
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0307TS168_4-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307TS168_4-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      10      I      10           -
LGA    M      11      M      11           -
LGA    T      12      T      12           -
LGA    -       -      F      13           -
LGA    -       -      S      14           -
LGA    -       -      G      15           -
LGA    -       -      Q      16           -
LGA    -       -      E      17           -
LGA    -       -      L      18           -
LGA    -       -      T      19           -
LGA    F      13      A      20           #
LGA    S      14      I      21           -
LGA    -       -      I      22           -
LGA    G      15      K      23           #
LGA    Q      16      M      24           -
LGA    -       -      A      25           -
LGA    E      17      K      26           #
LGA    L      18      S      27          3.247
LGA    -       -      M      28           -
LGA    -       -      V      29           -
LGA    T      19      M      30          2.683
LGA    A      20      A      31          2.278
LGA    I      21      D      32          4.031
LGA    I      22      G      33          4.673
LGA    K      23      K      34          1.981
LGA    M      24      -       -           -
LGA    A      25      -       -           -
LGA    K      26      -       -           -
LGA    S      27      -       -           -
LGA    M      28      -       -           -
LGA    V      29      -       -           -
LGA    M      30      -       -           -
LGA    A      31      -       -           -
LGA    D      32      -       -           -
LGA    G      33      -       -           -
LGA    K      34      -       -           -
LGA    I      35      -       -           -
LGA    K      36      -       -           -
LGA    P      37      -       -           -
LGA    A      38      -       -           -
LGA    E      39      -       -           -
LGA    I      40      -       -           -
LGA    A      41      -       -           -
LGA    V      42      -       -           -
LGA    M      43      -       -           -
LGA    T      44      -       -           -
LGA    R      45      -       -           -
LGA    E      46      -       -           -
LGA    F      47      -       -           -
LGA    M      48      -       -           -
LGA    R      49      -       -           -
LGA    F      50      -       -           -
LGA    G      51      -       -           -
LGA    I      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    D      55      -       -           -
LGA    Q      56      -       -           -
LGA    V      57      I      35          4.911
LGA    D      58      -       -           -
LGA    L      59      -       -           -
LGA    L      60      K      36          1.941
LGA    L      61      P      37          1.856
LGA    K      62      A      38          1.762
LGA    A      63      E      39          1.292
LGA    S      64      I      40          1.408
LGA    D      65      A      41          1.573
LGA    S      66      V      42          1.166
LGA    I      67      M      43          1.215
LGA    E      68      T      44          1.345
LGA    A      69      R      45          2.059
LGA    S      70      E      46          2.508
LGA    Q      71      F      47          1.952
LGA    A      72      M      48          1.422
LGA    V      73      R      49          0.887
LGA    A      74      F      50          1.286
LGA    L      75      G      51          2.740
LGA    -       -      I      52           -
LGA    I      76      L      53           #
LGA    A      77      Q      54           -
LGA    R      78      D      55           -
LGA    M      79      Q      56           -
LGA    D      80      V      57           -
LGA    E      81      D      58           -
LGA    E      82      L      59           -
LGA    R      83      L      60           -
LGA    K      84      L      61           -
LGA    K      85      K      62           -
LGA    Y      86      A      63           -
LGA    V      87      S      64           -
LGA    A      88      D      65           -
LGA    S      89      S      66           -
LGA    Y      90      I      67           -
LGA    L      91      E      68           -
LGA    G      92      A      69           -
LGA    V      93      S      70           -
LGA    I      94      Q      71           -
LGA    M      95      A      72           -
LGA    A      96      V      73           -
LGA    S      97      A      74           -
LGA    D      98      L      75           -
LGA    G      99      I      76           -
LGA    D     100      A      77           -
LGA    I     101      R      78           -
LGA    D     102      -       -           -
LGA    D     103      -       -           -
LGA    N     104      -       -           -
LGA    E     105      M      79          4.515
LGA    -       -      D      80           -
LGA    L     106      E      81          3.512
LGA    A     107      E      82          3.671
LGA    L     108      R      83          3.729
LGA    W     109      K      84          1.811
LGA    T     110      K      85          1.057
LGA    L     111      Y      86          2.797
LGA    I     112      V      87          3.493
LGA    S     113      A      88          2.863
LGA    T     114      S      89          3.200
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    L     115      G      92          1.021
LGA    C     116      V      93          5.163
LGA    G     117      I      94           -
LGA    -       -      M      95           -
LGA    -       -      A      96           -
LGA    -       -      S      97           -
LGA    -       -      D      98           -
LGA    -       -      G      99           -
LGA    L     118      D     100          2.730
LGA    P     119      I     101          3.846
LGA    -       -      D     102           -
LGA    T     120      D     103          5.021
LGA    -       -      N     104           -
LGA    -       -      E     105           -
LGA    M     121      L     106          3.418
LGA    T     122      A     107          2.474
LGA    -       -      L     108           -
LGA    -       -      W     109           -
LGA    V     123      T     110          3.275
LGA    M     124      L     111          2.097
LGA    E     125      I     112          2.401
LGA    A     126      S     113          1.759
LGA    I     127      T     114          1.001
LGA    N     128      L     115          2.476
LGA    N     129      C     116          3.883
LGA    M     130      G     117          2.842
LGA    K     131      L     118           #
LGA    N     132      P     119           -
LGA    -       -      T     120           -
LGA    -       -      M     121           -
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  123    5.0     48    2.84     4.17     25.189     1.634

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.861469 * X  +   0.079105 * Y  +  -0.501611 * Z  +  21.550524
  Y_new =  -0.083326 * X  +  -0.996424 * Y  +  -0.014032 * Z  +   9.210380
  Z_new =  -0.500927 * X  +   0.029709 * Y  +   0.864979 * Z  +  22.904636 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.034333   -3.107260  [ DEG:     1.9671   -178.0329 ]
  Theta =   0.524670    2.616923  [ DEG:    30.0614    149.9386 ]
  Phi   =  -3.045167    0.096426  [ DEG:  -174.4752      5.5248 ]
 
# 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: T0307TS168_4-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS168_4-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  123   5.0   48   2.84    4.17  25.189
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS168_4-D1
PFRMAT TS
TARGET T0307
MODEL 4
PARENT N/A
ATOM     10  CA  ILE    10      34.965  -4.292  29.104  1.00 25.00           C
ATOM     11  CA  MET    11      32.868  -1.180  29.698  1.00 25.00           C
ATOM     12  CA  THR    12      34.401   2.278  30.365  1.00 25.00           C
ATOM     13  CA  PHE    13      32.120   5.336  30.490  1.00 25.00           C
ATOM     14  CA  SER    14      34.531   7.943  29.133  1.00 25.00           C
ATOM     15  CA  GLY    15      32.024   8.746  26.452  1.00 25.00           C
ATOM     16  CA  GLN    16      33.149   5.493  24.773  1.00 25.00           C
ATOM     17  CA  GLU    17      29.498   4.411  24.366  1.00 25.00           C
ATOM     18  CA  LEU    18      28.639   7.808  22.819  1.00 25.00           C
ATOM     19  CA  THR    19      31.587   7.477  20.396  1.00 25.00           C
ATOM     20  CA  ALA    20      30.420   3.963  19.417  1.00 25.00           C
ATOM     21  CA  ILE    21      26.875   5.281  18.813  1.00 25.00           C
ATOM     22  CA  ILE    22      28.271   8.105  16.634  1.00 25.00           C
ATOM     23  CA  LYS    23      30.328   5.574  14.628  1.00 25.00           C
ATOM     24  CA  MET    24      27.216   3.396  14.136  1.00 25.00           C
ATOM     25  CA  ALA    25      25.238   6.451  12.946  1.00 25.00           C
ATOM     26  CA  LYS    26      28.035   7.336  10.484  1.00 25.00           C
ATOM     27  CA  SER    27      28.041   3.741   9.162  1.00 25.00           C
ATOM     28  CA  MET    28      24.239   3.873   8.716  1.00 25.00           C
ATOM     29  CA  VAL    29      24.551   7.189   6.825  1.00 25.00           C
ATOM     30  CA  MET    30      27.243   5.673   4.561  1.00 25.00           C
ATOM     31  CA  ALA    31      26.726   5.797   0.831  1.00 25.00           C
ATOM     32  CA  ASP    32      27.619   6.079  -2.857  1.00 25.00           C
ATOM     33  CA  GLY    33      28.638   6.643  -6.480  1.00 25.00           C
ATOM     34  CA  LYS    34      30.337   6.965  -9.814  1.00 25.00           C
ATOM     35  CA  ILE    35      32.028   7.822 -13.160  1.00 25.00           C
ATOM     36  CA  LYS    36      34.657   8.716 -15.799  1.00 25.00           C
ATOM     37  CA  PRO    37      38.105   9.534 -17.296  1.00 25.00           C
ATOM     38  CA  ALA    38      39.279   7.144 -14.543  1.00 25.00           C
ATOM     39  CA  GLU    39      40.770  10.084 -12.592  1.00 25.00           C
ATOM     40  CA  ILE    40      37.478  12.013 -12.937  1.00 25.00           C
ATOM     41  CA  ALA    41      35.532   8.963 -11.680  1.00 25.00           C
ATOM     42  CA  VAL    42      37.900   8.653  -8.687  1.00 25.00           C
ATOM     43  CA  MET    43      37.425  12.370  -7.896  1.00 25.00           C
ATOM     44  CA  THR    44      33.623  11.949  -8.079  1.00 25.00           C
ATOM     45  CA  ARG    45      33.819   8.939  -5.719  1.00 25.00           C
ATOM     46  CA  GLU    46      35.954  10.965  -3.270  1.00 25.00           C
ATOM     47  CA  PHE    47      33.417  13.832  -3.393  1.00 25.00           C
ATOM     48  CA  MET    48      30.564  11.370  -2.714  1.00 25.00           C
ATOM     49  CA  ARG    49      32.492   9.919   0.261  1.00 25.00           C
ATOM     50  CA  PHE    50      33.077  13.445   1.634  1.00 25.00           C
ATOM     51  CA  GLY    51      29.347  14.232   1.270  1.00 25.00           C
ATOM     52  CA  ILE    52      28.459  10.992   3.109  1.00 25.00           C
ATOM     53  CA  LEU    53      30.899  11.891   5.921  1.00 25.00           C
ATOM     54  CA  GLN    54      29.340  15.379   6.192  1.00 25.00           C
ATOM     55  CA  ASP    55      25.843  13.828   6.372  1.00 25.00           C
ATOM     56  CA  GLN    56      27.016  11.439   9.125  1.00 25.00           C
ATOM     57  CA  VAL    57      28.507  14.380  11.075  1.00 25.00           C
ATOM     58  CA  ASP    58      25.216  16.308  10.731  1.00 25.00           C
ATOM     59  CA  LEU    59      23.269  13.258  11.987  1.00 25.00           C
ATOM     60  CA  LEU    60      25.637  12.949  14.981  1.00 25.00           C
ATOM     61  CA  LEU    61      25.163  16.666  15.772  1.00 25.00           C
ATOM     62  CA  LYS    62      21.360  16.244  15.590  1.00 25.00           C
ATOM     63  CA  ALA    63      21.556  13.234  17.949  1.00 25.00           C
ATOM     64  CA  SER    64      23.691  15.262  20.398  1.00 25.00           C
ATOM     65  CA  ASP    65      21.155  18.128  20.275  1.00 25.00           C
ATOM     66  CA  SER    66      18.301  15.665  20.955  1.00 25.00           C
ATOM     67  CA  ILE    67      20.230  14.214  23.929  1.00 25.00           C
ATOM     68  CA  GLU    68      20.814  17.741  25.302  1.00 25.00           C
ATOM     69  CA  ALA    69      17.084  18.527  24.938  1.00 25.00           C
ATOM     70  CA  SER    70      16.197  15.288  26.777  1.00 25.00           C
ATOM     71  CA  GLN    71      18.636  16.186  29.589  1.00 25.00           C
ATOM     72  CA  ALA    72      17.077  19.675  29.860  1.00 25.00           C
ATOM     73  CA  VAL    73      13.579  18.124  30.040  1.00 25.00           C
ATOM     74  CA  ALA    74      14.754  15.735  32.793  1.00 25.00           C
ATOM     75  CA  LEU    75      16.244  18.675  34.743  1.00 25.00           C
ATOM     76  CA  ILE    76      12.953  20.604  34.399  1.00 25.00           C
ATOM     77  CA  ALA    77      11.007  17.553  35.655  1.00 25.00           C
ATOM     78  CA  ARG    78      13.375  17.244  38.649  1.00 25.00           C
ATOM     79  CA  MET    79      12.900  20.961  39.440  1.00 25.00           C
ATOM     80  CA  ASP    80       9.097  20.540  39.258  1.00 25.00           C
ATOM     81  CA  GLU    81       9.294  17.529  41.617  1.00 25.00           C
ATOM     82  CA  GLU    82      11.429  19.557  44.066  1.00 25.00           C
ATOM     83  CA  ARG    83       8.891  22.423  43.943  1.00 25.00           C
ATOM     84  CA  LYS    84       6.039  19.960  44.623  1.00 25.00           C
ATOM     85  CA  LYS    85       7.967  18.510  47.596  1.00 25.00           C
ATOM     86  CA  TYR    86       8.551  22.036  48.970  1.00 25.00           C
ATOM     87  CA  VAL    87       4.820  22.822  48.606  1.00 25.00           C
ATOM     88  CA  ALA    88       3.934  19.583  50.445  1.00 25.00           C
ATOM     89  CA  SER    89       6.373  20.482  53.257  1.00 25.00           C
ATOM     90  CA  TYR    90       4.814  23.970  53.527  1.00 25.00           C
ATOM     91  CA  LEU    91       1.316  22.419  53.708  1.00 25.00           C
ATOM     92  CA  GLY    92       2.491  20.030  56.462  1.00 25.00           C
ATOM     93  CA  VAL    93       3.981  22.971  58.411  1.00 25.00           C
ATOM     94  CA  ILE    94       0.690  24.898  58.066  1.00 25.00           C
ATOM     95  CA  MET    95      -1.256  21.848  59.323  1.00 25.00           C
ATOM     96  CA  ALA    96       1.112  21.541  62.318  1.00 25.00           C
ATOM     97  CA  SER    97       2.496  18.554  60.467  1.00 25.00           C
ATOM     98  CA  ASP    98       3.882  16.008  57.919  1.00 25.00           C
ATOM     99  CA  GLY    99       4.757  14.186  54.659  1.00 25.00           C
ATOM    100  CA  ASP   100       6.036  12.828  51.409  1.00 25.00           C
ATOM    101  CA  ILE   101       7.140  11.464  47.985  1.00 25.00           C
ATOM    102  CA  ASP   102       8.301  10.312  44.552  1.00 25.00           C
ATOM    103  CA  ASP   103       9.422   9.570  40.993  1.00 25.00           C
ATOM    104  CA  ASN   104      11.704  11.729  38.802  1.00 25.00           C
ATOM    105  CA  GLU   105      14.147   8.805  38.421  1.00 25.00           C
ATOM    106  CA  LEU   106      11.261   6.489  37.433  1.00 25.00           C
ATOM    107  CA  ALA   107      10.063   9.047  34.845  1.00 25.00           C
ATOM    108  CA  LEU   108      13.609   9.302  33.421  1.00 25.00           C
ATOM    109  CA  TRP   109      13.819   5.485  33.192  1.00 25.00           C
ATOM    110  CA  THR   110      10.443   5.384  31.384  1.00 25.00           C
ATOM    111  CA  LEU   111      11.649   8.064  28.930  1.00 25.00           C
ATOM    112  CA  ILE   112      14.849   6.064  28.278  1.00 25.00           C
ATOM    113  CA  SER   113      12.775   2.906  27.648  1.00 25.00           C
ATOM    114  CA  THR   114      10.538   4.832  25.207  1.00 25.00           C
ATOM    115  CA  LEU   115      13.632   6.149  23.374  1.00 25.00           C
ATOM    116  CA  CYS   116      14.408   4.169  20.290  1.00 25.00           C
ATOM    117  CA  GLY   117      11.105   2.894  18.949  1.00 25.00           C
ATOM    118  CA  LEU   118      12.048   3.452  15.279  1.00 25.00           C
ATOM    119  CA  PRO   119      12.757  -0.304  15.246  1.00 25.00           C
ATOM    120  CA  THR   120      13.235  -3.086  17.882  1.00 25.00           C
ATOM    121  CA  MET   121      14.714  -2.079  21.248  1.00 25.00           C
ATOM    122  CA  THR   122      18.102  -3.602  22.079  1.00 25.00           C
ATOM    123  CA  VAL   123      17.182  -5.534  25.256  1.00 25.00           C
ATOM    124  CA  MET   124      20.745  -5.091  26.586  1.00 25.00           C
ATOM    125  CA  GLU   125      20.578  -1.336  25.858  1.00 25.00           C
ATOM    126  CA  ALA   126      17.222  -1.105  27.690  1.00 25.00           C
ATOM    127  CA  ILE   127      18.705  -2.964  30.691  1.00 25.00           C
ATOM    128  CA  ASN   128      21.696  -0.571  30.726  1.00 25.00           C
ATOM    129  CA  ASN   129      19.324   2.434  30.622  1.00 25.00           C
ATOM    130  CA  MET   130      17.307   0.975  33.533  1.00 25.00           C
ATOM    131  CA  LYS   131      20.570   0.784  35.437  1.00 25.00           C
ATOM    132  CA  ASN   132      22.687   3.580  36.947  1.00 25.00           C
TER
END
