
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0346AL242_3
# Molecule2: number of CA atoms  172 ( 1335),  selected  172 , name T0346.pdb
# PARAMETERS: T0346AL242_3.T0346.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    Q      21      S       1          3.051
LGA    L      22      P       2          2.626
LGA    F      23      Q       3          3.001
LGA    S      24      C       4          4.182
LGA    D      25      H       5           #
LGA    I      26      F       6           -
LGA    -       -      D       7           -
LGA    -       -      I       8           -
LGA    -       -      E       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      R      12           -
LGA    -       -      E      13           -
LGA    -       -      P      14           -
LGA    -       -      V      15           -
LGA    -       -      G      16           -
LGA    -       -      R      17           -
LGA    -       -      I      18           -
LGA    -       -      M      19           -
LGA    -       -      F      20           -
LGA    C      27      Q      21          4.870
LGA    P      28      L      22          2.653
LGA    K      29      F      23          3.371
LGA    T      30      S      24          2.609
LGA    -       -      D      25           -
LGA    -       -      I      26           -
LGA    C      31      C      27          3.070
LGA    K      32      P      28          1.973
LGA    N      33      K      29          3.410
LGA    F      34      T      30          3.592
LGA    L      35      C      31          4.831
LGA    C      36      K      32          2.586
LGA    L      37      N      33          1.800
LGA    C      38      F      34          2.149
LGA    S      39      L      35          3.587
LGA    -       -      C      36           -
LGA    G      40      L      37          2.848
LGA    -       -      C      38           -
LGA    -       -      S      39           -
LGA    -       -      G      40           -
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      L      44           -
LGA    -       -      G      45           -
LGA    -       -      K      46           -
LGA    -       -      T      47           -
LGA    -       -      T      48           -
LGA    -       -      G      49           -
LGA    -       -      K      50           -
LGA    -       -      K      51           -
LGA    -       -      L      52           -
LGA    -       -      C      53           -
LGA    E      41      Y      54          2.391
LGA    -       -      K      55           -
LGA    -       -      G      56           -
LGA    K      42      S      57          2.794
LGA    G      43      T      58          3.760
LGA    -       -      F      59           -
LGA    -       -      H      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      V      63           -
LGA    -       -      K      64           -
LGA    -       -      N      65           -
LGA    -       -      F      66           -
LGA    -       -      M      67           -
LGA    -       -      I      68           -
LGA    -       -      Q      69           -
LGA    -       -      G      70           -
LGA    L      44      G      71          3.231
LGA    G      45      D      72           -
LGA    K      46      F      73           -
LGA    T      47      S      74           -
LGA    T      48      E      75           -
LGA    -       -      G      76           -
LGA    -       -      N      77           -
LGA    -       -      G      78           -
LGA    -       -      K      79           -
LGA    -       -      G      80           -
LGA    -       -      G      81           -
LGA    -       -      E      82           -
LGA    -       -      S      83           -
LGA    -       -      I      84           -
LGA    -       -      Y      85           -
LGA    -       -      G      86           -
LGA    -       -      G      87           -
LGA    -       -      Y      88           -
LGA    -       -      F      89           -
LGA    -       -      K      90           -
LGA    -       -      D      91           -
LGA    -       -      E      92           -
LGA    -       -      N      93           -
LGA    -       -      F      94           -
LGA    -       -      I      95           -
LGA    -       -      L      96           -
LGA    -       -      K      97           -
LGA    -       -      H      98           -
LGA    -       -      D      99           -
LGA    -       -      R     100           -
LGA    -       -      A     101           -
LGA    G      49      F     102          3.874
LGA    K      50      L     103          3.105
LGA    K      51      L     104          2.891
LGA    L      52      S     105          3.137
LGA    C      53      M     106          1.792
LGA    Y      54      A     107           -
LGA    -       -      N     108           -
LGA    -       -      R     109           -
LGA    -       -      G     110           -
LGA    -       -      K     111           -
LGA    -       -      H     112           -
LGA    -       -      T     113           -
LGA    -       -      N     114           -
LGA    -       -      G     115           -
LGA    -       -      S     116           -
LGA    -       -      Q     117           -
LGA    -       -      F     118           -
LGA    -       -      F     119           -
LGA    -       -      I     120           -
LGA    -       -      T     121           -
LGA    -       -      T     122           -
LGA    -       -      K     123           -
LGA    -       -      P     124           -
LGA    -       -      A     125           -
LGA    -       -      P     126           -
LGA    -       -      H     127           -
LGA    -       -      L     128           -
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      V     131           -
LGA    K      55      H     132          3.959
LGA    -       -      V     133           -
LGA    -       -      V     134           -
LGA    -       -      F     135           -
LGA    -       -      G     136           -
LGA    -       -      L     137           -
LGA    -       -      V     138           -
LGA    -       -      I     139           -
LGA    -       -      S     140           -
LGA    -       -      G     141           -
LGA    -       -      F     142           -
LGA    -       -      E     143           -
LGA    -       -      V     144           -
LGA    -       -      I     145           -
LGA    -       -      E     146           -
LGA    -       -      Q     147           -
LGA    -       -      I     148           -
LGA    -       -      E     149           -
LGA    -       -      N     150           -
LGA    -       -      L     151           -
LGA    -       -      K     152           -
LGA    -       -      T     153           -
LGA    -       -      D     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      S     157           -
LGA    -       -      R     158           -
LGA    -       -      P     159           -
LGA    -       -      Y     160           -
LGA    -       -      A     161           -
LGA    -       -      D     162           -
LGA    -       -      V     163           -
LGA    -       -      R     164           -
LGA    -       -      V     165           -
LGA    -       -      I     166           -
LGA    -       -      D     167           -
LGA    -       -      C     168           -
LGA    -       -      G     169           -
LGA    -       -      V     170           -
LGA    -       -      L     171           -
LGA    -       -      A     172           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35  172    5.0     28    3.21     3.57      9.135     0.846

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.115924 * X  +   0.145351 * Y  +  -0.982565 * Z  +  44.703903
  Y_new =   0.271478 * X  +   0.946931 * Y  +   0.172109 * Z  +   0.659314
  Z_new =   0.955438 * X  +  -0.286697 * Y  +   0.070313 * Z  +  33.207607 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.330291    1.811301  [ DEG:   -76.2201    103.7799 ]
  Theta =  -1.271139   -1.870454  [ DEG:   -72.8309   -107.1691 ]
  Phi   =   1.167222   -1.974370  [ DEG:    66.8769   -113.1231 ]
 
# 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: T0346AL242_3                                  
REMARK     2: T0346.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0346AL242_3.T0346.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35  172   5.0   28   3.21    3.57   9.135
REMARK  ---------------------------------------------------------- 
MOLECULE T0346AL242_3
REMARK Aligment from pdb entry: 1ji9_A
ATOM      1  N   GLN    21      36.116   1.953  26.171  1.00  0.00              
ATOM      2  CA  GLN    21      36.346   3.262  26.849  1.00  0.00              
ATOM      3  C   GLN    21      37.757   3.315  27.441  1.00  0.00              
ATOM      4  O   GLN    21      38.404   2.301  27.616  1.00  0.00              
ATOM      5  N   LEU    22      38.239   4.488  27.754  1.00  0.00              
ATOM      6  CA  LEU    22      39.607   4.600  28.338  1.00  0.00              
ATOM      7  C   LEU    22      39.724   3.707  29.570  1.00  0.00              
ATOM      8  O   LEU    22      40.804   3.347  29.991  1.00  0.00              
ATOM      9  N   PHE    23      38.608   3.353  30.137  1.00  0.00              
ATOM     10  CA  PHE    23      38.596   2.474  31.350  1.00  0.00              
ATOM     11  C   PHE    23      39.777   2.761  32.270  1.00  0.00              
ATOM     12  O   PHE    23      40.209   1.882  32.979  1.00  0.00              
ATOM     13  N   SER    24      40.331   3.947  32.265  1.00  0.00              
ATOM     14  CA  SER    24      41.515   4.167  33.145  1.00  0.00              
ATOM     15  C   SER    24      42.032   5.597  33.132  1.00  0.00              
ATOM     16  O   SER    24      41.841   6.352  32.199  1.00  0.00              
ATOM     17  N   ASP    25      42.771   5.915  34.150  1.00  0.00              
ATOM     18  CA  ASP    25      43.432   7.234  34.238  1.00  0.00              
ATOM     19  C   ASP    25      44.895   7.013  33.846  1.00  0.00              
ATOM     20  O   ASP    25      45.633   7.937  33.570  1.00  0.00              
ATOM     21  N   ILE    26      45.299   5.760  33.794  1.00  0.00              
ATOM     22  CA  ILE    26      46.704   5.433  33.388  1.00  0.00              
ATOM     23  C   ILE    26      46.725   4.858  31.971  1.00  0.00              
ATOM     24  O   ILE    26      47.763   4.535  31.427  1.00  0.00              
ATOM     25  N   CYS    27      45.576   4.719  31.388  1.00  0.00              
ATOM     26  CA  CYS    27      45.461   4.162  30.028  1.00  0.00              
ATOM     27  C   CYS    27      44.395   4.887  29.215  1.00  0.00              
ATOM     28  O   CYS    27      43.470   5.455  29.761  1.00  0.00              
ATOM     29  N   PRO    28      44.549   4.807  27.925  1.00  0.00              
ATOM     30  CA  PRO    28      43.587   5.415  27.002  1.00  0.00              
ATOM     31  C   PRO    28      42.532   4.366  26.642  1.00  0.00              
ATOM     32  O   PRO    28      42.507   3.290  27.205  1.00  0.00              
ATOM     33  N   LYS    29      41.676   4.651  25.711  1.00  0.00              
ATOM     34  CA  LYS    29      40.651   3.640  25.329  1.00  0.00              
ATOM     35  C   LYS    29      41.247   2.647  24.332  1.00  0.00              
ATOM     36  O   LYS    29      40.569   1.776  23.825  1.00  0.00              
ATOM     37  N   THR    30      42.508   2.783  24.038  1.00  0.00              
ATOM     38  CA  THR    30      43.149   1.860  23.062  1.00  0.00              
ATOM     39  C   THR    30      44.086   0.879  23.775  1.00  0.00              
ATOM     40  O   THR    30      44.583  -0.051  23.171  1.00  0.00              
ATOM     41  N   CYS    31      44.342   1.059  25.046  1.00  0.00              
ATOM     42  CA  CYS    31      45.242   0.124  25.745  1.00  0.00              
ATOM     43  C   CYS    31      44.840  -1.312  25.462  1.00  0.00              
ATOM     44  O   CYS    31      43.853  -1.799  25.975  1.00  0.00              
ATOM     45  N   LYS    32      45.598  -2.010  24.677  1.00  0.00              
ATOM     46  CA  LYS    32      45.239  -3.418  24.416  1.00  0.00              
ATOM     47  C   LYS    32      45.597  -4.250  25.634  1.00  0.00              
ATOM     48  O   LYS    32      45.249  -5.408  25.754  1.00  0.00              
ATOM     49  N   ASN    33      46.240  -3.632  26.562  1.00  0.00              
ATOM     50  CA  ASN    33      46.579  -4.314  27.821  1.00  0.00              
ATOM     51  C   ASN    33      45.307  -4.429  28.610  1.00  0.00              
ATOM     52  O   ASN    33      45.119  -5.287  29.439  1.00  0.00              
ATOM     53  N   PHE    34      44.443  -3.526  28.330  1.00  0.00              
ATOM     54  CA  PHE    34      43.143  -3.478  29.033  1.00  0.00              
ATOM     55  C   PHE    34      42.056  -3.984  28.113  1.00  0.00              
ATOM     56  O   PHE    34      40.905  -4.121  28.477  1.00  0.00              
ATOM     57  N   LEU    35      42.436  -4.244  26.913  1.00  0.00              
ATOM     58  CA  LEU    35      41.491  -4.728  25.903  1.00  0.00              
ATOM     59  C   LEU    35      40.952  -6.111  26.272  1.00  0.00              
ATOM     60  O   LEU    35      40.064  -6.634  25.627  1.00  0.00              
ATOM     61  N   CYS    36      40.738  -4.817  31.342  1.00  0.00              
ATOM     62  CA  CYS    36      41.428  -3.804  32.192  1.00  0.00              
ATOM     63  C   CYS    36      42.442  -4.509  33.094  1.00  0.00              
ATOM     64  O   CYS    36      42.140  -4.904  34.203  1.00  0.00              
ATOM     65  N   LEU    37      43.638  -4.686  32.609  1.00  0.00              
ATOM     66  CA  LEU    37      44.680  -5.384  33.404  1.00  0.00              
ATOM     67  C   LEU    37      44.927  -4.671  34.735  1.00  0.00              
ATOM     68  O   LEU    37      45.408  -5.264  35.680  1.00  0.00              
ATOM     69  N   CYS    38      44.595  -3.414  34.832  1.00  0.00              
ATOM     70  CA  CYS    38      44.814  -2.709  36.132  1.00  0.00              
ATOM     71  C   CYS    38      43.495  -2.593  36.900  1.00  0.00              
ATOM     72  O   CYS    38      43.393  -1.858  37.861  1.00  0.00              
ATOM     73  N   SER    39      42.486  -3.313  36.491  1.00  0.00              
ATOM     74  CA  SER    39      41.181  -3.241  37.206  1.00  0.00              
ATOM     75  C   SER    39      41.395  -3.231  38.715  1.00  0.00              
ATOM     76  O   SER    39      40.653  -2.624  39.460  1.00  0.00              
ATOM     77  N   GLY    40      42.404  -3.904  39.161  1.00  0.00              
ATOM     78  CA  GLY    40      42.686  -3.952  40.623  1.00  0.00              
ATOM     79  C   GLY    40      42.880  -2.533  41.156  1.00  0.00              
ATOM     80  O   GLY    40      43.914  -1.924  40.960  1.00  0.00              
ATOM     81  N   GLU    41      41.899  -2.002  41.832  1.00  0.00              
ATOM     82  CA  GLU    41      42.040  -0.623  42.379  1.00  0.00              
ATOM     83  C   GLU    41      42.717  -0.672  43.746  1.00  0.00              
ATOM     84  O   GLU    41      42.297  -0.036  44.692  1.00  0.00              
ATOM     85  N   LYS    42      43.771  -1.426  43.844  1.00  0.00              
ATOM     86  CA  LYS    42      44.508  -1.541  45.127  1.00  0.00              
ATOM     87  C   LYS    42      45.671  -0.547  45.142  1.00  0.00              
ATOM     88  O   LYS    42      45.493   0.628  45.393  1.00  0.00              
ATOM     89  N   GLY    43      46.856  -1.004  44.856  1.00  0.00              
ATOM     90  CA  GLY    43      48.025  -0.086  44.830  1.00  0.00              
ATOM     91  C   GLY    43      48.239   0.400  43.396  1.00  0.00              
ATOM     92  O   GLY    43      49.077   1.239  43.130  1.00  0.00              
ATOM     93  N   LEU    44      47.487  -0.130  42.467  1.00  0.00              
ATOM     94  CA  LEU    44      47.636   0.284  41.050  1.00  0.00              
ATOM     95  C   LEU    44      46.756   1.487  40.747  1.00  0.00              
ATOM     96  O   LEU    44      46.141   1.590  39.704  1.00  0.00              
ATOM     97  N   GLY    45      46.702   2.384  41.662  1.00  0.00              
ATOM     98  CA  GLY    45      45.879   3.608  41.496  1.00  0.00              
ATOM     99  C   GLY    45      45.952   4.127  40.056  1.00  0.00              
ATOM    100  O   GLY    45      47.016   4.245  39.481  1.00  0.00              
ATOM    101  N   LYS    46      44.826   4.442  39.474  1.00  0.00              
ATOM    102  CA  LYS    46      44.826   4.959  38.074  1.00  0.00              
ATOM    103  C   LYS    46      45.066   6.463  38.078  1.00  0.00              
ATOM    104  O   LYS    46      45.710   7.009  37.205  1.00  0.00              
ATOM    105  N   THR    47      44.557   7.124  39.071  1.00  0.00              
ATOM    106  CA  THR    47      44.744   8.595  39.187  1.00  0.00              
ATOM    107  C   THR    47      46.157   8.952  38.796  1.00  0.00              
ATOM    108  O   THR    47      46.434   9.983  38.217  1.00  0.00              
ATOM    109  N   THR    48      47.039   8.070  39.102  1.00  0.00              
ATOM    110  CA  THR    48      48.474   8.259  38.757  1.00  0.00              
ATOM    111  C   THR    48      48.614   8.908  37.379  1.00  0.00              
ATOM    112  O   THR    48      49.610   9.531  37.086  1.00  0.00              
ATOM    113  N   GLY    49      47.618   8.712  36.539  1.00  0.00              
ATOM    114  CA  GLY    49      47.603   9.242  35.143  1.00  0.00              
ATOM    115  C   GLY    49      48.226   8.226  34.210  1.00  0.00              
ATOM    116  O   GLY    49      47.999   8.225  33.016  1.00  0.00              
ATOM    117  N   LYS    50      49.000   7.358  34.760  1.00  0.00              
ATOM    118  CA  LYS    50      49.653   6.308  33.968  1.00  0.00              
ATOM    119  C   LYS    50      50.035   5.155  34.892  1.00  0.00              
ATOM    120  O   LYS    50      50.203   5.329  36.082  1.00  0.00              
ATOM    121  N   LYS    51      50.157   3.984  34.365  1.00  0.00              
ATOM    122  CA  LYS    51      50.527   2.823  35.234  1.00  0.00              
ATOM    123  C   LYS    51      51.855   2.202  34.800  1.00  0.00              
ATOM    124  O   LYS    51      52.614   2.784  34.050  1.00  0.00              
ATOM    125  N   LEU    52      52.145   1.026  35.288  1.00  0.00              
ATOM    126  CA  LEU    52      53.428   0.361  34.936  1.00  0.00              
ATOM    127  C   LEU    52      53.195  -1.103  34.551  1.00  0.00              
ATOM    128  O   LEU    52      54.101  -1.911  34.585  1.00  0.00              
ATOM    129  N   CYS    53      51.997  -1.454  34.172  1.00  0.00              
ATOM    130  CA  CYS    53      51.742  -2.879  33.776  1.00  0.00              
ATOM    131  C   CYS    53      51.579  -2.975  32.269  1.00  0.00              
ATOM    132  O   CYS    53      52.094  -3.863  31.619  1.00  0.00              
ATOM    133  N   TYR    54      50.856  -2.063  31.727  1.00  0.00              
ATOM    134  CA  TYR    54      50.610  -2.047  30.269  1.00  0.00              
ATOM    135  C   TYR    54      51.820  -1.491  29.536  1.00  0.00              
ATOM    136  O   TYR    54      52.221  -1.975  28.495  1.00  0.00              
ATOM    137  N   LYS    55      52.387  -0.471  30.085  1.00  0.00              
ATOM    138  CA  LYS    55      53.578   0.173  29.465  1.00  0.00              
ATOM    139  C   LYS    55      54.495  -0.882  28.839  1.00  0.00              
ATOM    140  O   LYS    55      54.373  -1.111  27.648  1.00  0.00              
END
