
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0363AL509_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL509_1-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    I      13      I      13          1.804
LGA    N      14      N      14          0.745
LGA    I      15      I      15          0.782
LGA    E      16      E      16          1.600
LGA    I      17      I      17          1.487
LGA    A      18      A      18          1.471
LGA    Y      19      Y      19          1.979
LGA    F      21      A      20          0.828
LGA    P      22      F      21          1.781
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    L      27      L      27          0.928
LGA    K      28      K      28          0.833
LGA    S      29      S      29          0.423
LGA    F      30      F      30          1.171
LGA    Q      31      Q      31          1.237
LGA    V      32      V      32          1.131
LGA    D      33      D      33          0.512
LGA    E      34      E      34          1.468
LGA    G      35      G      35          0.433
LGA    I      36      I      36          0.810
LGA    T      37      T      37          0.449
LGA    V      38      V      38          0.661
LGA    Q      39      Q      39          1.435
LGA    T      40      T      40          1.145
LGA    A      41      A      41          0.524
LGA    I      42      I      42          1.530
LGA    T      43      T      43          1.879
LGA    Q      44      Q      44          1.420
LGA    S      45      S      45          1.728
LGA    -       -      G      46           -
LGA    -       -      I      47           -
LGA    -       -      L      48           -
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28   46    5.0     28    1.25    92.86     57.494     2.080

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.588951 * X  +  -0.794071 * Y  +  -0.150293 * Z  +  45.830715
  Y_new =   0.727123 * X  +   0.439475 * Y  +   0.527403 * Z  + -27.458563
  Z_new =  -0.352746 * X  +  -0.419896 * Y  +   0.836217 * Z  +  35.909832 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.465356    2.676237  [ DEG:   -26.6629    153.3371 ]
  Theta =   0.360504    2.781089  [ DEG:    20.6554    159.3447 ]
  Phi   =   0.890003   -2.251590  [ DEG:    50.9934   -129.0066 ]
 
# 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: T0363AL509_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL509_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28   46   5.0   28   1.25   92.86  57.494
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL509_1-D1
REMARK Aligment from pdb entry: 1vjkA_
ATOM      1  N   ILE    13      18.434   5.308   8.994  1.00  0.00              
ATOM      2  CA  ILE    13      18.311   6.750   9.221  1.00  0.00              
ATOM      3  C   ILE    13      18.779   7.427   7.920  1.00  0.00              
ATOM      4  O   ILE    13      19.928   7.230   7.514  1.00  0.00              
ATOM      5  N   ASN    14      17.903   8.188   7.265  1.00  0.00              
ATOM      6  CA  ASN    14      18.273   8.853   6.023  1.00  0.00              
ATOM      7  C   ASN    14      18.480  10.326   6.282  1.00  0.00              
ATOM      8  O   ASN    14      17.545  11.022   6.739  1.00  0.00              
ATOM      9  N   ILE    15      19.686  10.809   6.017  1.00  0.00              
ATOM     10  CA  ILE    15      20.009  12.216   6.234  1.00  0.00              
ATOM     11  C   ILE    15      20.260  12.893   4.903  1.00  0.00              
ATOM     12  O   ILE    15      20.685  12.248   3.915  1.00  0.00              
ATOM     13  N   GLU    16      20.003  14.182   4.841  1.00  0.00              
ATOM     14  CA  GLU    16      20.250  14.980   3.667  1.00  0.00              
ATOM     15  C   GLU    16      21.535  15.724   3.902  1.00  0.00              
ATOM     16  O   GLU    16      21.611  16.556   4.818  1.00  0.00              
ATOM     17  N   ILE    17      22.547  15.455   3.100  1.00  0.00              
ATOM     18  CA  ILE    17      23.832  16.127   3.204  1.00  0.00              
ATOM     19  C   ILE    17      23.916  17.245   2.195  1.00  0.00              
ATOM     20  O   ILE    17      23.665  17.008   1.012  1.00  0.00              
ATOM     21  N   ALA    18      24.232  18.461   2.658  1.00  0.00              
ATOM     22  CA  ALA    18      24.383  19.617   1.769  1.00  0.00              
ATOM     23  C   ALA    18      25.839  20.024   1.788  1.00  0.00              
ATOM     24  O   ALA    18      26.394  20.351   2.852  1.00  0.00              
ATOM     25  N   TYR    19      26.466  20.002   0.623  1.00  0.00              
ATOM     26  CA  TYR    19      27.859  20.430   0.479  1.00  0.00              
ATOM     27  C   TYR    19      27.923  21.871   0.065  1.00  0.00              
ATOM     28  O   TYR    19      27.074  22.353  -0.705  1.00  0.00              
ATOM     29  N   PHE    21      28.968  22.553   0.549  1.00  0.00              
ATOM     30  CA  PHE    21      29.159  23.960   0.257  1.00  0.00              
ATOM     31  C   PHE    21      30.508  24.247  -0.343  1.00  0.00              
ATOM     32  O   PHE    21      31.492  23.573  -0.047  1.00  0.00              
ATOM     33  N   PRO    22      30.553  25.294  -1.166  1.00  0.00              
ATOM     34  CA  PRO    22      31.805  25.822  -1.700  1.00  0.00              
ATOM     35  C   PRO    22      32.615  24.703  -2.374  1.00  0.00              
ATOM     36  O   PRO    22      32.051  23.953  -3.181  1.00  0.00              
ATOM     37  N   LEU    27      24.162  18.210  -3.091  1.00  0.00              
ATOM     38  CA  LEU    27      23.505  17.562  -1.966  1.00  0.00              
ATOM     39  C   LEU    27      23.305  16.108  -2.286  1.00  0.00              
ATOM     40  O   LEU    27      23.291  15.708  -3.455  1.00  0.00              
ATOM     41  N   LYS    28      23.143  15.302  -1.244  1.00  0.00              
ATOM     42  CA  LYS    28      22.908  13.882  -1.410  1.00  0.00              
ATOM     43  C   LYS    28      22.257  13.308  -0.184  1.00  0.00              
ATOM     44  O   LYS    28      22.526  13.758   0.937  1.00  0.00              
ATOM     45  N   SER    29      21.385  12.341  -0.385  1.00  0.00              
ATOM     46  CA  SER    29      20.769  11.608   0.692  1.00  0.00              
ATOM     47  C   SER    29      21.623  10.432   1.053  1.00  0.00              
ATOM     48  O   SER    29      21.999   9.632   0.169  1.00  0.00              
ATOM     49  N   PHE    30      21.905  10.263   2.333  1.00  0.00              
ATOM     50  CA  PHE    30      22.721   9.163   2.787  1.00  0.00              
ATOM     51  C   PHE    30      21.961   8.341   3.815  1.00  0.00              
ATOM     52  O   PHE    30      21.585   8.837   4.896  1.00  0.00              
ATOM     53  N   GLN    31      21.703   7.090   3.472  1.00  0.00              
ATOM     54  CA  GLN    31      21.061   6.141   4.371  1.00  0.00              
ATOM     55  C   GLN    31      22.126   5.510   5.266  1.00  0.00              
ATOM     56  O   GLN    31      23.149   5.018   4.782  1.00  0.00              
ATOM     57  N   VAL    32      21.881   5.551   6.574  1.00  0.00              
ATOM     58  CA  VAL    32      22.814   5.079   7.572  1.00  0.00              
ATOM     59  C   VAL    32      22.122   4.058   8.455  1.00  0.00              
ATOM     60  O   VAL    32      20.910   4.107   8.602  1.00  0.00              
ATOM     61  N   ASP    33      22.868   3.118   9.044  1.00  0.00              
ATOM     62  CA  ASP    33      22.265   2.143   9.949  1.00  0.00              
ATOM     63  C   ASP    33      21.737   2.788  11.221  1.00  0.00              
ATOM     64  O   ASP    33      22.202   3.853  11.643  1.00  0.00              
ATOM     65  N   GLU    34      20.760   2.123  11.821  1.00  0.00              
ATOM     66  CA  GLU    34      20.248   2.480  13.126  1.00  0.00              
ATOM     67  C   GLU    34      21.396   2.807  14.087  1.00  0.00              
ATOM     68  O   GLU    34      22.392   2.091  14.137  1.00  0.00              
ATOM     69  N   GLY    35      21.241   3.906  14.824  1.00  0.00              
ATOM     70  CA  GLY    35      22.215   4.305  15.832  1.00  0.00              
ATOM     71  C   GLY    35      23.349   5.151  15.283  1.00  0.00              
ATOM     72  O   GLY    35      24.276   5.526  16.022  1.00  0.00              
ATOM     73  N   ILE    36      23.299   5.464  13.996  1.00  0.00              
ATOM     74  CA  ILE    36      24.380   6.223  13.393  1.00  0.00              
ATOM     75  C   ILE    36      24.611   7.535  14.078  1.00  0.00              
ATOM     76  O   ILE    36      23.666   8.240  14.470  1.00  0.00              
ATOM     77  N   THR    37      25.895   7.871  14.182  1.00  0.00              
ATOM     78  CA  THR    37      26.350   9.114  14.774  1.00  0.00              
ATOM     79  C   THR    37      27.003  10.003  13.718  1.00  0.00              
ATOM     80  O   THR    37      27.362   9.549  12.620  1.00  0.00              
ATOM     81  N   VAL    38      27.217  11.272  14.045  1.00  0.00              
ATOM     82  CA  VAL    38      27.927  12.179  13.142  1.00  0.00              
ATOM     83  C   VAL    38      29.250  11.571  12.635  1.00  0.00              
ATOM     84  O   VAL    38      29.554  11.625  11.422  1.00  0.00              
ATOM     85  N   GLN    39      30.032  10.953  13.531  1.00  0.00              
ATOM     86  CA  GLN    39      31.298  10.371  13.080  1.00  0.00              
ATOM     87  C   GLN    39      31.097   9.273  12.004  1.00  0.00              
ATOM     88  O   GLN    39      31.945   9.110  11.111  1.00  0.00              
ATOM     89  N   THR    40      29.989   8.529  12.095  1.00  0.00              
ATOM     90  CA  THR    40      29.713   7.468  11.099  1.00  0.00              
ATOM     91  C   THR    40      29.369   8.089   9.779  1.00  0.00              
ATOM     92  O   THR    40      29.779   7.574   8.730  1.00  0.00              
ATOM     93  N   ALA    41      28.643   9.194   9.808  1.00  0.00              
ATOM     94  CA  ALA    41      28.332   9.909   8.570  1.00  0.00              
ATOM     95  C   ALA    41      29.601  10.450   7.900  1.00  0.00              
ATOM     96  O   ALA    41      29.758  10.311   6.673  1.00  0.00              
ATOM     97  N   ILE    42      30.519  11.008   8.689  1.00  0.00              
ATOM     98  CA  ILE    42      31.777  11.492   8.136  1.00  0.00              
ATOM     99  C   ILE    42      32.530  10.346   7.465  1.00  0.00              
ATOM    100  O   ILE    42      33.061  10.504   6.335  1.00  0.00              
ATOM    101  N   THR    43      32.586   9.173   8.119  1.00  0.00              
ATOM    102  CA  THR    43      33.238   8.031   7.467  1.00  0.00              
ATOM    103  C   THR    43      32.574   7.604   6.179  1.00  0.00              
ATOM    104  O   THR    43      33.274   7.201   5.224  1.00  0.00              
ATOM    105  N   GLN    44      31.253   7.685   6.122  1.00  0.00              
ATOM    106  CA  GLN    44      30.545   7.320   4.910  1.00  0.00              
ATOM    107  C   GLN    44      30.795   8.337   3.796  1.00  0.00              
ATOM    108  O   GLN    44      30.928   7.933   2.634  1.00  0.00              
ATOM    109  N   SER    45      30.882   9.641   4.121  1.00  0.00              
ATOM    110  CA  SER    45      31.211  10.645   3.101  1.00  0.00              
ATOM    111  C   SER    45      32.575  10.331   2.485  1.00  0.00              
ATOM    112  O   SER    45      32.724  10.349   1.244  1.00  0.00              
END
