
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307TS168_5-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      F      13           -
LGA    -       -      S      14           -
LGA    -       -      G      15           -
LGA    S      14      Q      16          4.495
LGA    -       -      E      17           -
LGA    -       -      L      18           -
LGA    G      15      T      19          3.338
LGA    Q      16      A      20           #
LGA    E      17      I      21           #
LGA    L      18      I      22          2.972
LGA    T      19      K      23          3.433
LGA    A      20      M      24          5.007
LGA    I      21      A      25          3.036
LGA    I      22      K      26          1.246
LGA    K      23      S      27          3.711
LGA    M      24      M      28          2.979
LGA    A      25      V      29          0.924
LGA    K      26      M      30          2.723
LGA    S      27      A      31          3.234
LGA    M      28      D      32          3.655
LGA    V      29      G      33           #
LGA    M      30      K      34          1.205
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      I      35          4.393
LGA    Q      54      -       -           -
LGA    D      55      -       -           -
LGA    Q      56      K      36          2.502
LGA    V      57      P      37          2.156
LGA    D      58      A      38          1.672
LGA    L      59      E      39          1.168
LGA    L      60      I      40          1.152
LGA    L      61      A      41          0.786
LGA    K      62      V      42          0.416
LGA    A      63      M      43          0.746
LGA    S      64      T      44          1.188
LGA    D      65      R      45          1.645
LGA    S      66      E      46          1.620
LGA    I      67      F      47          1.224
LGA    E      68      M      48          1.458
LGA    A      69      R      49          2.334
LGA    S      70      F      50          3.398
LGA    Q      71      G      51          2.379
LGA    A      72      -       -           -
LGA    V      73      -       -           -
LGA    A      74      -       -           -
LGA    L      75      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      -       -           -
LGA    L     106      M      79           #
LGA    A     107      -       -           -
LGA    L     108      D      80           #
LGA    W     109      E      81          4.457
LGA    T     110      E      82          0.660
LGA    L     111      R      83          3.875
LGA    I     112      K      84          2.285
LGA    S     113      K      85          2.693
LGA    T     114      Y      86          4.899
LGA    -       -      V      87           -
LGA    L     115      A      88          1.547
LGA    -       -      S      89           -
LGA    -       -      Y      90           -
LGA    C     116      L      91           #
LGA    G     117      G      92           #
LGA    -       -      V      93           -
LGA    -       -      I      94           -
LGA    -       -      M      95           -
LGA    -       -      A      96           -
LGA    -       -      S      97           -
LGA    -       -      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    -       -      I     101           -
LGA    -       -      D     102           -
LGA    -       -      D     103           -
LGA    -       -      N     104           -
LGA    -       -      E     105           -
LGA    -       -      L     106           -
LGA    -       -      A     107           -
LGA    -       -      L     108           -
LGA    L     118      W     109          4.147
LGA    P     119      T     110          3.234
LGA    T     120      L     111          2.641
LGA    M     121      I     112          4.240
LGA    T     122      S     113          3.476
LGA    V     123      T     114          4.157
LGA    M     124      L     115          4.724
LGA    E     125      C     116          0.953
LGA    A     126      G     117          2.367
LGA    I     127      L     118           #
LGA    N     128      P     119           -
LGA    N     129      T     120           -
LGA    M     130      M     121           -
LGA    K     131      T     122           -
LGA    N     132      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     47    2.91     2.13     24.489     1.560

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.441106 * X  +   0.866122 * Y  +  -0.235070 * Z  +  19.188286
  Y_new =  -0.877536 * X  +  -0.471136 * Y  +  -0.089226 * Z  +  10.817025
  Z_new =  -0.188031 * X  +   0.166924 * Y  +   0.967874 * Z  +  28.736170 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.170785   -2.970808  [ DEG:     9.7853   -170.2148 ]
  Theta =   0.189157    2.952436  [ DEG:    10.8379    169.1621 ]
  Phi   =  -2.036573    1.105019  [ DEG:  -116.6870     63.3129 ]
 
# 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_5-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS168_5-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   47   2.91    2.13  24.489
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS168_5-D1
PFRMAT TS
TARGET T0307
MODEL 5
PARENT N/A
ATOM     10  CA  ILE    10      34.433   0.902  40.120  1.00 25.00           C
ATOM     11  CA  MET    11      31.577   3.266  41.015  1.00 25.00           C
ATOM     12  CA  THR    12      32.664   6.901  41.157  1.00 25.00           C
ATOM     13  CA  PHE    13      29.490   8.191  39.453  1.00 25.00           C
ATOM     14  CA  SER    14      28.799  11.644  38.191  1.00 25.00           C
ATOM     15  CA  GLY    15      28.557  13.248  34.806  1.00 25.00           C
ATOM     16  CA  GLN    16      30.373   9.971  34.014  1.00 25.00           C
ATOM     17  CA  GLU    17      27.058   8.352  32.988  1.00 25.00           C
ATOM     18  CA  LEU    18      26.272  11.339  30.723  1.00 25.00           C
ATOM     19  CA  THR    19      29.740  11.068  29.121  1.00 25.00           C
ATOM     20  CA  ALA    20      29.200   7.323  28.528  1.00 25.00           C
ATOM     21  CA  ILE    21      25.799   8.042  26.922  1.00 25.00           C
ATOM     22  CA  ILE    22      27.399  10.685  24.658  1.00 25.00           C
ATOM     23  CA  LYS    23      30.124   8.196  23.637  1.00 25.00           C
ATOM     24  CA  MET    24      27.457   5.565  22.841  1.00 25.00           C
ATOM     25  CA  ALA    25      25.537   8.116  20.725  1.00 25.00           C
ATOM     26  CA  LYS    26      28.750   9.008  18.842  1.00 25.00           C
ATOM     27  CA  SER    27      29.433   5.295  18.198  1.00 25.00           C
ATOM     28  CA  MET    28      25.862   4.840  16.891  1.00 25.00           C
ATOM     29  CA  VAL    29      26.298   7.858  14.575  1.00 25.00           C
ATOM     30  CA  MET    30      29.597   6.413  13.272  1.00 25.00           C
ATOM     31  CA  ALA    31      30.435   5.272   9.760  1.00 25.00           C
ATOM     32  CA  ASP    32      31.893   5.002   6.258  1.00 25.00           C
ATOM     33  CA  GLY    33      33.418   4.963   2.761  1.00 25.00           C
ATOM     34  CA  LYS    34      34.946   5.004  -0.703  1.00 25.00           C
ATOM     35  CA  ILE    35      36.672   5.169  -4.088  1.00 25.00           C
ATOM     36  CA  LYS    36      38.923   6.465  -6.818  1.00 25.00           C
ATOM     37  CA  PRO    37      41.484   8.470  -8.760  1.00 25.00           C
ATOM     38  CA  ALA    38      43.218   8.267  -5.351  1.00 25.00           C
ATOM     39  CA  GLU    39      42.546  11.991  -4.760  1.00 25.00           C
ATOM     40  CA  ILE    40      38.860  11.496  -5.676  1.00 25.00           C
ATOM     41  CA  ALA    41      38.628   8.540  -3.253  1.00 25.00           C
ATOM     42  CA  VAL    42      40.210  10.657  -0.481  1.00 25.00           C
ATOM     43  CA  MET    43      37.709  13.473  -1.171  1.00 25.00           C
ATOM     44  CA  THR    44      34.812  10.974  -1.007  1.00 25.00           C
ATOM     45  CA  ARG    45      36.135   9.622   2.323  1.00 25.00           C
ATOM     46  CA  GLU    46      36.389  13.187   3.699  1.00 25.00           C
ATOM     47  CA  PHE    47      32.792  13.897   2.589  1.00 25.00           C
ATOM     48  CA  MET    48      31.604  10.680   4.294  1.00 25.00           C
ATOM     49  CA  ARG    49      33.429  11.683   7.509  1.00 25.00           C
ATOM     50  CA  PHE    50      31.800  15.146   7.383  1.00 25.00           C
ATOM     51  CA  GLY    51      28.357  13.537   6.909  1.00 25.00           C
ATOM     52  CA  ILE    52      28.998  11.228   9.897  1.00 25.00           C
ATOM     53  CA  LEU    53      30.033  14.235  12.030  1.00 25.00           C
ATOM     54  CA  GLN    54      26.849  16.096  10.998  1.00 25.00           C
ATOM     55  CA  ASP    55      24.735  13.037  11.920  1.00 25.00           C
ATOM     56  CA  GLN    56      26.470  12.835  15.328  1.00 25.00           C
ATOM     57  CA  VAL    57      25.798  16.559  15.919  1.00 25.00           C
ATOM     58  CA  ASP    58      22.112  16.063  15.002  1.00 25.00           C
ATOM     59  CA  LEU    59      21.881  13.107  17.427  1.00 25.00           C
ATOM     60  CA  LEU    60      23.462  15.225  20.199  1.00 25.00           C
ATOM     61  CA  LEU    61      20.960  18.041  19.509  1.00 25.00           C
ATOM     62  CA  LYS    62      18.063  15.541  19.673  1.00 25.00           C
ATOM     63  CA  ALA    63      19.387  14.188  23.003  1.00 25.00           C
ATOM     64  CA  SER    64      19.640  17.754  24.378  1.00 25.00           C
ATOM     65  CA  ASP    65      16.045  18.463  23.268  1.00 25.00           C
ATOM     66  CA  SER    66      14.857  15.248  24.974  1.00 25.00           C
ATOM     67  CA  ILE    67      16.681  16.250  28.189  1.00 25.00           C
ATOM     68  CA  GLU    68      15.051  19.714  28.063  1.00 25.00           C
ATOM     69  CA  ALA    69      11.609  18.103  27.589  1.00 25.00           C
ATOM     70  CA  SER    70      12.250  15.795  30.576  1.00 25.00           C
ATOM     71  CA  GLN    71      13.286  18.802  32.710  1.00 25.00           C
ATOM     72  CA  ALA    72      10.101  20.662  31.678  1.00 25.00           C
ATOM     73  CA  VAL    73       7.987  17.605  32.600  1.00 25.00           C
ATOM     74  CA  ALA    74       9.722  17.403  36.008  1.00 25.00           C
ATOM     75  CA  LEU    75       9.049  21.125  36.599  1.00 25.00           C
ATOM     76  CA  ILE    76       5.364  20.631  35.682  1.00 25.00           C
ATOM     77  CA  ALA    77       5.133  17.675  38.106  1.00 25.00           C
ATOM     78  CA  ARG    78       6.714  19.793  40.878  1.00 25.00           C
ATOM     79  CA  MET    79       4.212  22.608  40.188  1.00 25.00           C
ATOM     80  CA  ASP    80       1.316  20.108  40.353  1.00 25.00           C
ATOM     81  CA  GLU    81       2.639  18.756  43.682  1.00 25.00           C
ATOM     82  CA  GLU    82       2.892  22.321  45.058  1.00 25.00           C
ATOM     83  CA  ARG    83      -0.704  23.031  43.948  1.00 25.00           C
ATOM     84  CA  LYS    84      -1.891  19.815  45.654  1.00 25.00           C
ATOM     85  CA  LYS    85      -0.067  20.818  48.869  1.00 25.00           C
ATOM     86  CA  TYR    86      -1.697  24.281  48.743  1.00 25.00           C
ATOM     87  CA  VAL    87      -5.139  22.671  48.269  1.00 25.00           C
ATOM     88  CA  ALA    88      -4.498  20.363  51.256  1.00 25.00           C
ATOM     89  CA  SER    89      -3.462  23.370  53.389  1.00 25.00           C
ATOM     90  CA  TYR    90      -6.647  25.230  52.358  1.00 25.00           C
ATOM     91  CA  LEU    91      -8.761  22.171  53.280  1.00 25.00           C
ATOM     92  CA  GLY    92      -7.026  21.969  56.688  1.00 25.00           C
ATOM     93  CA  VAL    93      -7.699  25.693  57.279  1.00 25.00           C
ATOM     94  CA  ILE    94     -11.384  25.197  56.362  1.00 25.00           C
ATOM     95  CA  MET    95     -11.615  22.241  58.786  1.00 25.00           C
ATOM     96  CA  ALA    96     -10.034  24.359  61.558  1.00 25.00           C
ATOM     97  CA  SER    97      -7.157  21.927  61.316  1.00 25.00           C
ATOM     98  CA  ASP    98      -4.891  19.835  59.030  1.00 25.00           C
ATOM     99  CA  GLY    99      -2.877  17.912  56.358  1.00 25.00           C
ATOM    100  CA  ASP   100      -1.079  16.143  53.458  1.00 25.00           C
ATOM    101  CA  ILE   101       1.014  14.707  50.586  1.00 25.00           C
ATOM    102  CA  ASP   102       2.784  13.289  47.558  1.00 25.00           C
ATOM    103  CA  ASP   103       4.702  12.097  44.490  1.00 25.00           C
ATOM    104  CA  ASN   104       6.866  14.173  42.108  1.00 25.00           C
ATOM    105  CA  GLU   105       9.888  11.951  42.875  1.00 25.00           C
ATOM    106  CA  LEU   106       7.789   8.820  42.196  1.00 25.00           C
ATOM    107  CA  ALA   107       6.610  10.303  38.867  1.00 25.00           C
ATOM    108  CA  LEU   108      10.233  11.092  37.907  1.00 25.00           C
ATOM    109  CA  TRP   109      11.269   7.508  38.773  1.00 25.00           C
ATOM    110  CA  THR   110       8.402   6.137  36.637  1.00 25.00           C
ATOM    111  CA  LEU   111       9.476   8.371  33.717  1.00 25.00           C
ATOM    112  CA  ILE   112      13.085   7.140  34.071  1.00 25.00           C
ATOM    113  CA  SER   113      11.872   3.507  34.071  1.00 25.00           C
ATOM    114  CA  THR   114       9.798   4.173  30.921  1.00 25.00           C
ATOM    115  CA  LEU   115      12.847   5.747  29.219  1.00 25.00           C
ATOM    116  CA  CYS   116      13.134   3.534  26.109  1.00 25.00           C
ATOM    117  CA  GLY   117      11.679   1.109  23.572  1.00 25.00           C
ATOM    118  CA  LEU   118      14.856  -0.836  22.634  1.00 25.00           C
ATOM    119  CA  PRO   119      14.649  -4.034  24.708  1.00 25.00           C
ATOM    120  CA  THR   120      18.311  -3.620  25.637  1.00 25.00           C
ATOM    121  CA  MET   121      17.302  -0.908  28.033  1.00 25.00           C
ATOM    122  CA  THR   122      18.632  -3.253  30.664  1.00 25.00           C
ATOM    123  CA  VAL   123      16.633  -4.248  33.775  1.00 25.00           C
ATOM    124  CA  MET   124      19.750  -3.786  35.954  1.00 25.00           C
ATOM    125  CA  GLU   125      20.344  -0.331  34.415  1.00 25.00           C
ATOM    126  CA  ALA   126      16.700   0.629  35.100  1.00 25.00           C
ATOM    127  CA  ILE   127      17.048  -0.539  38.730  1.00 25.00           C
ATOM    128  CA  ASN   128      20.250   1.529  39.112  1.00 25.00           C
ATOM    129  CA  ASN   129      18.467   4.600  37.678  1.00 25.00           C
ATOM    130  CA  MET   130      15.564   4.087  40.121  1.00 25.00           C
ATOM    131  CA  LYS   131      17.798   3.567  43.158  1.00 25.00           C
ATOM    132  CA  ASN   132      18.881   7.205  43.426  1.00 25.00           C
TER
END
