
#######################################################
#                                                     #
#                        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 T0311AL333_5-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311AL333_5-D1.T0311_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R       8           -
LGA    -       -      P       9           -
LGA    -       -      G      10           -
LGA    -       -      D      11           -
LGA    -       -      I      12           -
LGA    I      13      I      13          1.790
LGA    Q      14      Q      14          1.248
LGA    E      15      E      15          1.889
LGA    S      16      S      16          3.263
LGA    L      17      L      17          3.258
LGA    D      18      D      18          2.815
LGA    -       -      E      19           -
LGA    -       -      L      20           -
LGA    E      19      N      21          2.510
LGA    L      20      V      22          0.407
LGA    N      21      S      23          0.384
LGA    L      24      L      24          0.443
LGA    R      25      R      25          0.947
LGA    E      26      E      26          0.699
LGA    F      27      F      27          0.403
LGA    A      28      A      28          0.640
LGA    R      29      R      29          0.688
LGA    A      30      A      30          0.697
LGA    M      31      M      31          0.738
LGA    E      32      E      32          0.516
LGA    I      33      I      33          0.381
LGA    A      34      A      34          0.547
LGA    P      35      P      35          0.884
LGA    S      36      S      36          1.135
LGA    T      37      T      37          1.146
LGA    A      38      A      38          1.370
LGA    S      39      S      39          1.152
LGA    R      40      R      40          1.119
LGA    N      69      L      41          1.265
LGA    L      70      L      42          1.463
LGA    Q      71      T      43          1.164
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    -       -      A      46           -
LGA    -       -      A      47           -
LGA    -       -      L      48           -
LGA    -       -      T      49           -
LGA    -       -      P      50           -
LGA    -       -      E      51           -
LGA    -       -      M      52           -
LGA    -       -      A      53           -
LGA    -       -      I      54           -
LGA    -       -      K      55           -
LGA    -       -      L      56           -
LGA    -       -      S      57           -
LGA    -       -      V      58           -
LGA    -       -      V      59           -
LGA    -       -      I      60           -
LGA    -       -      G      61           -
LGA    -       -      S      62           -
LGA    -       -      S      63           -
LGA    -       -      P      64           -
LGA    -       -      Q      65           -
LGA    -       -      M      66           -
LGA    -       -      W      67           -
LGA    -       -      L      68           -
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      Q      71           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29   64    5.0     29    1.46    82.76     42.982     1.864

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.817365 * X  +   0.508901 * Y  +   0.270064 * Z  +   3.869580
  Y_new =   0.420931 * X  +  -0.847573 * Y  +   0.323168 * Z  +  15.524394
  Z_new =   0.393360 * X  +  -0.150468 * Y  +  -0.906988 * Z  +  20.494776 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.977191    0.164401  [ DEG:  -170.5805      9.4195 ]
  Theta =  -0.404283   -2.737310  [ DEG:   -23.1637   -156.8363 ]
  Phi   =   0.475564   -2.666029  [ DEG:    27.2478   -152.7522 ]
 
# 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: T0311AL333_5-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311AL333_5-D1.T0311_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29   64   5.0   29   1.46   82.76  42.982
REMARK  ---------------------------------------------------------- 
MOLECULE T0311AL333_5-D1
REMARK Aligment from pdb entry: 1d1l_A
ATOM     25  N   ILE    13      31.547   3.295  12.060  1.00  0.00              
ATOM     26  CA  ILE    13      30.835   2.053  12.443  1.00  0.00              
ATOM     27  C   ILE    13      30.746   1.910  13.982  1.00  0.00              
ATOM     28  O   ILE    13      29.670   1.770  14.610  1.00  0.00              
ATOM     29  N   GLN    14      31.892   2.022  14.632  1.00  0.00              
ATOM     30  CA  GLN    14      31.958   1.949  16.094  1.00  0.00              
ATOM     31  C   GLN    14      31.032   2.939  16.811  1.00  0.00              
ATOM     32  O   GLN    14      30.292   2.567  17.702  1.00  0.00              
ATOM     33  N   GLU    15      31.055   4.224  16.481  1.00  0.00              
ATOM     34  CA  GLU    15      30.171   5.142  17.197  1.00  0.00              
ATOM     35  C   GLU    15      28.716   4.817  16.927  1.00  0.00              
ATOM     36  O   GLU    15      27.851   5.014  17.753  1.00  0.00              
ATOM     37  N   SER    16      28.436   4.456  15.675  1.00  0.00              
ATOM     38  CA  SER    16      27.051   4.153  15.299  1.00  0.00              
ATOM     39  C   SER    16      26.526   2.972  16.148  1.00  0.00              
ATOM     40  O   SER    16      25.449   3.015  16.712  1.00  0.00              
ATOM     41  N   LEU    17      27.289   1.867  16.161  1.00  0.00              
ATOM     42  CA  LEU    17      26.867   0.677  16.910  1.00  0.00              
ATOM     43  C   LEU    17      26.699   0.968  18.383  1.00  0.00              
ATOM     44  O   LEU    17      25.790   0.453  19.039  1.00  0.00              
ATOM     45  N   ASP    18      27.605   1.812  18.904  1.00  0.00              
ATOM     46  CA  ASP    18      27.588   2.183  20.310  1.00  0.00              
ATOM     47  C   ASP    18      26.337   2.974  20.682  1.00  0.00              
ATOM     48  O   ASP    18      25.611   2.705  21.643  1.00  0.00              
ATOM     49  N   GLU    19      25.974   3.904  19.842  1.00  0.00              
ATOM     50  CA  GLU    19      24.768   4.609  20.140  1.00  0.00              
ATOM     51  C   GLU    19      23.507   3.840  19.851  1.00  0.00              
ATOM     52  O   GLU    19      22.562   3.980  20.610  1.00  0.00              
ATOM     53  N   LEU    20      23.418   3.111  18.718  1.00  0.00              
ATOM     54  CA  LEU    20      22.216   2.326  18.397  1.00  0.00              
ATOM     55  C   LEU    20      22.193   0.827  18.740  1.00  0.00              
ATOM     56  O   LEU    20      21.184   0.156  18.641  1.00  0.00              
ATOM     57  N   ASN    21      23.274   0.210  19.104  1.00  0.00              
ATOM     58  CA  ASN    21      23.136  -1.218  19.351  1.00  0.00              
ATOM     59  C   ASN    21      23.526  -2.052  18.127  1.00  0.00              
ATOM     60  O   ASN    21      23.193  -1.730  17.012  1.00  0.00              
ATOM     61  N   LEU    24      24.227  -3.133  18.352  1.00  0.00              
ATOM     62  CA  LEU    24      24.686  -4.009  17.276  1.00  0.00              
ATOM     63  C   LEU    24      23.547  -4.560  16.449  1.00  0.00              
ATOM     64  O   LEU    24      23.599  -4.725  15.231  1.00  0.00              
ATOM     65  N   ARG    25      22.472  -4.833  17.136  1.00  0.00              
ATOM     66  CA  ARG    25      21.372  -5.414  16.449  1.00  0.00              
ATOM     67  C   ARG    25      20.792  -4.495  15.382  1.00  0.00              
ATOM     68  O   ARG    25      20.549  -4.833  14.207  1.00  0.00              
ATOM     69  N   GLU    26      20.496  -3.308  15.822  1.00  0.00              
ATOM     70  CA  GLU    26      19.921  -2.379  14.883  1.00  0.00              
ATOM     71  C   GLU    26      20.895  -2.050  13.758  1.00  0.00              
ATOM     72  O   GLU    26      20.543  -1.759  12.622  1.00  0.00              
ATOM     73  N   PHE    27      22.169  -2.026  14.092  1.00  0.00              
ATOM     74  CA  PHE    27      23.153  -1.728  13.052  1.00  0.00              
ATOM     75  C   PHE    27      23.106  -2.803  11.946  1.00  0.00              
ATOM     76  O   PHE    27      23.119  -2.536  10.722  1.00  0.00              
ATOM     77  N   ALA    28      23.084  -4.073  12.408  1.00  0.00              
ATOM     78  CA  ALA    28      23.108  -5.225  11.463  1.00  0.00              
ATOM     79  C   ALA    28      21.896  -5.152  10.533  1.00  0.00              
ATOM     80  O   ALA    28      21.882  -5.300   9.291  1.00  0.00              
ATOM     81  N   ARG    29      20.804  -4.929  11.215  1.00  0.00              
ATOM     82  CA  ARG    29      19.563  -4.812  10.530  1.00  0.00              
ATOM     83  C   ARG    29      19.572  -3.668   9.535  1.00  0.00              
ATOM     84  O   ARG    29      19.220  -3.897   8.419  1.00  0.00              
ATOM     85  N   ALA    30      19.998  -2.457   9.958  1.00  0.00              
ATOM     86  CA  ALA    30      20.145  -1.275   9.124  1.00  0.00              
ATOM     87  C   ALA    30      20.997  -1.559   7.897  1.00  0.00              
ATOM     88  O   ALA    30      20.718  -1.106   6.800  1.00  0.00              
ATOM     89  N   MET    31      22.064  -2.315   8.064  1.00  0.00              
ATOM     90  CA  MET    31      22.909  -2.593   6.901  1.00  0.00              
ATOM     91  C   MET    31      22.524  -3.899   6.190  1.00  0.00              
ATOM     92  O   MET    31      23.050  -4.231   5.137  1.00  0.00              
ATOM     93  N   GLU    32      21.691  -4.700   6.826  1.00  0.00              
ATOM     94  CA  GLU    32      21.368  -5.974   6.246  1.00  0.00              
ATOM     95  C   GLU    32      22.511  -6.985   6.306  1.00  0.00              
ATOM     96  O   GLU    32      22.562  -7.839   5.442  1.00  0.00              
ATOM     97  N   ILE    33      23.438  -6.922   7.298  1.00  0.00              
ATOM     98  CA  ILE    33      24.511  -7.907   7.377  1.00  0.00              
ATOM     99  C   ILE    33      24.265  -8.912   8.487  1.00  0.00              
ATOM    100  O   ILE    33      23.379  -8.743   9.318  1.00  0.00              
ATOM    101  N   ALA    34      25.023 -10.004   8.457  1.00  0.00              
ATOM    102  CA  ALA    34      24.950 -11.016   9.498  1.00  0.00              
ATOM    103  C   ALA    34      25.552 -10.369  10.736  1.00  0.00              
ATOM    104  O   ALA    34      26.681  -9.821  10.687  1.00  0.00              
ATOM    105  N   PRO    35      24.812 -10.383  11.828  1.00  0.00              
ATOM    106  CA  PRO    35      25.167  -9.621  13.033  1.00  0.00              
ATOM    107  C   PRO    35      26.580  -9.688  13.512  1.00  0.00              
ATOM    108  O   PRO    35      27.151  -8.686  13.988  1.00  0.00              
ATOM    109  N   SER    36      27.147 -10.895  13.447  1.00  0.00              
ATOM    110  CA  SER    36      28.461 -11.034  14.041  1.00  0.00              
ATOM    111  C   SER    36      29.558 -10.335  13.247  1.00  0.00              
ATOM    112  O   SER    36      30.627 -10.004  13.782  1.00  0.00              
ATOM    113  N   THR    37      29.287 -10.039  11.986  1.00  0.00              
ATOM    114  CA  THR    37      30.244  -9.294  11.148  1.00  0.00              
ATOM    115  C   THR    37      30.546  -7.899  11.684  1.00  0.00              
ATOM    116  O   THR    37      31.614  -7.351  11.482  1.00  0.00              
ATOM    117  N   ALA    38      29.568  -7.313  12.356  1.00  0.00              
ATOM    118  CA  ALA    38      29.684  -5.991  12.944  1.00  0.00              
ATOM    119  C   ALA    38      30.774  -5.987  14.016  1.00  0.00              
ATOM    120  O   ALA    38      31.763  -5.243  14.034  1.00  0.00              
ATOM    121  N   SER    39      30.551  -6.904  14.935  1.00  0.00              
ATOM    122  CA  SER    39      31.408  -7.082  16.063  1.00  0.00              
ATOM    123  C   SER    39      32.855  -7.336  15.622  1.00  0.00              
ATOM    124  O   SER    39      33.825  -6.739  16.061  1.00  0.00              
ATOM    125  N   ARG    40      33.024  -8.229  14.687  1.00  0.00              
ATOM    126  CA  ARG    40      34.342  -8.476  14.148  1.00  0.00              
ATOM    127  C   ARG    40      35.005  -7.275  13.440  1.00  0.00              
ATOM    128  O   ARG    40      36.217  -7.161  13.469  1.00  0.00              
ATOM    129  N   ASN    69      34.263  -6.419  12.725  1.00  0.00              
ATOM    130  CA  ASN    69      34.891  -5.309  12.007  1.00  0.00              
ATOM    131  C   ASN    69      35.402  -4.259  12.989  1.00  0.00              
ATOM    132  O   ASN    69      36.459  -3.644  12.822  1.00  0.00              
ATOM    133  N   LEU    70      34.614  -4.084  14.039  1.00  0.00              
ATOM    134  CA  LEU    70      34.946  -3.176  15.133  1.00  0.00              
ATOM    135  C   LEU    70      36.252  -3.629  15.827  1.00  0.00              
ATOM    136  O   LEU    70      37.320  -2.998  15.720  1.00  0.00              
ATOM    137  N   GLN    71      36.154  -4.789  16.482  1.00  0.00              
ATOM    138  CA  GLN    71      37.261  -5.369  17.180  1.00  0.00              
ATOM    139  C   GLN    71      38.500  -5.405  16.313  1.00  0.00              
ATOM    140  O   GLN    71      39.591  -5.318  16.835  1.00  0.00              
END
