
#######################################################
#                                                     #
#                        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  129 (  129),  selected  129 , name T0302TS168_4-D1
# Molecule2: number of CA atoms  129 ( 2108),  selected  129 , name T0302_D1.pdb
# PARAMETERS: T0302TS168_4-D1.T0302_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V       3      V       3          2.723
LGA    S       4      S       4          2.989
LGA    P       5      P       5          2.797
LGA    E       6      -       -           -
LGA    E       7      E       6          2.972
LGA    A       8      E       7          3.205
LGA    V       9      A       8          1.669
LGA    K      10      V       9          0.279
LGA    W      11      K      10          1.526
LGA    G      12      W      11          3.432
LGA    E      13      G      12          3.550
LGA    S      14      E      13          3.272
LGA    F      15      S      14          4.686
LGA    D      16      -       -           -
LGA    K      17      F      15          1.249
LGA    L      18      D      16          3.090
LGA    -       -      K      17           -
LGA    -       -      L      18           -
LGA    L      19      L      19           #
LGA    S      20      S      20          1.792
LGA    H      21      H      21          1.961
LGA    R      22      R      22          2.138
LGA    D      23      D      23          0.755
LGA    G      24      G      24          1.987
LGA    L      25      L      25          1.808
LGA    E      26      E      26          1.429
LGA    A      27      A      27          2.068
LGA    F      28      F      28          1.123
LGA    T      29      T      29          1.000
LGA    R      30      R      30          2.509
LGA    F      31      F      31          2.322
LGA    L      32      L      32          0.452
LGA    K      33      K      33          1.581
LGA    T      34      T      34          2.091
LGA    E      35      E      35          1.318
LGA    F      36      F      36          3.150
LGA    S      37      S      37          3.134
LGA    E      38      E      38          2.493
LGA    E      39      E      39          2.775
LGA    N      40      N      40          1.903
LGA    I      41      I      41          1.089
LGA    E      42      E      42          1.482
LGA    F      43      F      43          0.876
LGA    W      44      W      44          1.057
LGA    I      45      I      45          0.581
LGA    A      46      A      46          0.819
LGA    C      47      C      47          1.098
LGA    E      48      E      48          1.057
LGA    D      49      D      49          0.912
LGA    F      50      F      50          1.355
LGA    K      51      K      51          1.377
LGA    K      52      K      52          2.855
LGA    S      53      S      53          3.587
LGA    K      54      K      54          4.029
LGA    G      55      G      55          1.943
LGA    P      56      P      56          0.802
LGA    Q      57      Q      57          0.612
LGA    Q      58      Q      58          0.916
LGA    I      59      I      59          1.000
LGA    H      60      H      60          0.897
LGA    L      61      L      61          0.835
LGA    K      62      K      62          0.797
LGA    A      63      A      63          0.275
LGA    K      64      K      64          1.300
LGA    A      65      A      65          1.243
LGA    I      66      I      66          0.589
LGA    Y      67      Y      67          0.946
LGA    E      68      E      68          2.293
LGA    K      69      K      69          1.897
LGA    F      70      F      70          0.571
LGA    -       -      I      71           -
LGA    I      71      Q      72          3.349
LGA    -       -      T      73           -
LGA    Q      72      D      74          4.348
LGA    T      73      A      75          3.766
LGA    D      74      P      76          3.191
LGA    A      75      K      77          5.537
LGA    P      76      E      78           #
LGA    K      77      V      79           -
LGA    E      78      -       -           -
LGA    V      79      N      80           #
LGA    N      80      L      81           -
LGA    L      81      D      82           #
LGA    D      82      -       -           -
LGA    F      83      F      83          2.933
LGA    H      84      H      84          3.178
LGA    T      85      T      85          2.365
LGA    K      86      K      86          2.002
LGA    E      87      E      87          2.176
LGA    V      88      V      88          1.707
LGA    I      89      I      89          1.602
LGA    T      90      T      90          1.847
LGA    N      91      N      91          2.434
LGA    S      92      S      92          2.975
LGA    I      93      I      93          2.918
LGA    T      94      T      94          2.493
LGA    Q      95      Q      95          3.315
LGA    P      96      P      96          1.673
LGA    T      97      T      97          2.287
LGA    L      98      L      98          4.104
LGA    H      99      H      99           #
LGA    S     100      S     100          3.497
LGA    F     101      F     101          1.297
LGA    D     102      D     102          0.883
LGA    A     103      A     103          1.274
LGA    A     104      A     104          1.135
LGA    Q     105      Q     105          0.942
LGA    S     106      S     106          1.711
LGA    R     107      R     107          1.108
LGA    V     108      V     108          1.251
LGA    Y     109      Y     109          1.716
LGA    Q     110      Q     110          2.157
LGA    L     111      L     111          1.911
LGA    M     112      M     112          2.682
LGA    E     113      E     113          3.010
LGA    Q     114      Q     114          2.560
LGA    D     115      D     115          3.006
LGA    S     116      S     116          1.908
LGA    Y     117      Y     117          0.654
LGA    T     118      T     118          2.839
LGA    R     119      R     119          1.817
LGA    F     120      F     120          1.701
LGA    L     121      L     121          2.538
LGA    K     122      K     122          2.131
LGA    S     123      S     123          4.251
LGA    D     124      D     124          3.344
LGA    I     125      I     125          3.496
LGA    Y     126      Y     126          2.228
LGA    L     127      L     127          1.932
LGA    D     128      D     128          3.597
LGA    L     129      L     129          5.024
LGA    M     130      M     130          4.385
LGA    E     131      E     131          2.574

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  129  129    5.0    118    2.40    87.29     63.139     4.724

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.507726 * X  +   0.163140 * Y  +  -0.845931 * Z  + 122.825989
  Y_new =  -0.347032 * X  +  -0.859993 * Y  +  -0.374140 * Z  +  -3.763188
  Z_new =  -0.788532 * X  +   0.483526 * Y  +  -0.380026 * Z  +   0.267338 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.236910   -0.904683  [ DEG:   128.1655    -51.8345 ]
  Theta =   0.908419    2.233174  [ DEG:    52.0486    127.9514 ]
  Phi   =  -0.599568    2.542024  [ DEG:   -34.3527    145.6473 ]
 
# 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: T0302TS168_4-D1                               
REMARK     2: T0302_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0302TS168_4-D1.T0302_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  129  129   5.0  118   2.40   87.29  63.139
REMARK  ---------------------------------------------------------- 
MOLECULE T0302TS168_4-D1
PFRMAT TS
TARGET T0302
MODEL 4
PARENT N/A
ATOM      3  CA  VAL     3     143.032   7.411   4.040  1.00 25.00           C
ATOM      4  CA  SER     4     144.547  10.358   2.062  1.00 25.00           C
ATOM      5  CA  PRO     5     143.602  12.851  -0.707  1.00 25.00           C
ATOM      6  CA  GLU     6     140.786  14.026  -3.022  1.00 25.00           C
ATOM      7  CA  GLU     7     142.105  11.762  -5.814  1.00 25.00           C
ATOM      8  CA  ALA     8     142.221   8.798  -3.391  1.00 25.00           C
ATOM      9  CA  VAL     9     138.621   9.518  -2.301  1.00 25.00           C
ATOM     10  CA  LYS    10     137.514   9.656  -5.965  1.00 25.00           C
ATOM     11  CA  TRP    11     139.256   6.315  -6.645  1.00 25.00           C
ATOM     12  CA  GLY    12     137.517   4.762  -3.607  1.00 25.00           C
ATOM     13  CA  GLU    13     134.136   6.067  -4.845  1.00 25.00           C
ATOM     14  CA  SER    14     134.808   4.593  -8.315  1.00 25.00           C
ATOM     15  CA  PHE    15     135.714   1.225  -6.733  1.00 25.00           C
ATOM     16  CA  ASP    16     132.485   1.294  -4.675  1.00 25.00           C
ATOM     17  CA  LYS    17     130.460   2.064  -7.832  1.00 25.00           C
ATOM     18  CA  LEU    18     132.150  -0.848  -9.657  1.00 25.00           C
ATOM     19  CA  LEU    19     131.347  -3.182  -6.727  1.00 25.00           C
ATOM     20  CA  SER    20     133.823  -3.769  -3.860  1.00 25.00           C
ATOM     21  CA  HIS    21     136.575  -1.683  -2.316  1.00 25.00           C
ATOM     22  CA  ARG    22     136.633  -1.251   1.469  1.00 25.00           C
ATOM     23  CA  ASP    23     136.924   1.332   4.281  1.00 25.00           C
ATOM     24  CA  GLY    24     135.098   3.919   2.129  1.00 25.00           C
ATOM     25  CA  LEU    25     132.321   1.385   1.395  1.00 25.00           C
ATOM     26  CA  GLU    26     131.993   0.625   5.134  1.00 25.00           C
ATOM     27  CA  ALA    27     131.765   4.370   5.901  1.00 25.00           C
ATOM     28  CA  PHE    28     129.054   4.776   3.227  1.00 25.00           C
ATOM     29  CA  THR    29     127.105   1.837   4.720  1.00 25.00           C
ATOM     30  CA  ARG    30     127.374   3.399   8.207  1.00 25.00           C
ATOM     31  CA  PHE    31     126.111   6.743   6.834  1.00 25.00           C
ATOM     32  CA  LEU    32     123.162   4.967   5.156  1.00 25.00           C
ATOM     33  CA  LYS    33     122.331   3.186   8.443  1.00 25.00           C
ATOM     34  CA  THR    34     122.449   6.528  10.312  1.00 25.00           C
ATOM     35  CA  GLU    35     120.016   7.970   7.733  1.00 25.00           C
ATOM     36  CA  PHE    36     117.220   6.047   6.024  1.00 25.00           C
ATOM     37  CA  SER    37     118.182   4.219   2.786  1.00 25.00           C
ATOM     38  CA  GLU    38     120.221   1.304   4.173  1.00 25.00           C
ATOM     39  CA  GLU    39     117.625  -1.512   4.170  1.00 25.00           C
ATOM     40  CA  ASN    40     118.812  -2.635   0.706  1.00 25.00           C
ATOM     41  CA  ILE    41     122.443  -2.638   1.924  1.00 25.00           C
ATOM     42  CA  GLU    42     121.443  -4.724   4.977  1.00 25.00           C
ATOM     43  CA  PHE    43     119.607  -7.207   2.710  1.00 25.00           C
ATOM     44  CA  TRP    44     122.693  -7.467   0.456  1.00 25.00           C
ATOM     45  CA  ILE    45     124.905  -8.105   3.517  1.00 25.00           C
ATOM     46  CA  ALA    46     122.498 -10.831   4.719  1.00 25.00           C
ATOM     47  CA  CYS    47     122.570 -12.457   1.252  1.00 25.00           C
ATOM     48  CA  GLU    48     126.399 -12.375   1.265  1.00 25.00           C
ATOM     49  CA  ASP    49     126.446 -13.987   4.739  1.00 25.00           C
ATOM     50  CA  PHE    50     124.048 -16.719   3.531  1.00 25.00           C
ATOM     51  CA  LYS    51     126.282 -17.368   0.488  1.00 25.00           C
ATOM     52  CA  LYS    52     129.056 -19.602   1.815  1.00 25.00           C
ATOM     53  CA  SER    53     126.303 -22.121   2.249  1.00 25.00           C
ATOM     54  CA  LYS    54     124.921 -25.354   0.898  1.00 25.00           C
ATOM     55  CA  GLY    55     124.563 -26.963   4.328  1.00 25.00           C
ATOM     56  CA  PRO    56     120.783 -27.399   4.303  1.00 25.00           C
ATOM     57  CA  GLN    57     118.736 -26.702   7.463  1.00 25.00           C
ATOM     58  CA  GLN    58     121.046 -23.778   8.344  1.00 25.00           C
ATOM     59  CA  ILE    59     120.659 -22.372   4.803  1.00 25.00           C
ATOM     60  CA  HIS    60     116.850 -22.666   5.076  1.00 25.00           C
ATOM     61  CA  LEU    61     116.927 -20.851   8.449  1.00 25.00           C
ATOM     62  CA  LYS    62     119.076 -18.069   6.929  1.00 25.00           C
ATOM     63  CA  ALA    63     116.620 -17.732   4.009  1.00 25.00           C
ATOM     64  CA  LYS    64     113.691 -17.512   6.468  1.00 25.00           C
ATOM     65  CA  ALA    65     115.532 -14.807   8.457  1.00 25.00           C
ATOM     66  CA  ILE    66     116.189 -12.848   5.233  1.00 25.00           C
ATOM     67  CA  TYR    67     112.487 -13.115   4.289  1.00 25.00           C
ATOM     68  CA  GLU    68     111.483 -11.863   7.766  1.00 25.00           C
ATOM     69  CA  LYS    69     113.901  -8.912   7.428  1.00 25.00           C
ATOM     70  CA  PHE    70     112.432  -8.070   3.993  1.00 25.00           C
ATOM     71  CA  ILE    71     108.892  -8.195   5.448  1.00 25.00           C
ATOM     72  CA  GLN    72     106.437 -10.826   6.524  1.00 25.00           C
ATOM     73  CA  THR    73     104.303  -8.106   8.209  1.00 25.00           C
ATOM     74  CA  ASP    74     106.435  -6.390  10.888  1.00 25.00           C
ATOM     75  CA  ALA    75     106.223  -3.430   8.439  1.00 25.00           C
ATOM     76  CA  PRO    76     106.019   0.065   7.026  1.00 25.00           C
ATOM     77  CA  LYS    77     104.181  -0.890   3.769  1.00 25.00           C
ATOM     78  CA  GLU    78     103.274   1.314   0.763  1.00 25.00           C
ATOM     79  CA  VAL    79     106.000  -0.007  -1.443  1.00 25.00           C
ATOM     80  CA  ASN    80     103.118  -1.008  -3.786  1.00 25.00           C
ATOM     81  CA  LEU    81     105.540  -3.411  -5.467  1.00 25.00           C
ATOM     82  CA  ASP    82     103.109  -5.420  -7.594  1.00 25.00           C
ATOM     83  CA  PHE    83     105.855  -7.841  -8.388  1.00 25.00           C
ATOM     84  CA  HIS    84     106.951 -11.102 -10.072  1.00 25.00           C
ATOM     85  CA  THR    85     110.410 -10.802  -8.457  1.00 25.00           C
ATOM     86  CA  LYS    86     108.789 -10.225  -5.034  1.00 25.00           C
ATOM     87  CA  GLU    87     106.569 -13.305  -5.539  1.00 25.00           C
ATOM     88  CA  VAL    88     109.638 -15.392  -6.487  1.00 25.00           C
ATOM     89  CA  ILE    89     111.468 -14.168  -3.354  1.00 25.00           C
ATOM     90  CA  THR    90     108.440 -15.086  -1.196  1.00 25.00           C
ATOM     91  CA  ASN    91     108.337 -18.572  -2.780  1.00 25.00           C
ATOM     92  CA  SER    92     112.077 -19.022  -2.089  1.00 25.00           C
ATOM     93  CA  ILE    93     111.558 -17.960   1.553  1.00 25.00           C
ATOM     94  CA  THR    94     110.128 -21.450   1.880  1.00 25.00           C
ATOM     95  CA  GLN    95     111.930 -24.737   1.089  1.00 25.00           C
ATOM     96  CA  PRO    96     114.978 -23.059  -0.493  1.00 25.00           C
ATOM     97  CA  THR    97     118.195 -23.615  -2.553  1.00 25.00           C
ATOM     98  CA  LEU    98     120.033 -20.411  -3.499  1.00 25.00           C
ATOM     99  CA  HIS    99     118.470 -18.515  -6.406  1.00 25.00           C
ATOM    100  CA  SER   100     115.771 -16.077  -5.207  1.00 25.00           C
ATOM    101  CA  PHE   101     118.152 -14.721  -2.531  1.00 25.00           C
ATOM    102  CA  ASP   102     120.891 -14.257  -5.167  1.00 25.00           C
ATOM    103  CA  ALA   103     118.427 -12.399  -7.435  1.00 25.00           C
ATOM    104  CA  ALA   104     117.411 -10.134  -4.518  1.00 25.00           C
ATOM    105  CA  GLN   105     121.095  -9.403  -3.770  1.00 25.00           C
ATOM    106  CA  SER   106     121.700  -8.547  -7.454  1.00 25.00           C
ATOM    107  CA  ARG   107     118.673  -6.201  -7.430  1.00 25.00           C
ATOM    108  CA  VAL   108     119.988  -4.498  -4.261  1.00 25.00           C
ATOM    109  CA  TYR   109     123.425  -4.061  -5.893  1.00 25.00           C
ATOM    110  CA  GLN   110     121.784  -2.541  -9.002  1.00 25.00           C
ATOM    111  CA  LEU   111     119.783  -0.131  -6.798  1.00 25.00           C
ATOM    112  CA  MET   112     122.987   0.887  -4.961  1.00 25.00           C
ATOM    113  CA  GLU   113     124.742   1.497  -8.310  1.00 25.00           C
ATOM    114  CA  GLN   114     121.796   3.642  -9.491  1.00 25.00           C
ATOM    115  CA  ASP   115     120.207   6.465  -7.537  1.00 25.00           C
ATOM    116  CA  SER   116     121.788   6.315  -4.064  1.00 25.00           C
ATOM    117  CA  TYR   117     125.576   6.282  -4.039  1.00 25.00           C
ATOM    118  CA  THR   118     127.178   9.259  -5.838  1.00 25.00           C
ATOM    119  CA  ARG   119     124.339  11.537  -4.647  1.00 25.00           C
ATOM    120  CA  PHE   120     124.811  10.290  -1.057  1.00 25.00           C
ATOM    121  CA  LEU   121     128.574  10.966  -1.290  1.00 25.00           C
ATOM    122  CA  LYS   122     128.818  13.748  -3.897  1.00 25.00           C
ATOM    123  CA  SER   123     127.057  16.704  -2.165  1.00 25.00           C
ATOM    124  CA  ASP   124     128.967  17.601   1.042  1.00 25.00           C
ATOM    125  CA  ILE   125     129.540  15.231   3.995  1.00 25.00           C
ATOM    126  CA  TYR   126     132.294  13.422   2.042  1.00 25.00           C
ATOM    127  CA  LEU   127     133.950  16.777   1.223  1.00 25.00           C
ATOM    128  CA  ASP   128     133.807  17.777   4.918  1.00 25.00           C
ATOM    129  CA  LEU   129     135.386  14.432   5.909  1.00 25.00           C
ATOM    130  CA  MET   130     138.166  14.951   3.327  1.00 25.00           C
ATOM    131  CA  GLU   131     138.406  18.754   3.175  1.00 25.00           C
TER
END
