
#######################################################
#                                                     #
#                        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  143 (  143),  selected  143 , name T0338TS168_3-D1
# Molecule2: number of CA atoms  143 ( 1129),  selected  143 , name T0338_D1.pdb
# PARAMETERS: T0338TS168_3-D1.T0338_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       1           -
LGA    -       -      S       2           -
LGA    -       -      S       3           -
LGA    -       -      R       4           -
LGA    -       -      W       5           -
LGA    -       -      F       6           -
LGA    -       -      F       7           -
LGA    -       -      T       8           -
LGA    -       -      R       9           -
LGA    -       -      E      10           -
LGA    -       -      Q      11           -
LGA    -       -      L      12           -
LGA    -       -      E      13           -
LGA    -       -      N      14           -
LGA    -       -      T      15           -
LGA    -       -      P      16           -
LGA    -       -      S      17           -
LGA    -       -      R      18           -
LGA    -       -      R      19           -
LGA    -       -      C      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      E      23           -
LGA    -       -      A      24           -
LGA    -       -      D      25           -
LGA    -       -      K      26           -
LGA    -       -      E      27           -
LGA    -       -      L      28           -
LGA    A       1      S      29           #
LGA    S       2      -       -           -
LGA    S       3      -       -           -
LGA    R       4      C      30           #
LGA    W       5      R      31           -
LGA    -       -      Q      32           -
LGA    -       -      Q      33           -
LGA    F       6      A      34          3.192
LGA    F       7      A      35          3.613
LGA    -       -      N      36           -
LGA    -       -      L      37           -
LGA    T       8      I      38          2.859
LGA    R       9      Q      39          3.426
LGA    E      10      E      40          4.034
LGA    Q      11      M      41          5.239
LGA    L      12      G      42          5.040
LGA    E      13      Q      43          4.329
LGA    N      14      R      44           #
LGA    T      15      -       -           -
LGA    P      16      -       -           -
LGA    S      17      -       -           -
LGA    R      18      -       -           -
LGA    R      19      -       -           -
LGA    C      20      -       -           -
LGA    G      21      -       -           -
LGA    V      22      -       -           -
LGA    E      23      -       -           -
LGA    A      24      -       -           -
LGA    D      25      -       -           -
LGA    K      26      -       -           -
LGA    E      27      -       -           -
LGA    L      28      -       -           -
LGA    S      29      -       -           -
LGA    C      30      -       -           -
LGA    R      31      L      45           #
LGA    Q      32      N      46          4.766
LGA    Q      33      -       -           -
LGA    A      34      -       -           -
LGA    A      35      V      47          0.856
LGA    N      36      S      48          1.509
LGA    L      37      -       -           -
LGA    I      38      -       -           -
LGA    Q      39      Q      49          2.546
LGA    E      40      L      50          1.161
LGA    M      41      T      51          4.026
LGA    G      42      I      52          3.969
LGA    Q      43      N      53          3.162
LGA    R      44      T      54           #
LGA    L      45      A      55           -
LGA    N      46      I      56           -
LGA    V      47      V      57           -
LGA    S      48      Y      58           -
LGA    Q      49      M      59           -
LGA    L      50      H      60           -
LGA    T      51      R      61           -
LGA    I      52      F      62           -
LGA    N      53      Y      63           -
LGA    T      54      M      64           -
LGA    A      55      H      65           -
LGA    I      56      H      66           -
LGA    V      57      S      67           -
LGA    Y      58      F      68           -
LGA    M      59      T      69           -
LGA    H      60      K      70           -
LGA    R      61      F      71           -
LGA    F      62      N      72           -
LGA    Y      63      K      73           -
LGA    M      64      N      74           -
LGA    H      65      I      75           -
LGA    H      66      I      76           -
LGA    S      67      S      77           -
LGA    F      68      S      78           -
LGA    T      69      T      79           -
LGA    K      70      A      80           -
LGA    F      71      -       -           -
LGA    N      72      -       -           -
LGA    K      73      -       -           -
LGA    N      74      -       -           -
LGA    I      75      -       -           -
LGA    I      76      -       -           -
LGA    S      77      -       -           -
LGA    S      78      L      81           #
LGA    T      79      F      82          2.844
LGA    A      80      -       -           -
LGA    L      81      -       -           -
LGA    F      82      L      83          2.034
LGA    L      83      A      84          1.961
LGA    A      84      A      85           -
LGA    A      85      K      86           -
LGA    K      86      V      87           -
LGA    V      87      E      88           -
LGA    E      88      E      89           -
LGA    E      89      Q      90           -
LGA    Q      90      A      91           -
LGA    A      91      R      92           -
LGA    R      92      K      93           -
LGA    K      93      L      94           -
LGA    L      94      E      95           -
LGA    E      95      H      96           -
LGA    H      96      -       -           -
LGA    V      97      -       -           -
LGA    I      98      -       -           -
LGA    K      99      -       -           -
LGA    V     100      -       -           -
LGA    A     101      V      97           #
LGA    H     102      I      98          4.618
LGA    -       -      K      99           -
LGA    -       -      V     100           -
LGA    -       -      A     101           -
LGA    A     103      H     102          3.661
LGA    C     104      A     103           -
LGA    L     105      C     104           -
LGA    -       -      L     105           -
LGA    H     106      H     106          4.918
LGA    -       -      P     107           -
LGA    -       -      L     108           -
LGA    -       -      E     109           -
LGA    P     107      P     110          4.334
LGA    L     108      L     111           -
LGA    E     109      L     112           #
LGA    P     110      D     113           #
LGA    L     111      T     114          5.648
LGA    L     112      K     115          2.275
LGA    D     113      C     116          2.432
LGA    -       -      D     117           -
LGA    T     114      A     118          1.669
LGA    K     115      Y     119          1.486
LGA    C     116      L     120          1.536
LGA    D     117      Q     121          1.041
LGA    A     118      Q     122          0.790
LGA    Y     119      T     123          0.998
LGA    L     120      R     124          0.860
LGA    Q     121      E     125          0.565
LGA    Q     122      L     126          0.691
LGA    T     123      V     127          0.709
LGA    R     124      I     128          0.590
LGA    E     125      L     129          0.480
LGA    L     126      E     130          0.417
LGA    V     127      T     131          0.512
LGA    I     128      I     132          0.514
LGA    L     129      M     133          0.885
LGA    E     130      L     134          1.227
LGA    T     131      Q     135          1.613
LGA    I     132      T     136          1.733
LGA    M     133      L     137          2.459
LGA    L     134      G     138          2.962
LGA    Q     135      F     139           -
LGA    T     136      -       -           -
LGA    L     137      -       -           -
LGA    G     138      -       -           -
LGA    F     139      -       -           -
LGA    E     140      -       -           -
LGA    I     141      E     140          2.404
LGA    T     142      I     141           #
LGA    I     143      T     142           -
LGA    -       -      I     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  143  143    5.0     48    2.83    10.42     22.774     1.637

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.237901 * X  +   0.801609 * Y  +  -0.548476 * Z  + -24.593456
  Y_new =   0.680668 * X  +  -0.540425 * Y  +  -0.494603 * Z  +  33.819138
  Z_new =  -0.692888 * X  +  -0.255664 * Y  +  -0.674197 * Z  +  45.703091 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.779134    0.362458  [ DEG:  -159.2327     20.7673 ]
  Theta =   0.765487    2.376106  [ DEG:    43.8592    136.1408 ]
  Phi   =   1.234557   -1.907036  [ DEG:    70.7349   -109.2651 ]
 
# 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: T0338TS168_3-D1                               
REMARK     2: T0338_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS168_3-D1.T0338_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  143  143   5.0   48   2.83   10.42  22.774
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS168_3-D1
PFRMAT TS
TARGET T0338
MODEL 3
PARENT N/A
ATOM      1  CA  ALA     1       1.393  29.673  67.173  1.00 25.00           C
ATOM      2  CA  SER     2       0.715  33.306  66.158  1.00 25.00           C
ATOM      3  CA  SER     3      -2.054  32.897  63.623  1.00 25.00           C
ATOM      4  CA  ARG     4      -5.346  31.832  65.333  1.00 25.00           C
ATOM      5  CA  TRP     5      -7.149  34.370  63.091  1.00 25.00           C
ATOM      6  CA  PHE     6      -9.522  31.693  61.970  1.00 25.00           C
ATOM      7  CA  PHE     7     -12.753  30.864  63.887  1.00 25.00           C
ATOM      8  CA  THR     8     -16.152  32.299  64.804  1.00 25.00           C
ATOM      9  CA  ARG     9     -17.928  34.185  67.590  1.00 25.00           C
ATOM     10  CA  GLU    10     -16.680  36.817  70.076  1.00 25.00           C
ATOM     11  CA  GLN    11     -15.622  39.088  67.180  1.00 25.00           C
ATOM     12  CA  LEU    12     -19.069  38.671  65.562  1.00 25.00           C
ATOM     13  CA  GLU    13     -20.761  39.550  68.884  1.00 25.00           C
ATOM     14  CA  ASN    14     -20.714  42.378  71.339  1.00 25.00           C
ATOM     15  CA  THR    15     -20.680  44.583  68.261  1.00 25.00           C
ATOM     16  CA  PRO    16     -22.826  47.270  69.949  1.00 25.00           C
ATOM     17  CA  SER    17     -21.727  50.317  71.977  1.00 25.00           C
ATOM     18  CA  ARG    18     -20.705  53.991  71.367  1.00 25.00           C
ATOM     19  CA  ARG    19     -22.943  55.200  68.527  1.00 25.00           C
ATOM     20  CA  CYS    20     -26.603  54.737  67.592  1.00 25.00           C
ATOM     21  CA  GLY    21     -27.758  54.341  64.012  1.00 25.00           C
ATOM     22  CA  VAL    22     -31.421  53.725  63.126  1.00 25.00           C
ATOM     23  CA  GLU    23     -35.032  52.622  62.803  1.00 25.00           C
ATOM     24  CA  ALA    24     -34.600  49.193  61.176  1.00 25.00           C
ATOM     25  CA  ASP    25     -36.171  46.623  63.541  1.00 25.00           C
ATOM     26  CA  LYS    26     -37.171  44.446  60.553  1.00 25.00           C
ATOM     27  CA  GLU    27     -33.605  44.660  59.173  1.00 25.00           C
ATOM     28  CA  LEU    28     -32.196  43.651  62.588  1.00 25.00           C
ATOM     29  CA  SER    29     -34.605  40.676  62.730  1.00 25.00           C
ATOM     30  CA  CYS    30     -33.529  39.607  59.213  1.00 25.00           C
ATOM     31  CA  ARG    31     -29.847  39.842  60.240  1.00 25.00           C
ATOM     32  CA  GLN    32     -30.555  37.718  63.348  1.00 25.00           C
ATOM     33  CA  GLN    33     -32.343  35.110  61.189  1.00 25.00           C
ATOM     34  CA  ALA    34     -29.368  35.028  58.779  1.00 25.00           C
ATOM     35  CA  ALA    35     -26.965  34.554  61.723  1.00 25.00           C
ATOM     36  CA  ASN    36     -29.127  31.688  63.058  1.00 25.00           C
ATOM     37  CA  LEU    37     -29.132  30.047  59.598  1.00 25.00           C
ATOM     38  CA  ILE    38     -25.321  30.371  59.412  1.00 25.00           C
ATOM     39  CA  GLN    39     -24.993  28.788  62.884  1.00 25.00           C
ATOM     40  CA  GLU    40     -27.270  25.903  61.812  1.00 25.00           C
ATOM     41  CA  MET    41     -25.160  25.376  58.659  1.00 25.00           C
ATOM     42  CA  GLY    42     -21.967  25.333  60.774  1.00 25.00           C
ATOM     43  CA  GLN    43     -23.540  22.764  63.140  1.00 25.00           C
ATOM     44  CA  ARG    44     -24.539  20.587  60.151  1.00 25.00           C
ATOM     45  CA  LEU    45     -28.237  20.812  61.204  1.00 25.00           C
ATOM     46  CA  ASN    46     -30.984  18.137  61.385  1.00 25.00           C
ATOM     47  CA  VAL    47     -31.759  18.084  57.652  1.00 25.00           C
ATOM     48  CA  SER    48     -32.606  17.578  53.937  1.00 25.00           C
ATOM     49  CA  GLN    49     -30.367  19.608  51.629  1.00 25.00           C
ATOM     50  CA  LEU    50     -29.865  21.824  54.712  1.00 25.00           C
ATOM     51  CA  THR    51     -26.985  23.646  52.965  1.00 25.00           C
ATOM     52  CA  ILE    52     -29.177  24.196  49.873  1.00 25.00           C
ATOM     53  CA  ASN    53     -31.985  25.581  52.079  1.00 25.00           C
ATOM     54  CA  THR    54     -29.508  27.948  53.790  1.00 25.00           C
ATOM     55  CA  ALA    55     -28.250  29.139  50.374  1.00 25.00           C
ATOM     56  CA  ILE    56     -31.853  29.755  49.234  1.00 25.00           C
ATOM     57  CA  VAL    57     -32.550  31.747  52.430  1.00 25.00           C
ATOM     58  CA  TYR    58     -29.393  33.836  51.845  1.00 25.00           C
ATOM     59  CA  MET    59     -30.483  34.517  48.237  1.00 25.00           C
ATOM     60  CA  HIS    60     -33.950  35.588  49.460  1.00 25.00           C
ATOM     61  CA  ARG    61     -32.346  37.934  52.028  1.00 25.00           C
ATOM     62  CA  PHE    62     -30.126  39.445  49.298  1.00 25.00           C
ATOM     63  CA  TYR    63     -33.190  39.972  47.063  1.00 25.00           C
ATOM     64  CA  MET    64     -35.037  41.676  49.954  1.00 25.00           C
ATOM     65  CA  HIS    65     -32.020  43.954  50.569  1.00 25.00           C
ATOM     66  CA  HIS    66     -31.156  42.321  53.903  1.00 25.00           C
ATOM     67  CA  SER    67     -29.012  45.396  54.348  1.00 25.00           C
ATOM     68  CA  PHE    68     -31.770  47.875  53.711  1.00 25.00           C
ATOM     69  CA  THR    69     -33.490  51.229  53.307  1.00 25.00           C
ATOM     70  CA  LYS    70     -31.577  51.388  50.061  1.00 25.00           C
ATOM     71  CA  PHE    71     -28.614  48.950  49.845  1.00 25.00           C
ATOM     72  CA  ASN    72     -27.321  45.391  49.219  1.00 25.00           C
ATOM     73  CA  LYS    73     -27.407  42.057  47.389  1.00 25.00           C
ATOM     74  CA  ASN    74     -23.610  41.577  47.251  1.00 25.00           C
ATOM     75  CA  ILE    75     -23.554  40.746  50.989  1.00 25.00           C
ATOM     76  CA  ILE    76     -26.373  38.203  50.491  1.00 25.00           C
ATOM     77  CA  SER    77     -24.454  36.606  47.588  1.00 25.00           C
ATOM     78  CA  SER    78     -21.304  36.392  49.756  1.00 25.00           C
ATOM     79  CA  THR    79     -23.321  34.753  52.569  1.00 25.00           C
ATOM     80  CA  ALA    80     -24.774  32.224  50.086  1.00 25.00           C
ATOM     81  CA  LEU    81     -21.255  31.431  48.797  1.00 25.00           C
ATOM     82  CA  PHE    82     -20.028  30.924  52.390  1.00 25.00           C
ATOM     83  CA  LEU    83     -22.976  28.581  53.092  1.00 25.00           C
ATOM     84  CA  ALA    84     -22.183  26.591  49.918  1.00 25.00           C
ATOM     85  CA  ALA    85     -18.514  26.313  50.979  1.00 25.00           C
ATOM     86  CA  LYS    86     -19.584  25.089  54.446  1.00 25.00           C
ATOM     87  CA  VAL    87     -21.884  22.481  52.842  1.00 25.00           C
ATOM     88  CA  GLU    88     -19.018  21.299  50.594  1.00 25.00           C
ATOM     89  CA  GLU    89     -16.235  19.687  52.677  1.00 25.00           C
ATOM     90  CA  GLN    90     -13.582  19.462  55.403  1.00 25.00           C
ATOM     91  CA  ALA    91      -9.961  20.007  56.325  1.00 25.00           C
ATOM     92  CA  ARG    92      -8.215  22.811  54.339  1.00 25.00           C
ATOM     93  CA  LYS    93     -10.661  25.164  52.637  1.00 25.00           C
ATOM     94  CA  LEU    94     -13.727  27.384  53.050  1.00 25.00           C
ATOM     95  CA  GLU    95     -12.259  28.265  56.476  1.00 25.00           C
ATOM     96  CA  HIS    96      -9.471  30.278  54.791  1.00 25.00           C
ATOM     97  CA  VAL    97     -12.062  32.140  52.673  1.00 25.00           C
ATOM     98  CA  ILE    98     -14.104  32.923  55.816  1.00 25.00           C
ATOM     99  CA  LYS    99     -10.958  34.231  57.565  1.00 25.00           C
ATOM    100  CA  VAL   100     -10.161  36.436  54.537  1.00 25.00           C
ATOM    101  CA  ALA   101     -13.739  37.805  54.562  1.00 25.00           C
ATOM    102  CA  HIS   102     -13.446  38.567  58.305  1.00 25.00           C
ATOM    103  CA  ALA   103     -10.126  40.376  57.702  1.00 25.00           C
ATOM    104  CA  CYS   104     -11.725  42.428  54.891  1.00 25.00           C
ATOM    105  CA  LEU   105     -11.618  45.736  56.870  1.00 25.00           C
ATOM    106  CA  HIS   106      -9.062  46.094  59.672  1.00 25.00           C
ATOM    107  CA  PRO   107      -6.820  48.818  58.296  1.00 25.00           C
ATOM    108  CA  LEU   108      -3.920  50.261  56.330  1.00 25.00           C
ATOM    109  CA  GLU   109      -5.602  53.630  55.898  1.00 25.00           C
ATOM    110  CA  PRO   110      -5.166  53.450  52.146  1.00 25.00           C
ATOM    111  CA  LEU   111      -8.698  52.044  51.845  1.00 25.00           C
ATOM    112  CA  LEU   112     -11.881  51.741  49.737  1.00 25.00           C
ATOM    113  CA  ASP   113      -9.860  50.230  46.856  1.00 25.00           C
ATOM    114  CA  THR   114      -8.256  47.720  49.264  1.00 25.00           C
ATOM    115  CA  LYS   115     -11.713  46.766  50.608  1.00 25.00           C
ATOM    116  CA  CYS   116     -12.994  46.270  47.033  1.00 25.00           C
ATOM    117  CA  ASP   117      -9.971  44.060  46.231  1.00 25.00           C
ATOM    118  CA  ALA   118     -10.619  41.986  49.384  1.00 25.00           C
ATOM    119  CA  TYR   119     -14.296  41.580  48.393  1.00 25.00           C
ATOM    120  CA  LEU   120     -13.250  40.457  44.883  1.00 25.00           C
ATOM    121  CA  GLN   121     -10.816  37.917  46.395  1.00 25.00           C
ATOM    122  CA  GLN   122     -13.585  36.584  48.679  1.00 25.00           C
ATOM    123  CA  THR   123     -15.937  36.252  45.675  1.00 25.00           C
ATOM    124  CA  ARG   124     -13.229  34.362  43.734  1.00 25.00           C
ATOM    125  CA  GLU   125     -12.696  32.015  46.712  1.00 25.00           C
ATOM    126  CA  LEU   126     -16.468  31.382  46.919  1.00 25.00           C
ATOM    127  CA  VAL   127     -16.569  30.613  43.169  1.00 25.00           C
ATOM    128  CA  ILE   128     -13.641  28.176  43.565  1.00 25.00           C
ATOM    129  CA  LEU   129     -15.435  26.455  46.478  1.00 25.00           C
ATOM    130  CA  GLU   130     -18.619  26.152  44.370  1.00 25.00           C
ATOM    131  CA  THR   131     -16.598  24.641  41.489  1.00 25.00           C
ATOM    132  CA  ILE   132     -14.995  22.132  43.898  1.00 25.00           C
ATOM    133  CA  MET   133     -18.452  21.177  45.242  1.00 25.00           C
ATOM    134  CA  LEU   134     -19.732  20.681  41.667  1.00 25.00           C
ATOM    135  CA  GLN   135     -16.710  18.471  40.865  1.00 25.00           C
ATOM    136  CA  THR   136     -17.358  16.397  44.019  1.00 25.00           C
ATOM    137  CA  LEU   137     -21.033  15.991  43.026  1.00 25.00           C
ATOM    138  CA  GLY   138     -21.133  13.537  45.894  1.00 25.00           C
ATOM    139  CA  PHE   139     -19.758  16.453  48.004  1.00 25.00           C
ATOM    140  CA  GLU   140     -22.918  16.208  50.082  1.00 25.00           C
ATOM    141  CA  ILE   141     -24.662  18.276  47.354  1.00 25.00           C
ATOM    142  CA  THR   142     -26.708  16.760  44.474  1.00 25.00           C
ATOM    143  CA  ILE   143     -26.680  20.123  42.767  1.00 25.00           C
TER
END
