0.00              
ATOM     72  O   THR    26      33.741 -12.839   2.551  1.00  0.00              
ATOM     73  N   LEU    27      35.898 -13.365   2.214  1.00  0.00              
ATOM     74  CA  LEU    27      35.932 -14.158   3.419  1.00  0.00              
ATOM     75  C   LEU    27      35.723 -13.226   4.610  1.00  0.00              
ATOM     76  O   LEU    27      34.952 -13.553   5.508  1.00  0.00              
ATOM     77  N   LYS    28      36.370 -12.061   4.606  1.00  0.00              
ATOM     78  CA  LYS    28      36.202 -11.112   5.712  1.00  0.00              
ATOM     79  C   LYS    28      34.747 -10.701   5.861  1.00  0.00              
ATOM     80  O   LYS    28      34.226 -10.655   6.976  1.00  0.00              
ATOM     81  N   GLN    29      34.094 -10.411   4.741  1.00  0.00              
ATOM     82  CA  GLN    29      32.691 -10.024   4.791  1.00  0.00              
ATOM     83  C   GLN    29      31.858 -11.176   5.385  1.00  0.00              
ATOM     84  O   GLN    29      30.906 -10.945   6.160  1.00  0.00              
ATOM     85  N   LYS    30      32.226 -12.407   5.021  1.00  0.00              
ATOM     86  CA  LYS    30      31.516 -13.593   5.509  1.00  0.00              
ATOM     87  C   LYS    30      31.746 -13.786   7.000  1.00  0.00              
ATOM     88  O   LYS    30      30.829 -14.178   7.717  1.00  0.00              
ATOM     89  N   VAL    31      32.971 -13.511   7.458  1.00  0.00              
ATOM     90  CA  VAL    31      33.294 -13.639   8.878  1.00  0.00              
ATOM     91  C   VAL    31      32.469 -12.586   9.613  1.00  0.00              
ATOM     92  O   VAL    31      31.979 -12.842  10.707  1.00  0.00              
ATOM     93  N   LYS    32      32.303 -11.411   9.004  1.00  0.00              
ATOM     94  CA  LYS    32      31.492 -10.366   9.623  1.00  0.00              
ATOM     95  C   LYS    32      30.018 -10.783   9.680  1.00  0.00              
ATOM     96  O   LYS    32      29.409 -10.751  10.749  1.00  0.00              
ATOM     97  N   SER    33      29.442 -11.182   8.544  1.00  0.00              
ATOM     98  CA  SER    33      28.045 -11.598   8.559  1.00  0.00              
ATOM     99  C   SER    33      27.899 -12.693   9.610  1.00  0.00              
ATOM    100  O   SER    33      27.000 -12.640  10.441  1.00  0.00              
ATOM    101  N   SER    34      28.808 -13.662   9.599  1.00  0.00              
ATOM    102  CA  SER    34      28.748 -14.745  10.566  1.00  0.00              
ATOM    103  C   SER    34      28.843 -14.224  11.990  1.00  0.00              
ATOM    104  O   SER    34      28.171 -14.724  12.882  1.00  0.00              
ATOM    105  N   GLY    35      29.673 -13.214  12.212  1.00  0.00              
ATOM    106  CA  GLY    35      29.840 -12.650  13.552  1.00  0.00              
ATOM    107  C   GLY    35      28.497 -12.155  14.119  1.00  0.00              
ATOM    108  O   GLY    35      28.151 -12.434  15.270  1.00  0.00              
ATOM    109  N   ALA    36      27.749 -11.423  13.295  1.00  0.00              
ATOM    110  CA  ALA    36      26.446 -10.886  13.674  1.00  0.00              
ATOM    111  C   ALA    36      25.480 -11.953  14.127  1.00  0.00              
ATOM    112  O   ALA    36      24.749 -11.765  15.104  1.00  0.00              
ATOM    113  N   VAL    37      25.459 -13.072  13.416  1.00  0.00              
ATOM    114  CA  VAL    37      24.552 -14.151  13.776  1.00  0.00              
ATOM    115  C   VAL    37      25.012 -14.815  15.071  1.00  0.00              
ATOM    116  O   VAL    37      24.182 -15.158  15.926  1.00  0.00              
END
