
#######################################################
#                                                     #
#                        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  145 (  145),  selected  145 , name T0380TS393_4
# Molecule2: number of CA atoms  142 ( 1146),  selected  142 , name T0380.pdb
# PARAMETERS: T0380TS393_4.T0380.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      I       2           -
LGA    -       -      D       3           -
LGA    I       2      E       4           #
LGA    D       3      K       5          3.428
LGA    -       -      F       6           -
LGA    -       -      L       7           -
LGA    E       4      I       8          3.038
LGA    K       5      E       9          2.218
LGA    F       6      S      10          1.775
LGA    L       7      N      11          2.277
LGA    I       8      E      12          2.455
LGA    E       9      L      13          1.861
LGA    S      10      V      14          1.813
LGA    N      11      E      15          2.506
LGA    E      12      S      16          2.668
LGA    L      13      S      17          3.586
LGA    V      14      K      18          3.387
LGA    E      15      -       -           -
LGA    S      16      -       -           -
LGA    S      17      -       -           -
LGA    K      18      I      19          2.112
LGA    I      19      V      20          3.128
LGA    V      20      M      21          4.240
LGA    M      21      V      22          1.713
LGA    V      22      G      23          2.370
LGA    G      23      T      24          0.761
LGA    T      24      N      25          3.800
LGA    N      25      G      26          2.102
LGA    G      26      E      27          4.813
LGA    E      27      -       -           -
LGA    N      28      -       -           -
LGA    G      29      N      28          4.805
LGA    Y      30      G      29          2.967
LGA    P      31      Y      30          3.494
LGA    N      32      P      31          2.140
LGA    I      33      N      32          2.956
LGA    K      34      I      33          1.749
LGA    A      35      -       -           -
LGA    M      36      K      34          1.752
LGA    M      37      A      35          1.101
LGA    R      38      M      36          2.651
LGA    L      39      M      37          1.381
LGA    K      40      R      38          2.174
LGA    H      41      L      39          2.854
LGA    D      42      K      40          4.445
LGA    G      43      -       -           -
LGA    L      44      -       -           -
LGA    K      45      H      41          3.564
LGA    K      46      D      42           #
LGA    -       -      G      43           -
LGA    -       -      L      44           -
LGA    -       -      K      45           -
LGA    -       -      K      46           -
LGA    -       -      F      47           -
LGA    F      47      W      48          3.276
LGA    W      48      L      49          3.399
LGA    L      49      S      50           #
LGA    S      50      T      51           #
LGA    T      51      N      52           #
LGA    N      52      T      53          2.846
LGA    T      53      S      54          4.996
LGA    S      54      T      55          2.580
LGA    T      55      -       -           -
LGA    R      56      R      56          3.784
LGA    M      57      M      57          4.026
LGA    V      58      V      58          1.655
LGA    E      59      E      59          1.798
LGA    R      60      R      60          3.372
LGA    L      61      L      61          2.045
LGA    K      62      K      62          1.371
LGA    K      63      K      63          3.392
LGA    N      64      N      64          3.743
LGA    N      65      -       -           -
LGA    K      66      N      65          0.903
LGA    I      67      K      66          2.066
LGA    C      68      I      67          1.443
LGA    L      69      C      68          1.251
LGA    Y      70      L      69          2.188
LGA    F      71      Y      70          2.451
LGA    V      72      F      71          4.764
LGA    D      73      V      72          1.641
LGA    D      74      D      73          2.573
LGA    -       -      D      74           -
LGA    N      75      N      75          3.572
LGA    K      76      K      76          3.502
LGA    F      77      F      77          3.416
LGA    A      78      A      78          2.483
LGA    G      79      G      79          2.876
LGA    L      80      L      80          4.283
LGA    -       -      M      81           -
LGA    M      81      L      82          3.060
LGA    L      82      V      83           #
LGA    V      83      G      84           #
LGA    G      84      T      85           #
LGA    T      85      I      86           #
LGA    I      86      E      87          2.417
LGA    E      87      I      88          2.375
LGA    I      88      -       -           -
LGA    L      89      L      89          2.414
LGA    H      90      H      90          0.967
LGA    D      91      D      91          2.903
LGA    R      92      -       -           -
LGA    A      93      R      92          2.486
LGA    S      94      A      93           #
LGA    -       -      S      94           -
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    -       -      M      97           -
LGA    -       -      L      98           -
LGA    -       -      W      99           -
LGA    -       -      T     100           -
LGA    -       -      D     101           -
LGA    -       -      G     102           -
LGA    -       -      C     103           -
LGA    -       -      E     104           -
LGA    -       -      I     105           -
LGA    -       -      Y     106           -
LGA    -       -      Y     107           -
LGA    -       -      P     108           -
LGA    -       -      L     109           -
LGA    -       -      G     110           -
LGA    K      95      I     111           #
LGA    E      96      D     112          2.029
LGA    M      97      -       -           -
LGA    L      98      -       -           -
LGA    W      99      -       -           -
LGA    T     100      D     113          5.274
LGA    D     101      P     114           -
LGA    G     102      D     115           -
LGA    C     103      Y     116           #
LGA    E     104      T     117           #
LGA    I     105      A     118          3.122
LGA    Y     106      L     119          2.887
LGA    Y     107      C     120          4.949
LGA    P     108      F     121           #
LGA    L     109      T     122           #
LGA    G     110      A     123           #
LGA    I     111      -       -           -
LGA    D     112      -       -           -
LGA    D     113      -       -           -
LGA    P     114      E     124          3.436
LGA    D     115      W     125           -
LGA    Y     116      G     126           -
LGA    T     117      -       -           -
LGA    A     118      -       -           -
LGA    L     119      -       -           -
LGA    C     120      -       -           -
LGA    F     121      -       -           -
LGA    T     122      -       -           -
LGA    A     123      -       -           -
LGA    E     124      -       -           -
LGA    W     125      -       -           -
LGA    G     126      -       -           -
LGA    N     127      -       -           -
LGA    Y     128      -       -           -
LGA    Y     129      -       -           -
LGA    R     130      -       -           -
LGA    H     131      -       -           -
LGA    L     132      -       -           -
LGA    K     133      -       -           -
LGA    N     134      -       -           -
LGA    I     135      -       -           -
LGA    T     136      -       -           -
LGA    F     137      -       -           -
LGA    K     138      -       -           -
LGA    I     139      N     127           #
LGA    D     140      Y     128           -
LGA    -       -      Y     129           -
LGA    -       -      R     130           -
LGA    -       -      H     131           -
LGA    -       -      L     132           -
LGA    -       -      K     133           -
LGA    E     141      N     134           #
LGA    I     142      I     135           -
LGA    Y     143      T     136           #
LGA    N     144      F     137           -
LGA    Y     145      K     138           -
LGA    -       -      I     139           -
LGA    -       -      D     140           -
LGA    -       -      E     141           -
LGA    -       -      I     142           -
LGA    -       -      Y     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  145  142    5.0     77    2.97    24.68     31.566     2.510

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.433022 * X  +  -0.449707 * Y  +   0.781188 * Z  +  -7.097338
  Y_new =  -0.645103 * X  +  -0.759910 * Y  +  -0.079869 * Z  +  -7.165334
  Z_new =   0.629551 * X  +  -0.469362 * Y  +  -0.619165 * Z  +  16.447681 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.492956    0.648637  [ DEG:  -142.8359     37.1641 ]
  Theta =  -0.680975   -2.460618  [ DEG:   -39.0170   -140.9830 ]
  Phi   =  -0.979630    2.161962  [ DEG:   -56.1287    123.8713 ]
 
# 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: T0380TS393_4                                  
REMARK     2: T0380.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0380TS393_4.T0380.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  145  142   5.0   77   2.97   24.68  31.566
REMARK  ---------------------------------------------------------- 
MOLECULE T0380TS393_4
PFRMAT TS
TARGET T0380
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1     -17.087   0.384   0.115  1.00 25.00           C
ATOM      2  CA  ILE     2     -19.178   0.904   3.315  1.00 25.00           C
ATOM      3  CA  ASP     3     -19.634   4.642   3.392  1.00 25.00           C
ATOM      4  CA  GLU     4     -18.175   8.157   3.347  1.00 25.00           C
ATOM      5  CA  LYS     5     -18.212   8.852   7.112  1.00 25.00           C
ATOM      6  CA  PHE     6     -17.193   5.228   7.817  1.00 25.00           C
ATOM      7  CA  LEU     7     -14.329   5.517   5.291  1.00 25.00           C
ATOM      8  CA  ILE     8     -13.162   8.767   6.949  1.00 25.00           C
ATOM      9  CA  GLU     9     -13.251   7.074  10.383  1.00 25.00           C
ATOM     10  CA  SER    10     -11.206   4.139   9.018  1.00 25.00           C
ATOM     11  CA  ASN    11      -8.646   6.576   7.541  1.00 25.00           C
ATOM     12  CA  GLU    12      -8.400   8.391  10.905  1.00 25.00           C
ATOM     13  CA  LEU    13      -7.864   5.049  12.697  1.00 25.00           C
ATOM     14  CA  VAL    14      -5.116   4.120  10.196  1.00 25.00           C
ATOM     15  CA  GLU    15      -3.426   7.510  10.757  1.00 25.00           C
ATOM     16  CA  SER    16      -3.047   7.338  14.539  1.00 25.00           C
ATOM     17  CA  SER    17      -4.684   4.988  16.969  1.00 25.00           C
ATOM     18  CA  LYS    18      -5.108   1.639  15.126  1.00 25.00           C
ATOM     19  CA  ILE    19      -6.994  -0.269  12.393  1.00 25.00           C
ATOM     20  CA  VAL    20      -7.375  -3.254  14.790  1.00 25.00           C
ATOM     21  CA  MET    21      -7.865  -5.996  17.339  1.00 25.00           C
ATOM     22  CA  VAL    22      -8.061  -7.900  20.691  1.00 25.00           C
ATOM     23  CA  GLY    23      -9.623 -10.353  23.193  1.00 25.00           C
ATOM     24  CA  THR    24      -7.856 -13.622  22.710  1.00 25.00           C
ATOM     25  CA  ASN    25      -8.204 -14.625  26.407  1.00 25.00           C
ATOM     26  CA  GLY    26      -7.124 -11.397  28.102  1.00 25.00           C
ATOM     27  CA  GLU    27      -7.547  -9.164  31.154  1.00 25.00           C
ATOM     28  CA  ASN    28      -9.247  -9.676  34.453  1.00 25.00           C
ATOM     29  CA  GLY    29     -11.963 -12.041  35.621  1.00 25.00           C
ATOM     30  CA  TYR    30     -14.715 -13.137  33.191  1.00 25.00           C
ATOM     31  CA  PRO    31     -14.968  -9.891  31.191  1.00 25.00           C
ATOM     32  CA  ASN    32     -12.107  -8.024  29.392  1.00 25.00           C
ATOM     33  CA  ILE    33     -10.690  -6.458  26.219  1.00 25.00           C
ATOM     34  CA  LYS    34      -6.971  -6.407  25.414  1.00 25.00           C
ATOM     35  CA  ALA    35      -7.901  -3.447  23.248  1.00 25.00           C
ATOM     36  CA  MET    36      -4.844  -4.017  21.031  1.00 25.00           C
ATOM     37  CA  MET    37      -2.120  -2.242  19.087  1.00 25.00           C
ATOM     38  CA  ARG    38      -0.270  -1.867  15.765  1.00 25.00           C
ATOM     39  CA  LEU    39      -1.558  -3.377  12.464  1.00 25.00           C
ATOM     40  CA  LYS    40      -1.277  -3.068   8.648  1.00 25.00           C
ATOM     41  CA  HIS    41      -1.179  -2.701   4.853  1.00 25.00           C
ATOM     42  CA  ASP    42      -2.433  -1.749   1.347  1.00 25.00           C
ATOM     43  CA  GLY    43      -2.034  -5.164  -0.281  1.00 25.00           C
ATOM     44  CA  LEU    44      -5.771  -5.614   0.312  1.00 25.00           C
ATOM     45  CA  LYS    45      -7.149  -7.564   3.237  1.00 25.00           C
ATOM     46  CA  LYS    46      -7.034  -6.137   6.717  1.00 25.00           C
ATOM     47  CA  PHE    47      -5.824  -6.613  10.276  1.00 25.00           C
ATOM     48  CA  TRP    48      -4.546  -7.265  13.764  1.00 25.00           C
ATOM     49  CA  LEU    49      -2.799  -6.826  17.160  1.00 25.00           C
ATOM     50  CA  SER    50      -2.261  -8.623  20.508  1.00 25.00           C
ATOM     51  CA  THR    51      -0.391 -11.894  21.033  1.00 25.00           C
ATOM     52  CA  ASN    52       3.020 -13.531  20.428  1.00 25.00           C
ATOM     53  CA  THR    53       3.820 -16.474  18.144  1.00 25.00           C
ATOM     54  CA  SER    54       4.230 -18.746  21.132  1.00 25.00           C
ATOM     55  CA  THR    55       3.445 -17.274  24.605  1.00 25.00           C
ATOM     56  CA  ARG    56       1.127 -19.654  26.446  1.00 25.00           C
ATOM     57  CA  MET    57      -1.585 -17.147  25.428  1.00 25.00           C
ATOM     58  CA  VAL    58      -0.650 -17.595  21.742  1.00 25.00           C
ATOM     59  CA  GLU    59      -0.838 -21.400  22.130  1.00 25.00           C
ATOM     60  CA  ARG    60      -4.284 -21.085  23.772  1.00 25.00           C
ATOM     61  CA  LEU    61      -5.474 -18.844  20.904  1.00 25.00           C
ATOM     62  CA  LYS    62      -4.191 -21.391  18.348  1.00 25.00           C
ATOM     63  CA  LYS    63      -6.023 -24.202  20.193  1.00 25.00           C
ATOM     64  CA  ASN    64      -9.117 -22.086  19.532  1.00 25.00           C
ATOM     65  CA  ASN    65      -8.795 -19.680  16.537  1.00 25.00           C
ATOM     66  CA  LYS    66      -9.566 -16.595  18.638  1.00 25.00           C
ATOM     67  CA  ILE    67     -11.703 -13.572  19.432  1.00 25.00           C
ATOM     68  CA  CYS    68     -12.769  -9.970  18.932  1.00 25.00           C
ATOM     69  CA  LEU    69     -12.830  -6.925  16.674  1.00 25.00           C
ATOM     70  CA  TYR    70     -12.134  -3.363  17.739  1.00 25.00           C
ATOM     71  CA  PHE    71      -9.866  -0.310  18.013  1.00 25.00           C
ATOM     72  CA  VAL    72      -9.707   3.070  19.690  1.00 25.00           C
ATOM     73  CA  ASP    73     -10.183   5.879  17.096  1.00 25.00           C
ATOM     74  CA  ASP    74     -11.533   8.961  18.840  1.00 25.00           C
ATOM     75  CA  ASN    75     -10.279  11.733  16.494  1.00 25.00           C
ATOM     76  CA  LYS    76     -13.221  12.305  14.085  1.00 25.00           C
ATOM     77  CA  PHE    77     -15.639  10.167  16.036  1.00 25.00           C
ATOM     78  CA  ALA    78     -15.748   6.344  15.803  1.00 25.00           C
ATOM     79  CA  GLY    79     -13.922   3.134  15.040  1.00 25.00           C
ATOM     80  CA  LEU    80     -12.397   0.156  13.268  1.00 25.00           C
ATOM     81  CA  MET    81     -13.437  -3.503  12.904  1.00 25.00           C
ATOM     82  CA  LEU    82     -11.213  -6.437  11.830  1.00 25.00           C
ATOM     83  CA  VAL    83     -10.048  -9.407   9.712  1.00 25.00           C
ATOM     84  CA  GLY    84      -9.365 -12.887   8.323  1.00 25.00           C
ATOM     85  CA  THR    85      -7.105 -15.958   8.096  1.00 25.00           C
ATOM     86  CA  ILE    86      -4.397 -17.279  10.511  1.00 25.00           C
ATOM     87  CA  GLU    87      -3.105 -18.031  14.026  1.00 25.00           C
ATOM     88  CA  ILE    88       0.095 -16.050  14.691  1.00 25.00           C
ATOM     89  CA  LEU    89       0.583 -15.616  10.943  1.00 25.00           C
ATOM     90  CA  HIS    90       3.132 -18.314  10.112  1.00 25.00           C
ATOM     91  CA  ASP    91       5.311 -20.492   7.934  1.00 25.00           C
ATOM     92  CA  ARG    92       8.506 -18.886   9.097  1.00 25.00           C
ATOM     93  CA  ALA    93       8.546 -16.308   6.266  1.00 25.00           C
ATOM     94  CA  SER    94       5.507 -14.547   7.793  1.00 25.00           C
ATOM     95  CA  LYS    95       7.235 -14.474  11.210  1.00 25.00           C
ATOM     96  CA  GLU    96      10.388 -12.998   9.613  1.00 25.00           C
ATOM     97  CA  MET    97       8.278 -10.321   7.867  1.00 25.00           C
ATOM     98  CA  LEU    98       6.571  -9.465  11.186  1.00 25.00           C
ATOM     99  CA  TRP    99       9.987  -9.177  12.896  1.00 25.00           C
ATOM    100  CA  THR   100      11.220  -6.871  10.098  1.00 25.00           C
ATOM    101  CA  ASP   101       8.089  -4.697  10.477  1.00 25.00           C
ATOM    102  CA  GLY   102       4.729  -5.333   8.706  1.00 25.00           C
ATOM    103  CA  CYS   103       2.138  -6.952  10.899  1.00 25.00           C
ATOM    104  CA  GLU   104      -0.627  -8.347   8.697  1.00 25.00           C
ATOM    105  CA  ILE   105      -2.074 -10.901  11.140  1.00 25.00           C
ATOM    106  CA  TYR   106      -5.571 -11.865  12.035  1.00 25.00           C
ATOM    107  CA  TYR   107      -8.015 -14.635  12.832  1.00 25.00           C
ATOM    108  CA  PRO   108     -10.914 -16.591  11.393  1.00 25.00           C
ATOM    109  CA  LEU   109     -13.297 -17.979   8.730  1.00 25.00           C
ATOM    110  CA  GLY   110     -15.211 -17.135   5.567  1.00 25.00           C
ATOM    111  CA  ILE   111     -18.523 -17.738   7.338  1.00 25.00           C
ATOM    112  CA  ASP   112     -19.492 -18.710  10.828  1.00 25.00           C
ATOM    113  CA  ASP   113     -19.741 -15.012  11.429  1.00 25.00           C
ATOM    114  CA  PRO   114     -16.621 -12.918  12.008  1.00 25.00           C
ATOM    115  CA  ASP   115     -14.348 -14.125  14.805  1.00 25.00           C
ATOM    116  CA  TYR   116     -12.229 -11.078  13.921  1.00 25.00           C
ATOM    117  CA  THR   117      -8.978 -10.805  15.764  1.00 25.00           C
ATOM    118  CA  ALA   118      -5.666 -11.111  17.588  1.00 25.00           C
ATOM    119  CA  LEU   119      -2.179 -11.708  16.093  1.00 25.00           C
ATOM    120  CA  CYS   120       1.056  -9.693  16.616  1.00 25.00           C
ATOM    121  CA  PHE   121       2.014  -6.683  18.733  1.00 25.00           C
ATOM    122  CA  THR   122       3.421  -4.168  21.210  1.00 25.00           C
ATOM    123  CA  ALA   123       2.016  -0.988  22.681  1.00 25.00           C
ATOM    124  CA  GLU   124       3.681  -0.471  26.052  1.00 25.00           C
ATOM    125  CA  TRP   125       0.104   0.210  27.145  1.00 25.00           C
ATOM    126  CA  GLY   126      -2.029  -2.016  29.351  1.00 25.00           C
ATOM    127  CA  ASN   127       1.031  -4.236  29.032  1.00 25.00           C
ATOM    128  CA  TYR   128      -0.422  -4.976  25.567  1.00 25.00           C
ATOM    129  CA  TYR   129      -1.671  -8.383  26.791  1.00 25.00           C
ATOM    130  CA  ARG   130      -3.295  -6.722  29.836  1.00 25.00           C
ATOM    131  CA  HIS   131      -1.549  -9.137  32.271  1.00 25.00           C
ATOM    132  CA  LEU   132      -3.593 -12.281  31.642  1.00 25.00           C
ATOM    133  CA  LYS   133      -6.846 -13.815  32.911  1.00 25.00           C
ATOM    134  CA  ASN   134     -10.212 -13.992  31.188  1.00 25.00           C
ATOM    135  CA  ILE   135     -12.718 -13.349  28.362  1.00 25.00           C
ATOM    136  CA  THR   136     -15.199 -11.708  25.992  1.00 25.00           C
ATOM    137  CA  PHE   137     -14.481  -8.906  23.537  1.00 25.00           C
ATOM    138  CA  LYS   138     -15.661  -6.306  21.121  1.00 25.00           C
ATOM    139  CA  ILE   139     -18.853  -4.279  20.861  1.00 25.00           C
ATOM    140  CA  ASP   140     -22.377  -2.992  21.206  1.00 25.00           C
ATOM    141  CA  GLU   141     -26.027  -1.794  21.637  1.00 25.00           C
ATOM    142  CA  ILE   142     -29.772  -1.400  21.857  1.00 25.00           C
ATOM    143  CA  TYR   143     -31.886  -2.014  18.824  1.00 25.00           C
ATOM    144  CA  ASN   144     -34.040   0.804  17.333  1.00 25.00           C
ATOM    145  CA  TYR   145     -34.361   3.785  15.050  1.00 25.00           C
TER
END
