
#######################################################
#                                                     #
#                        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 T0287AL242_2
# Molecule2: number of CA atoms  161 ( 1350),  selected  161 , name T0287.pdb
# PARAMETERS: T0287AL242_2.T0287.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K      21           -
LGA    -       -      L      22           -
LGA    -       -      I      23           -
LGA    -       -      E      24           -
LGA    -       -      S      25           -
LGA    -       -      L      26           -
LGA    -       -      Q      27           -
LGA    -       -      E      28           -
LGA    -       -      N      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      L      32           -
LGA    -       -      N      33           -
LGA    -       -      T      34           -
LGA    -       -      D      35           -
LGA    -       -      E      36           -
LGA    -       -      K      37           -
LGA    -       -      K      38           -
LGA    -       -      K      39           -
LGA    -       -      I      40           -
LGA    -       -      I      41           -
LGA    -       -      D      42           -
LGA    -       -      Q      43           -
LGA    -       -      I      44           -
LGA    -       -      K      45           -
LGA    -       -      T      46           -
LGA    -       -      M      47           -
LGA    -       -      H      48           -
LGA    -       -      D      49           -
LGA    -       -      F      50           -
LGA    -       -      F      51           -
LGA    -       -      K      52           -
LGA    -       -      Q      53           -
LGA    -       -      M      54           -
LGA    -       -      H      55           -
LGA    -       -      T      56           -
LGA    -       -      N      57           -
LGA    -       -      K      58           -
LGA    -       -      G      59           -
LGA    -       -      A      60           -
LGA    -       -      L      61           -
LGA    -       -      D      62           -
LGA    -       -      K      63           -
LGA    -       -      V      64           -
LGA    -       -      L      65           -
LGA    -       -      R      66           -
LGA    -       -      N      67           -
LGA    -       -      Y      68           -
LGA    -       -      M      69           -
LGA    -       -      K      70           -
LGA    -       -      D      71           -
LGA    -       -      Y      72           -
LGA    -       -      R      73           -
LGA    -       -      A      74           -
LGA    -       -      V      75           -
LGA    -       -      I      76           -
LGA    -       -      K      77           -
LGA    -       -      S      78           -
LGA    S       2      I      79          3.109
LGA    N       3      G      80          0.645
LGA    N       4      V      81          0.663
LGA    M       5      D      82          0.861
LGA    R       6      K      83          0.376
LGA    K       7      F      84          0.456
LGA    L       8      K      85          0.531
LGA    F       9      K      86          0.476
LGA    S      10      V      87          1.068
LGA    M      11      Y      88          0.897
LGA    I      12      R      89          1.093
LGA    A      13      L      90          0.976
LGA    D      14      L      91          1.261
LGA    S      15      E      92          1.279
LGA    K      16      S      93          1.144
LGA    D      17      E      94          0.952
LGA    K      18      T      95          1.047
LGA    K      19      M      96          0.491
LGA    E      20      E      97          0.779
LGA    K      21      L      98          0.718
LGA    L      22      L      99          0.490
LGA    I      23      H     100          0.236
LGA    E      24      A     101          0.679
LGA    S      25      I     102          0.805
LGA    L      26      A     103          0.485
LGA    Q      27      E     104          0.721
LGA    E      28      N     105          0.992
LGA    N      29      P     106          2.919
LGA    -       -      N     107           -
LGA    -       -      F     108           -
LGA    -       -      L     109           -
LGA    -       -      F     110           -
LGA    -       -      S     111           -
LGA    -       -      K     112           -
LGA    -       -      F     113           -
LGA    -       -      D     114           -
LGA    -       -      R     115           -
LGA    -       -      S     116           -
LGA    -       -      I     117           -
LGA    -       -      L     118           -
LGA    -       -      G     119           -
LGA    -       -      I     120           -
LGA    -       -      F     121           -
LGA    -       -      L     122           -
LGA    -       -      P     123           -
LGA    -       -      F     124           -
LGA    -       -      F     125           -
LGA    -       -      S     126           -
LGA    -       -      K     127           -
LGA    -       -      P     128           -
LGA    -       -      I     129           -
LGA    -       -      M     130           -
LGA    -       -      F     131           -
LGA    -       -      K     132           -
LGA    -       -      M     133           -
LGA    -       -      S     134           -
LGA    -       -      I     135           -
LGA    -       -      R     136           -
LGA    -       -      E     137           -
LGA    -       -      M     138           -
LGA    -       -      D     139           -
LGA    -       -      S     140           -
LGA    -       -      Q     141           -
LGA    -       -      I     142           -
LGA    -       -      E     143           -
LGA    -       -      L     144           -
LGA    -       -      Y     145           -
LGA    -       -      G     146           -
LGA    -       -      T     147           -
LGA    -       -      K     148           -
LGA    -       -      L     149           -
LGA    -       -      P     150           -
LGA    -       -      L     151           -
LGA    -       -      L     152           -
LGA    -       -      K     153           -
LGA    -       -      L     154           -
LGA    -       -      F     155           -
LGA    -       -      V     156           -
LGA    -       -      M     157           -
LGA    -       -      T     158           -
LGA    -       -      D     159           -
LGA    -       -      E     160           -
LGA    -       -      E     161           -
LGA    -       -      M     162           -
LGA    -       -      N     163           -
LGA    -       -      F     164           -
LGA    -       -      Y     165           -
LGA    -       -      A     166           -
LGA    -       -      N     167           -
LGA    -       -      L     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      I     171           -
LGA    -       -      E     172           -
LGA    -       -      Q     173           -
LGA    -       -      Y     174           -
LGA    -       -      N     175           -
LGA    -       -      D     176           -
LGA    -       -      Y     177           -
LGA    -       -      V     178           -
LGA    -       -      R     179           -
LGA    -       -      D     180           -
LGA    -       -      L     181           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28  161    5.0     28    1.13     7.14     16.936     2.276

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.946312 * X  +   0.164720 * Y  +  -0.278138 * Z  + 136.432556
  Y_new =   0.283470 * X  +   0.836407 * Y  +  -0.469115 * Z  + 127.165848
  Z_new =   0.155364 * X  +  -0.522773 * Y  +  -0.838195 * Z  +  91.133507 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.583937    0.557656  [ DEG:  -148.0487     31.9513 ]
  Theta =  -0.155996   -2.985597  [ DEG:    -8.9379   -171.0621 ]
  Phi   =   2.850547   -0.291046  [ DEG:   163.3243    -16.6757 ]
 
# 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: T0287AL242_2                                  
REMARK     2: T0287.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0287AL242_2.T0287.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28  161   5.0   28   1.13    7.14  16.936
REMARK  ---------------------------------------------------------- 
MOLECULE T0287AL242_2
REMARK Aligment from pdb entry: 1fav_C
ATOM      1  N   SER     2     113.601  95.252  37.072  1.00  0.00              
ATOM      2  CA  SER     2     112.740  96.437  37.191  1.00  0.00              
ATOM      3  C   SER     2     113.537  97.737  37.111  1.00  0.00              
ATOM      4  O   SER     2     114.501  97.928  37.853  1.00  0.00              
ATOM      5  N   ASN     3     113.124  98.642  36.227  1.00  0.00              
ATOM      6  CA  ASN     3     113.847  99.897  36.063  1.00  0.00              
ATOM      7  C   ASN     3     113.303 101.113  36.811  1.00  0.00              
ATOM      8  O   ASN     3     113.623 101.286  37.986  1.00  0.00              
ATOM      9  N   ASN     4     112.491 101.964  36.176  1.00  0.00              
ATOM     10  CA  ASN     4     112.037 103.143  36.936  1.00  0.00              
ATOM     11  C   ASN     4     110.877 102.914  37.853  1.00  0.00              
ATOM     12  O   ASN     4     110.749 103.593  38.868  1.00  0.00              
ATOM     13  N   MET     5     110.032 101.955  37.517  1.00  0.00              
ATOM     14  CA  MET     5     108.881 101.712  38.353  1.00  0.00              
ATOM     15  C   MET     5     109.219 101.112  39.702  1.00  0.00              
ATOM     16  O   MET     5     108.568 101.429  40.691  1.00  0.00              
ATOM     17  N   ARG     6     110.223 100.244  39.760  1.00  0.00              
ATOM     18  CA  ARG     6     110.571  99.659  41.045  1.00  0.00              
ATOM     19  C   ARG     6     111.385 100.662  41.862  1.00  0.00              
ATOM     20  O   ARG     6     111.522 100.511  43.083  1.00  0.00              
ATOM     21  N   LYS     7     111.918 101.685  41.191  1.00  0.00              
ATOM     22  CA  LYS     7     112.695 102.722  41.869  1.00  0.00              
ATOM     23  C   LYS     7     111.747 103.722  42.517  1.00  0.00              
ATOM     24  O   LYS     7     112.067 104.348  43.529  1.00  0.00              
ATOM     25  N   LEU     8     110.566 103.861  41.934  1.00  0.00              
ATOM     26  CA  LEU     8     109.584 104.790  42.467  1.00  0.00              
ATOM     27  C   LEU     8     108.882 104.232  43.711  1.00  0.00              
ATOM     28  O   LEU     8     108.721 104.959  44.703  1.00  0.00              
ATOM     29  N   PHE     9     108.487 102.953  43.670  1.00  0.00              
ATOM     30  CA  PHE     9     107.806 102.334  44.809  1.00  0.00              
ATOM     31  C   PHE     9     108.740 102.478  45.983  1.00  0.00              
ATOM     32  O   PHE     9     108.326 102.634  47.131  1.00  0.00              
ATOM     33  N   SER    10     110.020 102.424  45.660  1.00  0.00              
ATOM     34  CA  SER    10     111.061 102.551  46.649  1.00  0.00              
ATOM     35  C   SER    10     111.026 103.967  47.210  1.00  0.00              
ATOM     36  O   SER    10     110.841 104.158  48.403  1.00  0.00              
ATOM     37  N   MET    11     111.180 104.957  46.342  1.00  0.00              
ATOM     38  CA  MET    11     111.175 106.336  46.773  1.00  0.00              
ATOM     39  C   MET    11     109.928 106.702  47.555  1.00  0.00              
ATOM     40  O   MET    11     110.009 107.373  48.586  1.00  0.00              
ATOM     41  N   ILE    12     108.773 106.255  47.069  1.00  0.00              
ATOM     42  CA  ILE    12     107.502 106.568  47.717  1.00  0.00              
ATOM     43  C   ILE    12     107.303 105.872  49.053  1.00  0.00              
ATOM     44  O   ILE    12     106.689 106.429  49.963  1.00  0.00              
ATOM     45  N   ALA    13     107.819 104.651  49.157  1.00  0.00              
ATOM     46  CA  ALA    13     107.742 103.879  50.393  1.00  0.00              
ATOM     47  C   ALA    13     108.606 104.648  51.375  1.00  0.00              
ATOM     48  O   ALA    13     108.167 105.053  52.458  1.00  0.00              
ATOM     49  N   ASP    14     109.846 104.853  50.954  1.00  0.00              
ATOM     50  CA  ASP    14     110.833 105.568  51.736  1.00  0.00              
ATOM     51  C   ASP    14     110.313 106.962  52.049  1.00  0.00              
ATOM     52  O   ASP    14     110.599 107.515  53.113  1.00  0.00              
ATOM     53  N   SER    15     109.540 107.521  51.120  1.00  0.00              
ATOM     54  CA  SER    15     108.975 108.853  51.287  1.00  0.00              
ATOM     55  C   SER    15     107.674 108.800  52.045  1.00  0.00              
ATOM     56  O   SER    15     106.910 109.753  52.054  1.00  0.00              
ATOM     57  N   LYS    16     107.408 107.676  52.676  1.00  0.00              
ATOM     58  CA  LYS    16     106.181 107.553  53.420  1.00  0.00              
ATOM     59  C   LYS    16     106.546 107.525  54.893  1.00  0.00              
ATOM     60  O   LYS    16     105.916 108.191  55.711  1.00  0.00              
ATOM     61  N   ASP    17     107.590 106.772  55.220  1.00  0.00              
ATOM     62  CA  ASP    17     108.048 106.660  56.593  1.00  0.00              
ATOM     63  C   ASP    17     108.483 108.015  57.109  1.00  0.00              
ATOM     64  O   ASP    17     108.064 108.432  58.180  1.00  0.00              
ATOM     65  N   LYS    18     109.305 108.711  56.331  1.00  0.00              
ATOM     66  CA  LYS    18     109.788 110.035  56.713  1.00  0.00              
ATOM     67  C   LYS    18     108.625 110.964  57.003  1.00  0.00              
ATOM     68  O   LYS    18     108.609 111.625  58.039  1.00  0.00              
ATOM     69  N   LYS    19     107.651 111.018  56.095  1.00  0.00              
ATOM     70  CA  LYS    19     106.497 111.883  56.305  1.00  0.00              
ATOM     71  C   LYS    19     105.748 111.457  57.556  1.00  0.00              
ATOM     72  O   LYS    19     105.141 112.278  58.249  1.00  0.00              
ATOM     73  N   GLU    20     105.806 110.160  57.835  1.00  0.00              
ATOM     74  CA  GLU    20     105.162 109.566  59.001  1.00  0.00              
ATOM     75  C   GLU    20     105.925 109.958  60.262  1.00  0.00              
ATOM     76  O   GLU    20     105.342 110.155  61.325  1.00  0.00              
ATOM     77  N   LYS    21     107.240 110.069  60.120  1.00  0.00              
ATOM     78  CA  LYS    21     108.132 110.421  61.216  1.00  0.00              
ATOM     79  C   LYS    21     108.135 111.922  61.520  1.00  0.00              
ATOM     80  O   LYS    21     107.946 112.324  62.670  1.00  0.00              
ATOM     81  N   LEU    22     108.352 112.733  60.481  1.00  0.00              
ATOM     82  CA  LEU    22     108.404 114.202  60.560  1.00  0.00              
ATOM     83  C   LEU    22     107.217 114.780  61.329  1.00  0.00              
ATOM     84  O   LEU    22     107.347 115.765  62.047  1.00  0.00              
ATOM     85  N   ILE    23     106.058 114.161  61.168  1.00  0.00              
ATOM     86  CA  ILE    23     104.854 114.620  61.831  1.00  0.00              
ATOM     87  C   ILE    23     104.892 114.269  63.304  1.00  0.00              
ATOM     88  O   ILE    23     104.422 115.032  64.143  1.00  0.00              
ATOM     89  N   GLU    24     105.444 113.102  63.608  1.00  0.00              
ATOM     90  CA  GLU    24     105.552 112.640  64.978  1.00  0.00              
ATOM     91  C   GLU    24     106.309 113.711  65.714  1.00  0.00              
ATOM     92  O   GLU    24     105.783 114.352  66.617  1.00  0.00              
ATOM     93  N   SER    25     107.555 113.903  65.297  1.00  0.00              
ATOM     94  CA  SER    25     108.436 114.894  65.893  1.00  0.00              
ATOM     95  C   SER    25     107.800 116.277  66.006  1.00  0.00              
ATOM     96  O   SER    25     107.920 116.946  67.032  1.00  0.00              
ATOM     97  N   LEU    26     107.126 116.698  64.943  1.00  0.00              
ATOM     98  CA  LEU    26     106.472 117.996  64.903  1.00  0.00              
ATOM     99  C   LEU    26     105.496 118.149  66.060  1.00  0.00              
ATOM    100  O   LEU    26     105.310 119.247  66.587  1.00  0.00              
ATOM    101  N   GLN    27     104.875 117.038  66.449  1.00  0.00              
ATOM    102  CA  GLN    27     103.926 117.025  67.558  1.00  0.00              
ATOM    103  C   GLN    27     104.711 117.157  68.857  1.00  0.00              
ATOM    104  O   GLN    27     104.383 117.965  69.734  1.00  0.00              
ATOM    105  N   GLU    28     105.768 116.362  68.972  1.00  0.00              
ATOM    106  CA  GLU    28     106.602 116.395  70.166  1.00  0.00              
ATOM    107  C   GLU    28     107.429 117.693  70.132  1.00  0.00              
ATOM    108  O   GLU    28     108.632 117.718  70.328  1.00  0.00              
ATOM    109  N   ASN    29     106.736 118.797  69.892  1.00  0.00              
ATOM    110  CA  ASN    29     107.367 120.105  69.811  1.00  0.00              
ATOM    111  C   ASN    29     106.633 120.975  70.802  1.00  0.00              
ATOM    112  O   ASN    29     105.410 120.725  70.887  1.00  0.00              
END
