
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0319AL243_2
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL243_2.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A      58      M       1           -
LGA    V      59      K       2           #
LGA    L      60      F       3          5.553
LGA    T      61      L       4          3.307
LGA    -       -      T       5           -
LGA    -       -      T       6           -
LGA    -       -      N       7           -
LGA    -       -      F       8           -
LGA    -       -      L       9           -
LGA    -       -      K      10           -
LGA    -       -      C      11           -
LGA    -       -      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      P      24           -
LGA    -       -      L      25           -
LGA    -       -      Q      26           -
LGA    -       -      Y      27           -
LGA    -       -      D      28           -
LGA    -       -      G      29           -
LGA    -       -      S      30           -
LGA    -       -      K      31           -
LGA    -       -      C      32           -
LGA    -       -      Q      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      D      37           -
LGA    -       -      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    -       -      L      48           -
LGA    V      62      N      49           #
LGA    A      63      I      50          3.134
LGA    A      64      V      51          5.040
LGA    E      65      D      52          4.875
LGA    L      66      R      53          2.951
LGA    G      67      V      54          3.057
LGA    N      68      D      55          3.276
LGA    -       -      W      56           -
LGA    -       -      P      57           -
LGA    -       -      A      58           -
LGA    -       -      V      59           -
LGA    -       -      L      60           -
LGA    -       -      T      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      G      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      A      70           -
LGA    -       -      L      71           -
LGA    -       -      P      72           -
LGA    -       -      P      73           -
LGA    -       -      T      74           -
LGA    N      69      K      75           #
LGA    A      70      P      76          4.356
LGA    L      71      -       -           -
LGA    P      72      -       -           -
LGA    P      73      S      77          1.232
LGA    T      74      F      78          3.487
LGA    K      75      P      79           #
LGA    P      76      S      80           #
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    D      88      L      85          1.334
LGA    D      89      T      86          0.812
LGA    M      90      D      87          0.820
LGA    A      91      D      88          0.725
LGA    I      92      D      89          0.403
LGA    L      93      M      90          0.644
LGA    N      94      A      91          0.833
LGA    D      95      I      92          0.565
LGA    L      96      L      93          0.757
LGA    H      97      N      94          1.016
LGA    T      98      D      95          0.425
LGA    L      99      L      96          0.955
LGA    L     100      H      97          1.627
LGA    L     101      T      98          0.471
LGA    Q     102      L      99          2.796
LGA    S     104      L     100           -
LGA    -       -      L     101           -
LGA    -       -      Q     102           -
LGA    I     105      T     103          3.264
LGA    A     106      S     104           -
LGA    E     107      I     105           -
LGA    G     108      A     106           -
LGA    E     109      E     107           -
LGA    M     110      G     108           -
LGA    -       -      E     109           -
LGA    -       -      M     110           -
LGA    -       -      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      H     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    -       -      Y     120           -
LGA    -       -      I     121           -
LGA    -       -      K     122           -
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    -       -      P     126           -
LGA    -       -      N     127           -
LGA    -       -      L     128           -
LGA    -       -      L     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      V     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41  135    5.0     27    2.66     7.41     14.647     0.977

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.039852 * X  +  -0.431281 * Y  +   0.901337 * Z  +  48.262833
  Y_new =   0.315620 * X  +   0.850437 * Y  +   0.420881 * Z  + -50.674007
  Z_new =  -0.948048 * X  +   0.301253 * Y  +   0.102229 * Z  +  -8.280529 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.243644   -1.897948  [ DEG:    71.2556   -108.7444 ]
  Theta =   1.247044    1.894548  [ DEG:    71.4504    108.5496 ]
  Phi   =   1.696399   -1.445194  [ DEG:    97.1965    -82.8035 ]
 
# 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: T0319AL243_2                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL243_2.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41  135   5.0   27   2.66    7.41  14.647
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL243_2
REMARK Aligment from pdb entry: 2f6sA
ATOM      1  N   ALA    58      25.114   2.134  17.475  1.00  0.00              
ATOM      2  CA  ALA    58      25.887   0.938  17.187  1.00  0.00              
ATOM      3  C   ALA    58      25.225  -0.298  17.781  1.00  0.00              
ATOM      4  O   ALA    58      25.301  -1.386  17.211  1.00  0.00              
ATOM      5  N   VAL    59      24.563  -0.127  18.919  1.00  0.00              
ATOM      6  CA  VAL    59      23.884  -1.239  19.562  1.00  0.00              
ATOM      7  C   VAL    59      22.806  -1.807  18.650  1.00  0.00              
ATOM      8  O   VAL    59      22.681  -3.020  18.535  1.00  0.00              
ATOM      9  N   LEU    60      22.047  -0.931  17.989  1.00  0.00              
ATOM     10  CA  LEU    60      20.984  -1.364  17.077  1.00  0.00              
ATOM     11  C   LEU    60      21.554  -2.146  15.893  1.00  0.00              
ATOM     12  O   LEU    60      20.905  -3.075  15.374  1.00  0.00              
ATOM     13  N   THR    61      22.761  -1.759  15.470  1.00  0.00              
ATOM     14  CA  THR    61      23.424  -2.413  14.353  1.00  0.00              
ATOM     15  C   THR    61      23.903  -3.778  14.824  1.00  0.00              
ATOM     16  O   THR    61      23.827  -4.755  14.074  1.00  0.00              
ATOM     17  N   VAL    62      24.376  -3.849  16.067  1.00  0.00              
ATOM     18  CA  VAL    62      24.804  -5.127  16.611  1.00  0.00              
ATOM     19  C   VAL    62      23.614  -6.061  16.742  1.00  0.00              
ATOM     20  O   VAL    62      23.689  -7.222  16.330  1.00  0.00              
ATOM     21  N   ALA    63      22.511  -5.556  17.286  1.00  0.00              
ATOM     22  CA  ALA    63      21.310  -6.359  17.404  1.00  0.00              
ATOM     23  C   ALA    63      20.946  -6.916  16.009  1.00  0.00              
ATOM     24  O   ALA    63      20.696  -8.122  15.839  1.00  0.00              
ATOM     25  N   ALA    64      20.933  -6.029  15.015  1.00  0.00              
ATOM     26  CA  ALA    64      20.541  -6.387  13.654  1.00  0.00              
ATOM     27  C   ALA    64      21.453  -7.480  13.085  1.00  0.00              
ATOM     28  O   ALA    64      20.992  -8.400  12.431  1.00  0.00              
ATOM     29  N   GLU    65      22.743  -7.387  13.384  1.00  0.00              
ATOM     30  CA  GLU    65      23.716  -8.386  12.975  1.00  0.00              
ATOM     31  C   GLU    65      23.330  -9.784  13.448  1.00  0.00              
ATOM     32  O   GLU    65      23.385 -10.722  12.667  1.00  0.00              
ATOM     33  N   LEU    66      22.921  -9.902  14.711  1.00  0.00              
ATOM     34  CA  LEU    66      22.428 -11.157  15.265  1.00  0.00              
ATOM     35  C   LEU    66      21.077 -11.563  14.683  1.00  0.00              
ATOM     36  O   LEU    66      20.949 -12.645  14.099  1.00  0.00              
ATOM     37  N   GLY    67      20.077 -10.694  14.847  1.00  0.00              
ATOM     38  CA  GLY    67      18.685 -10.980  14.447  1.00  0.00              
ATOM     39  C   GLY    67      18.512 -11.377  12.991  1.00  0.00              
ATOM     40  O   GLY    67      17.684 -12.202  12.681  1.00  0.00              
ATOM     41  N   ASN    68      19.260 -10.751  12.092  1.00  0.00              
ATOM     42  CA  ASN    68      19.076 -11.004  10.665  1.00  0.00              
ATOM     43  C   ASN    68      19.644 -12.365  10.256  1.00  0.00              
ATOM     44  O   ASN    68      19.262 -12.900   9.231  1.00  0.00              
ATOM     45  N   ASN    69      20.582 -12.900  11.047  1.00  0.00              
ATOM     46  CA  ASN    69      21.299 -14.111  10.694  1.00  0.00              
ATOM     47  C   ASN    69      22.588 -13.854   9.916  1.00  0.00              
ATOM     48  O   ASN    69      23.312 -14.790   9.563  1.00  0.00              
ATOM     49  N   ALA    70      22.887 -12.587   9.645  1.00  0.00              
ATOM     50  CA  ALA    70      24.110 -12.228   8.932  1.00  0.00              
ATOM     51  C   ALA    70      25.328 -12.678   9.692  1.00  0.00              
ATOM     52  O   ALA    70      26.354 -13.043   9.099  1.00  0.00              
ATOM     53  N   LEU    71      25.217 -12.666  11.014  1.00  0.00              
ATOM     54  CA  LEU    71      26.310 -13.119  11.877  1.00  0.00              
ATOM     55  C   LEU    71      26.821 -14.523  11.455  1.00  0.00              
ATOM     56  O   LEU    71      28.002 -14.809  11.571  1.00  0.00              
ATOM     57  N   PRO    72      25.935 -15.362  10.924  1.00  0.00              
ATOM     58  CA  PRO    72      26.293 -16.738  10.590  1.00  0.00              
ATOM     59  C   PRO    72      27.317 -16.833   9.451  1.00  0.00              
ATOM     60  O   PRO    72      27.901 -17.889   9.231  1.00  0.00              
ATOM     61  N   PRO    73      27.540 -15.745   8.725  1.00  0.00              
ATOM     62  CA  PRO    73      28.519 -15.796   7.637  1.00  0.00              
ATOM     63  C   PRO    73      29.723 -14.858   7.814  1.00  0.00              
ATOM     64  O   PRO    73      30.502 -14.654   6.883  1.00  0.00              
ATOM     65  N   THR    74      29.883 -14.288   9.003  1.00  0.00              
ATOM     66  CA  THR    74      31.133 -13.664   9.341  1.00  0.00              
ATOM     67  C   THR    74      32.201 -14.776   9.426  1.00  0.00              
ATOM     68  O   THR    74      31.976 -15.826  10.024  1.00  0.00              
ATOM     69  N   LYS    75      33.359 -14.538   8.832  1.00  0.00              
ATOM     70  CA  LYS    75      34.448 -15.492   8.908  1.00  0.00              
ATOM     71  C   LYS    75      34.938 -15.580  10.361  1.00  0.00              
ATOM     72  O   LYS    75      35.143 -14.561  11.002  1.00  0.00              
ATOM     73  N   PRO    76      35.140 -16.800  10.863  1.00  0.00              
ATOM     74  CA  PRO    76      35.436 -17.026  12.287  1.00  0.00              
ATOM     75  C   PRO    76      36.931 -17.121  12.616  1.00  0.00              
ATOM     76  O   PRO    76      37.672 -17.862  11.965  1.00  0.00              
ATOM     77  N   ASP    88      37.359 -16.399  13.649  1.00  0.00              
ATOM     78  CA  ASP    88      38.677 -16.612  14.236  1.00  0.00              
ATOM     79  C   ASP    88      39.821 -15.933  13.513  1.00  0.00              
ATOM     80  O   ASP    88      40.979 -16.191  13.823  1.00  0.00              
ATOM     81  N   ASP    89      39.503 -15.051  12.566  1.00  0.00              
ATOM     82  CA  ASP    89      40.512 -14.410  11.712  1.00  0.00              
ATOM     83  C   ASP    89      40.466 -12.889  11.867  1.00  0.00              
ATOM     84  O   ASP    89      39.494 -12.339  12.425  1.00  0.00              
ATOM     85  N   MET    90      41.507 -12.220  11.362  1.00  0.00              
ATOM     86  CA  MET    90      41.537 -10.760  11.332  1.00  0.00              
ATOM     87  C   MET    90      40.445 -10.220  10.452  1.00  0.00              
ATOM     88  O   MET    90      39.753  -9.286  10.852  1.00  0.00              
ATOM     89  N   ALA    91      40.326 -10.781   9.243  1.00  0.00              
ATOM     90  CA  ALA    91      39.296 -10.331   8.301  1.00  0.00              
ATOM     91  C   ALA    91      37.934 -10.404   8.957  1.00  0.00              
ATOM     92  O   ALA    91      37.125  -9.488   8.821  1.00  0.00              
ATOM     93  N   ILE    92      37.727 -11.471   9.720  1.00  0.00              
ATOM     94  CA  ILE    92      36.484 -11.698  10.413  1.00  0.00              
ATOM     95  C   ILE    92      36.231 -10.669  11.478  1.00  0.00              
ATOM     96  O   ILE    92      35.095 -10.235  11.669  1.00  0.00              
ATOM     97  N   LEU    93      37.294 -10.288  12.175  1.00  0.00              
ATOM     98  CA  LEU    93      37.210  -9.316  13.247  1.00  0.00              
ATOM     99  C   LEU    93      36.878  -7.968  12.622  1.00  0.00              
ATOM    100  O   LEU    93      36.088  -7.180  13.183  1.00  0.00              
ATOM    101  N   ASN    94      37.466  -7.715  11.455  1.00  0.00              
ATOM    102  CA  ASN    94      37.169  -6.508  10.711  1.00  0.00              
ATOM    103  C   ASN    94      35.706  -6.478  10.255  1.00  0.00              
ATOM    104  O   ASN    94      35.054  -5.439  10.368  1.00  0.00              
ATOM    105  N   ASP    95      35.184  -7.601   9.759  1.00  0.00              
ATOM    106  CA  ASP    95      33.777  -7.670   9.354  1.00  0.00              
ATOM    107  C   ASP    95      32.867  -7.237  10.494  1.00  0.00              
ATOM    108  O   ASP    95      31.935  -6.441  10.297  1.00  0.00              
ATOM    109  N   LEU    96      33.145  -7.764  11.680  1.00  0.00              
ATOM    110  CA  LEU    96      32.378  -7.444  12.857  1.00  0.00              
ATOM    111  C   LEU    96      32.398  -5.947  13.102  1.00  0.00              
ATOM    112  O   LEU    96      31.338  -5.307  13.256  1.00  0.00              
ATOM    113  N   HIS    97      33.604  -5.396  13.106  1.00  0.00              
ATOM    114  CA  HIS    97      33.820  -3.988  13.395  1.00  0.00              
ATOM    115  C   HIS    97      33.131  -3.120  12.353  1.00  0.00              
ATOM    116  O   HIS    97      32.464  -2.147  12.695  1.00  0.00              
ATOM    117  N   THR    98      33.284  -3.488  11.085  1.00  0.00              
ATOM    118  CA  THR    98      32.702  -2.748  10.004  1.00  0.00              
ATOM    119  C   THR    98      31.218  -2.711  10.260  1.00  0.00              
ATOM    120  O   THR    98      30.599  -1.663  10.159  1.00  0.00              
ATOM    121  N   LEU    99      30.653  -3.860  10.621  1.00  0.00              
ATOM    122  CA  LEU    99      29.241  -3.960  10.762  1.00  0.00              
ATOM    123  C   LEU    99      28.719  -3.109  11.919  1.00  0.00              
ATOM    124  O   LEU    99      27.674  -2.426  11.754  1.00  0.00              
ATOM    125  N   LEU   100      29.409  -3.134  13.071  1.00  0.00              
ATOM    126  CA  LEU   100      28.969  -2.348  14.232  1.00  0.00              
ATOM    127  C   LEU   100      29.152  -0.837  14.066  1.00  0.00              
ATOM    128  O   LEU   100      28.482  -0.063  14.748  1.00  0.00              
ATOM    129  N   LEU   101      30.058  -0.405  13.184  1.00  0.00              
ATOM    130  CA  LEU   101      30.460   1.013  13.201  1.00  0.00              
ATOM    131  C   LEU   101      30.352   1.755  11.875  1.00  0.00              
ATOM    132  O   LEU   101      30.615   2.939  11.789  1.00  0.00              
ATOM    133  N   GLN   102      29.945   1.031  10.860  1.00  0.00              
ATOM    134  CA  GLN   102      29.719   1.554   9.529  1.00  0.00              
ATOM    135  C   GLN   102      28.786   2.777   9.637  1.00  0.00              
ATOM    136  O   GLN   102      27.747   2.730  10.319  1.00  0.00              
ATOM    137  N   SER   104      29.191   3.884   9.012  1.00  0.00              
ATOM    138  CA  SER   104      28.401   5.109   9.036  1.00  0.00              
ATOM    139  C   SER   104      28.491   5.855  10.360  1.00  0.00              
ATOM    140  O   SER   104      27.884   6.919  10.513  1.00  0.00              
ATOM    141  N   ILE   105      29.232   5.294  11.317  1.00  0.00              
ATOM    142  CA  ILE   105      29.505   5.974  12.576  1.00  0.00              
ATOM    143  C   ILE   105      30.976   6.363  12.628  1.00  0.00              
ATOM    144  O   ILE   105      31.288   7.552  12.651  1.00  0.00              
ATOM    145  N   ALA   106      31.878   5.381  12.636  1.00  0.00              
ATOM    146  CA  ALA   106      33.301   5.696  12.615  1.00  0.00              
ATOM    147  C   ALA   106      33.793   5.723  11.181  1.00  0.00              
ATOM    148  O   ALA   106      33.522   4.792  10.422  1.00  0.00              
ATOM    149  N   GLU   107      34.536   6.769  10.820  1.00  0.00              
ATOM    150  CA  GLU   107      35.116   6.865   9.482  1.00  0.00              
ATOM    151  C   GLU   107      35.967   5.627   9.234  1.00  0.00              
ATOM    152  O   GLU   107      36.051   5.146   8.111  1.00  0.00              
ATOM    153  N   GLY   108      36.029  -0.931  10.454  1.00  0.00              
ATOM    154  CA  GLY   108      36.575  -2.119   9.793  1.00  0.00              
ATOM    155  C   GLY   108      38.048  -2.004   9.422  1.00  0.00              
ATOM    156  O   GLY   108      38.618  -2.958   8.911  1.00  0.00              
ATOM    157  N   GLU   109      38.674  -0.853   9.690  1.00  0.00              
ATOM    158  CA  GLU   109      40.063  -0.626   9.269  1.00  0.00              
ATOM    159  C   GLU   109      41.039  -0.703  10.428  1.00  0.00              
ATOM    160  O   GLU   109      40.744  -0.214  11.530  1.00  0.00              
ATOM    161  N   MET   110      42.187  -1.327  10.182  1.00  0.00              
ATOM    162  CA  MET   110      43.299  -1.353  11.119  1.00  0.00              
ATOM    163  C   MET   110      43.802   0.084  11.353  1.00  0.00              
ATOM    164  O   MET   110      43.970   0.845  10.394  1.00  0.00              
END
