
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0300AL381_2
# Molecule2: number of CA atoms   89 (  695),  selected   89 , name T0300
# PARAMETERS: T0300AL381_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          2.406
LGA    Y      10      A      47          1.507
LGA    E      11      K      48          1.510
LGA    E      12      R      49          1.168
LGA    M      13      E      50          1.329
LGA    V      14      S      51          0.896
LGA    K      15      I      52          0.183
LGA    E      16      I      53          0.599
LGA    V      17      V      54          1.426
LGA    E      18      S      55          1.552
LGA    R      19      S      56          0.998
LGA    L      20      S      57          0.725
LGA    K      21      R      58          1.254
LGA    L      22      A      59          1.271
LGA    E      23      L      60          0.437
LGA    N      24      G      61          0.265
LGA    K      25      A      62          0.376
LGA    T      26      V      63          0.718
LGA    L      27      A      64          1.245
LGA    K      28      M      65          0.235
LGA    Q      29      R      66          0.971
LGA    K      30      K      67          1.372
LGA    V      31      I      68          0.914
LGA    K      32      E      69          0.557
LGA    S      33      A      70          1.002
LGA    S      34      K      71          0.811
LGA    G      35      V      72          1.458
LGA    A      36      R      73          1.539
LGA    -       -      S      74           -
LGA    V      37      R      75          3.093
LGA    E     101      A      76          4.394
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)   30   89    5.0     30    1.48     6.67     31.958     1.904

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.780378 * X  +   0.475020 * Y  +   0.406653 * Z  +  41.686489
  Y_new =  -0.223105 * X  +  -0.819035 * Y  +   0.528588 * Z  + -14.476289
  Z_new =   0.584152 * X  +   0.321772 * Y  +   0.745137 * Z  +   0.917737 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.407641   -2.733951  [ DEG:    23.3561   -156.6439 ]
  Theta =  -0.623835   -2.517757  [ DEG:   -35.7431   -144.2569 ]
  Phi   =  -2.863127    0.278465  [ DEG:  -164.0451     15.9549 ]
 
# 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: T0300AL381_2                                  
REMARK     2: T0300                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0300AL381_2.T0300 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30   89   5.0   30   1.48    6.67  31.958
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL381_2
REMARK Aligment from pdb entry: 1u2uA
ATOM      1  N   THR     9      56.807 -16.235 -12.667  1.00  0.00              
ATOM      2  CA  THR     9      55.426 -16.023 -12.245  1.00  0.00              
ATOM      3  C   THR     9      55.126 -14.543 -12.033  1.00  0.00              
ATOM      4  O   THR     9      54.203 -14.184 -11.300  1.00  0.00              
ATOM      5  N   TYR    10      55.909 -13.692 -12.677  1.00  0.00              
ATOM      6  CA  TYR    10      55.737 -12.253 -12.568  1.00  0.00              
ATOM      7  C   TYR    10      54.401 -11.819 -13.146  1.00  0.00              
ATOM      8  O   TYR    10      53.716 -10.959 -12.591  1.00  0.00              
ATOM      9  N   GLU    11      54.019 -12.444 -14.240  1.00  0.00              
ATOM     10  CA  GLU    11      52.752 -12.155 -14.872  1.00  0.00              
ATOM     11  C   GLU    11      51.645 -12.944 -14.181  1.00  0.00              
ATOM     12  O   GLU    11      50.463 -12.776 -14.477  1.00  0.00              
ATOM     13  N   GLU    12      52.050 -13.801 -13.242  1.00  0.00              
ATOM     14  CA  GLU    12      51.119 -14.616 -12.485  1.00  0.00              
ATOM     15  C   GLU    12      50.680 -13.890 -11.220  1.00  0.00              
ATOM     16  O   GLU    12      49.504 -13.927 -10.859  1.00  0.00              
ATOM     17  N   MET    13      51.619 -13.216 -10.545  1.00  0.00              
ATOM     18  CA  MET    13      51.271 -12.484  -9.332  1.00  0.00              
ATOM     19  C   MET    13      50.207 -11.445  -9.642  1.00  0.00              
ATOM     20  O   MET    13      49.231 -11.300  -8.906  1.00  0.00              
ATOM     21  N   VAL    14      50.404 -10.724 -10.742  1.00  0.00              
ATOM     22  CA  VAL    14      49.455  -9.695 -11.154  1.00  0.00              
ATOM     23  C   VAL    14      48.039 -10.253 -11.180  1.00  0.00              
ATOM     24  O   VAL    14      47.066  -9.523 -10.997  1.00  0.00              
ATOM     25  N   LYS    15      47.938 -11.558 -11.403  1.00  0.00              
ATOM     26  CA  LYS    15      46.648 -12.226 -11.447  1.00  0.00              
ATOM     27  C   LYS    15      46.385 -12.967 -10.139  1.00  0.00              
ATOM     28  O   LYS    15      45.235 -13.202  -9.767  1.00  0.00              
ATOM     29  N   GLU    16      47.460 -13.327  -9.441  1.00  0.00              
ATOM     30  CA  GLU    16      47.346 -14.035  -8.172  1.00  0.00              
ATOM     31  C   GLU    16      46.751 -13.132  -7.096  1.00  0.00              
ATOM     32  O   GLU    16      46.190 -13.614  -6.112  1.00  0.00              
ATOM     33  N   VAL    17      46.869 -11.821  -7.291  1.00  0.00              
ATOM     34  CA  VAL    17      46.335 -10.860  -6.334  1.00  0.00              
ATOM     35  C   VAL    17      44.839 -10.672  -6.555  1.00  0.00              
ATOM     36  O   VAL    17      44.039 -10.851  -5.637  1.00  0.00              
ATOM     37  N   GLU    18      44.464 -10.330  -7.784  1.00  0.00              
ATOM     38  CA  GLU    18      43.061 -10.141  -8.124  1.00  0.00              
ATOM     39  C   GLU    18      42.260 -11.401  -7.808  1.00  0.00              
ATOM     40  O   GLU    18      41.050 -11.345  -7.592  1.00  0.00              
ATOM     41  N   ARG    19      42.953 -12.538  -7.778  1.00  0.00              
ATOM     42  CA  ARG    19      42.320 -13.816  -7.482  1.00  0.00              
ATOM     43  C   ARG    19      41.851 -13.859  -6.030  1.00  0.00              
ATOM     44  O   ARG    19      40.677 -14.104  -5.755  1.00  0.00              
ATOM     45  N   LEU    20      42.775 -13.614  -5.103  1.00  0.00              
ATOM     46  CA  LEU    20      42.445 -13.622  -3.684  1.00  0.00              
ATOM     47  C   LEU    20      41.710 -12.348  -3.292  1.00  0.00              
ATOM     48  O   LEU    20      40.696 -12.395  -2.602  1.00  0.00              
ATOM     49  N   LYS    21      42.224 -11.204  -3.738  1.00  0.00              
ATOM     50  CA  LYS    21      41.604  -9.918  -3.429  1.00  0.00              
ATOM     51  C   LYS    21      40.102  -9.958  -3.696  1.00  0.00              
ATOM     52  O   LYS    21      39.329  -9.244  -3.059  1.00  0.00              
ATOM     53  N   LEU    22      39.695 -10.806  -4.638  1.00  0.00              
ATOM     54  CA  LEU    22      38.286 -10.948  -4.981  1.00  0.00              
ATOM     55  C   LEU    22      37.588 -11.893  -4.008  1.00  0.00              
ATOM     56  O   LEU    22      36.409 -11.721  -3.699  1.00  0.00              
ATOM     57  N   GLU    23      38.328 -12.887  -3.523  1.00  0.00              
ATOM     58  CA  GLU    23      37.786 -13.858  -2.579  1.00  0.00              
ATOM     59  C   GLU    23      37.950 -13.361  -1.147  1.00  0.00              
ATOM     60  O   GLU    23      36.973 -13.229  -0.409  1.00  0.00              
ATOM     61  N   ASN    24      39.193 -13.077  -0.765  1.00  0.00              
ATOM     62  CA  ASN    24      39.495 -12.583   0.574  1.00  0.00              
ATOM     63  C   ASN    24      38.544 -11.452   0.965  1.00  0.00              
ATOM     64  O   ASN    24      38.169 -11.318   2.131  1.00  0.00              
ATOM     65  N   LYS    25      38.160 -10.643  -0.015  1.00  0.00              
ATOM     66  CA  LYS    25      37.254  -9.525   0.225  1.00  0.00              
ATOM     67  C   LYS    25      35.803  -9.997   0.293  1.00  0.00              
ATOM     68  O   LYS    25      34.997  -9.451   1.046  1.00  0.00              
ATOM     69  N   THR    26      35.475 -11.009  -0.502  1.00  0.00              
ATOM     70  CA  THR    26      34.120 -11.547  -0.535  1.00  0.00              
ATOM     71  C   THR    26      33.769 -12.240   0.779  1.00  0.00              
ATOM     72  O   THR    26      32.604 -12.287   1.174  1.00  0.00              
ATOM     73  N   LEU    27      34.781 -12.780   1.450  1.00  0.00              
ATOM     74  CA  LEU    27      34.572 -13.474   2.716  1.00  0.00              
ATOM     75  C   LEU    27      34.613 -12.503   3.890  1.00  0.00              
ATOM     76  O   LEU    27      33.704 -12.479   4.717  1.00  0.00              
ATOM     77  N   LYS    28      35.675 -11.705   3.961  1.00  0.00              
ATOM     78  CA  LYS    28      35.836 -10.734   5.042  1.00  0.00              
ATOM     79  C   LYS    28      34.557  -9.929   5.265  1.00  0.00              
ATOM     80  O   LYS    28      34.290  -9.468   6.375  1.00  0.00              
ATOM     81  N   GLN    29      33.772  -9.761   4.208  1.00  0.00              
ATOM     82  CA  GLN    29      32.526  -9.007   4.293  1.00  0.00              
ATOM     83  C   GLN    29      31.377  -9.892   4.771  1.00  0.00              
ATOM     84  O   GLN    29      30.435  -9.412   5.402  1.00  0.00              
ATOM     85  N   LYS    30      31.457 -11.182   4.463  1.00  0.00              
ATOM     86  CA  LYS    30      30.416 -12.125   4.861  1.00  0.00              
ATOM     87  C   LYS    30      30.707 -12.710   6.239  1.00  0.00              
ATOM     88  O   LYS    30      29.791 -12.987   7.014  1.00  0.00              
ATOM     89  N   VAL    31      31.986 -12.893   6.538  1.00  0.00              
ATOM     90  CA  VAL    31      32.405 -13.445   7.820  1.00  0.00              
ATOM     91  C   VAL    31      32.191 -12.439   8.946  1.00  0.00              
ATOM     92  O   VAL    31      31.951 -12.816  10.092  1.00  0.00              
ATOM     93  N   LYS    32      32.281 -11.157   8.608  1.00  0.00              
ATOM     94  CA  LYS    32      32.099 -10.092   9.587  1.00  0.00              
ATOM     95  C   LYS    32      30.689 -10.110  10.176  1.00  0.00              
ATOM     96  O   LYS    32      30.445  -9.536  11.236  1.00  0.00              
ATOM     97  N   SER    33      29.763 -10.766   9.481  1.00  0.00              
ATOM     98  CA  SER    33      28.381 -10.847   9.940  1.00  0.00              
ATOM     99  C   SER    33      28.023 -12.265  10.381  1.00  0.00              
ATOM    100  O   SER    33      27.281 -12.453  11.345  1.00  0.00              
ATOM    101  N   SER    34      28.549 -13.258   9.670  1.00  0.00              
ATOM    102  CA  SER    34      28.275 -14.656   9.992  1.00  0.00              
ATOM    103  C   SER    34      28.645 -14.972  11.440  1.00  0.00              
ATOM    104  O   SER    34      27.786 -15.331  12.245  1.00  0.00              
ATOM    105  N   GLY    35      29.927 -14.839  11.763  1.00  0.00              
ATOM    106  CA  GLY    35      30.407 -15.114  13.114  1.00  0.00              
ATOM    107  C   GLY    35      30.355 -13.858  13.979  1.00  0.00              
ATOM    108  O   GLY    35      31.375 -13.406  14.498  1.00  0.00              
ATOM    109  N   ALA    36      29.159 -13.301  14.131  1.00  0.00              
ATOM    110  CA  ALA    36      28.975 -12.099  14.937  1.00  0.00              
ATOM    111  C   ALA    36      29.022 -12.430  16.425  1.00  0.00              
ATOM    112  O   ALA    36      29.648 -11.718  17.211  1.00  0.00              
ATOM    113  N   VAL    37      28.357 -13.516  16.806  1.00  0.00              
ATOM    114  CA  VAL    37      28.323 -13.944  18.201  1.00  0.00              
ATOM    115  C   VAL    37      29.476 -14.893  18.508  1.00  0.00              
ATOM    116  O   VAL    37      30.043 -14.865  19.601  1.00  0.00              
ATOM    117  N   GLU   101      29.818 -15.733  17.537  1.00  0.00              
ATOM    118  CA  GLU   101      30.901 -16.680  17.723  1.00  0.00              
ATOM    119  C   GLU   101      32.261 -16.066  17.450  1.00  0.00              
ATOM    120  O   GLU   101      33.000 -16.537  16.588  1.00  0.00              
END
