
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0350TS168_5
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350TS168_5.T0350.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    N       2      D      17           #
LGA    I       3      T      18           #
LGA    E       4      Q      19           -
LGA    R       5      -       -           -
LGA    L       6      I      20          5.615
LGA    T       7      H      21          2.619
LGA    T       8      N      22           #
LGA    L       9      Q      23          3.732
LGA    Q      10      K      24          3.778
LGA    -       -      D      25           -
LGA    P      11      N      26          4.198
LGA    V      12      D      27          2.015
LGA    W      13      N      28          4.002
LGA    D      14      E      29          1.686
LGA    R      15      V      30          2.755
LGA    Y      16      P      31          3.898
LGA    D      17      -       -           -
LGA    T      18      -       -           -
LGA    Q      19      -       -           -
LGA    I      20      V      32           #
LGA    H      21      H      33           -
LGA    N      22      Q      34           -
LGA    Q      23      V      35           -
LGA    K      24      -       -           -
LGA    D      25      -       -           -
LGA    N      26      -       -           -
LGA    D      27      -       -           -
LGA    N      28      -       -           -
LGA    E      29      -       -           -
LGA    V      30      -       -           -
LGA    P      31      -       -           -
LGA    V      32      -       -           -
LGA    H      33      -       -           -
LGA    Q      34      -       -           -
LGA    V      35      -       -           -
LGA    S      36      -       -           -
LGA    Y      37      S      36          5.444
LGA    T      38      Y      37           #
LGA    N      39      T      38          5.312
LGA    L      40      N      39          3.153
LGA    A      41      L      40          3.512
LGA    E      42      A      41          2.947
LGA    M      43      E      42          1.012
LGA    V      44      M      43          2.167
LGA    G      45      V      44          2.871
LGA    E      46      G      45          0.977
LGA    M      47      E      46          3.770
LGA    N      48      M      47          4.758
LGA    K      49      N      48          3.512
LGA    L      50      -       -           -
LGA    L      51      K      49           #
LGA    E      52      L      50           -
LGA    P      53      L      51          4.954
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    S      54      S      54          5.189
LGA    Q      55      Q      55          2.335
LGA    V      56      V      56          2.056
LGA    H      57      H      57           -
LGA    L      58      L      58          5.102
LGA    K      59      K      59           #
LGA    F      60      F      60          3.402
LGA    E      61      E      61          2.287
LGA    L      62      L      62          2.823
LGA    H      63      H      63          1.916
LGA    D      64      D      64          1.363
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    K      65      E      68          2.119
LGA    L      66      Y      69           #
LGA    N      67      -       -           -
LGA    E      68      Y      70           #
LGA    Y      69      V      71          4.989
LGA    Y      70      K      72          1.861
LGA    V      71      V      73          2.910
LGA    K      72      I      74          2.968
LGA    V      73      -       -           -
LGA    I      74      E      75           #
LGA    E      75      D      76          3.219
LGA    D      76      -       -           -
LGA    S      77      S      77          1.604
LGA    T      78      T      78           #
LGA    N      79      N      79          1.902
LGA    E      80      E      80          2.505
LGA    V      81      V      81           #
LGA    I      82      I      82          2.222
LGA    R      83      R      83          1.487
LGA    E      84      E      84          3.961
LGA    I      85      I      85          2.859
LGA    P      86      P      86          3.059
LGA    P      87      P      87          2.784
LGA    K      88      K      88          2.963
LGA    R      89      R      89          2.782
LGA    W      90      W      90          3.670
LGA    L      91      L      91          3.737
LGA    D      92      D      92          1.937
LGA    F      93      F      93          1.656
LGA    Y      94      Y      94          2.507
LGA    A      95      A      95          2.164
LGA    A      96      A      96          1.826
LGA    M      97      M      97          1.587
LGA    T      98      T      98          1.624
LGA    E      99      E      99          2.142
LGA    F     100      F     100          2.369
LGA    L     101      L     101          2.809
LGA    G     102      G     102          2.715
LGA    L     103      L     103          3.337
LGA    F     104      F     104          3.696
LGA    V     105      V     105          6.673
LGA    D     106      D     106           -
LGA    E     107      E     107           -
LGA    K     108      K     108           -
LGA    K     109      K     109           -
LGA    L     110      -       -           -
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117  109    5.0     65    3.25    56.92     35.752     1.941

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.581691 * X  +   0.598513 * Y  +   0.550834 * Z  +   1.891304
  Y_new =  -0.149968 * X  +   0.744495 * Y  +  -0.650567 * Z  +   0.255224
  Z_new =  -0.799466 * X  +   0.295821 * Y  +   0.522823 * Z  + -20.041246 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.514904   -2.626689  [ DEG:    29.5018   -150.4982 ]
  Theta =   0.926405    2.215187  [ DEG:    53.0791    126.9209 ]
  Phi   =  -0.252319    2.889273  [ DEG:   -14.4568    165.5432 ]
 
# 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: T0350TS168_5                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS168_5.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   65   3.25   56.92  35.752
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS168_5
PFRMAT TS
TARGET T0350
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      11.071 -22.873 -20.774  1.00 25.00           C
ATOM      2  CA  ASN     2      10.030 -19.213 -21.202  1.00 25.00           C
ATOM      3  CA  ILE     3       6.655 -19.586 -22.914  1.00 25.00           C
ATOM      4  CA  GLU     4       3.513 -21.069 -24.463  1.00 25.00           C
ATOM      5  CA  ARG     5       2.426 -18.846 -27.276  1.00 25.00           C
ATOM      6  CA  LEU     6       3.761 -15.482 -26.166  1.00 25.00           C
ATOM      7  CA  THR     7       2.641 -12.299 -24.353  1.00 25.00           C
ATOM      8  CA  THR     8       0.628 -10.929 -27.299  1.00 25.00           C
ATOM      9  CA  LEU     9      -1.838  -9.566 -24.659  1.00 25.00           C
ATOM     10  CA  GLN    10      -5.635  -9.893 -24.758  1.00 25.00           C
ATOM     11  CA  PRO    11      -7.292 -10.074 -21.337  1.00 25.00           C
ATOM     12  CA  VAL    12      -9.769  -7.424 -22.409  1.00 25.00           C
ATOM     13  CA  TRP    13      -7.651  -5.049 -20.299  1.00 25.00           C
ATOM     14  CA  ASP    14     -10.436  -2.633 -19.264  1.00 25.00           C
ATOM     15  CA  ARG    15      -8.922   0.102 -21.477  1.00 25.00           C
ATOM     16  CA  TYR    16      -8.753  -2.342 -24.422  1.00 25.00           C
ATOM     17  CA  ASP    17     -12.418  -3.306 -23.864  1.00 25.00           C
ATOM     18  CA  THR    18     -13.405   0.394 -23.791  1.00 25.00           C
ATOM     19  CA  GLN    19     -11.490   0.995 -27.053  1.00 25.00           C
ATOM     20  CA  ILE    20     -13.259  -1.992 -28.670  1.00 25.00           C
ATOM     21  CA  HIS    21     -16.651  -0.633 -27.526  1.00 25.00           C
ATOM     22  CA  ASN    22     -15.796   2.804 -28.984  1.00 25.00           C
ATOM     23  CA  GLN    23     -16.093   2.607 -32.756  1.00 25.00           C
ATOM     24  CA  LYS    24     -19.852   1.993 -33.041  1.00 25.00           C
ATOM     25  CA  ASP    25     -23.349   2.620 -31.551  1.00 25.00           C
ATOM     26  CA  ASN    26     -24.955   4.823 -28.849  1.00 25.00           C
ATOM     27  CA  ASP    27     -24.385   4.990 -25.082  1.00 25.00           C
ATOM     28  CA  ASN    28     -24.066   7.814 -22.496  1.00 25.00           C
ATOM     29  CA  GLU    29     -20.961   8.977 -20.631  1.00 25.00           C
ATOM     30  CA  VAL    30     -18.084  10.613 -18.742  1.00 25.00           C
ATOM     31  CA  PRO    31     -14.395   9.833 -18.923  1.00 25.00           C
ATOM     32  CA  VAL    32     -11.758  10.182 -21.585  1.00 25.00           C
ATOM     33  CA  HIS    33     -11.406  13.396 -23.563  1.00 25.00           C
ATOM     34  CA  GLN    34      -8.762  14.227 -26.121  1.00 25.00           C
ATOM     35  CA  VAL    35      -7.832  12.040 -29.143  1.00 25.00           C
ATOM     36  CA  SER    36      -6.674  13.445 -32.522  1.00 25.00           C
ATOM     37  CA  TYR    37      -4.311  10.468 -32.358  1.00 25.00           C
ATOM     38  CA  THR    38      -1.665  13.176 -31.785  1.00 25.00           C
ATOM     39  CA  ASN    39      -3.006  13.775 -28.248  1.00 25.00           C
ATOM     40  CA  LEU    40      -2.871  10.014 -27.535  1.00 25.00           C
ATOM     41  CA  ALA    41       0.739   9.878 -28.805  1.00 25.00           C
ATOM     42  CA  GLU    42       1.666  12.841 -26.563  1.00 25.00           C
ATOM     43  CA  MET    43       0.049  11.104 -23.557  1.00 25.00           C
ATOM     44  CA  VAL    44       2.000   7.900 -24.328  1.00 25.00           C
ATOM     45  CA  GLY    45       5.254   9.906 -24.552  1.00 25.00           C
ATOM     46  CA  GLU    46       4.489  11.569 -21.188  1.00 25.00           C
ATOM     47  CA  MET    47       3.816   8.142 -19.619  1.00 25.00           C
ATOM     48  CA  ASN    48       7.130   6.825 -21.013  1.00 25.00           C
ATOM     49  CA  LYS    49       8.968   9.866 -19.584  1.00 25.00           C
ATOM     50  CA  LEU    50       7.331   9.282 -16.171  1.00 25.00           C
ATOM     51  CA  LEU    51       8.377   5.600 -16.271  1.00 25.00           C
ATOM     52  CA  GLU    52      11.967   6.618 -17.135  1.00 25.00           C
ATOM     53  CA  PRO    53      11.989   9.102 -14.220  1.00 25.00           C
ATOM     54  CA  SER    54      10.695   6.657 -11.569  1.00 25.00           C
ATOM     55  CA  GLN    55      13.454   5.969  -9.034  1.00 25.00           C
ATOM     56  CA  VAL    56      13.718   2.604 -10.726  1.00 25.00           C
ATOM     57  CA  HIS    57      14.665  -0.185 -13.211  1.00 25.00           C
ATOM     58  CA  LEU    58      11.474   0.855 -14.989  1.00 25.00           C
ATOM     59  CA  LYS    59      12.880   1.577 -18.453  1.00 25.00           C
ATOM     60  CA  PHE    60      10.990   3.587 -21.144  1.00 25.00           C
ATOM     61  CA  GLU    61      11.880   5.896 -24.041  1.00 25.00           C
ATOM     62  CA  LEU    62       9.575   5.619 -27.033  1.00 25.00           C
ATOM     63  CA  HIS    63      11.647   6.232 -30.146  1.00 25.00           C
ATOM     64  CA  ASP    64      11.342   4.864 -33.670  1.00 25.00           C
ATOM     65  CA  LYS    65      10.253   1.761 -35.536  1.00 25.00           C
ATOM     66  CA  LEU    66       9.585  -1.494 -33.666  1.00 25.00           C
ATOM     67  CA  ASN    67      12.981  -2.734 -32.576  1.00 25.00           C
ATOM     68  CA  GLU    68      15.420  -0.503 -30.597  1.00 25.00           C
ATOM     69  CA  TYR    69      12.061   1.221 -30.251  1.00 25.00           C
ATOM     70  CA  TYR    70      13.283   1.719 -26.643  1.00 25.00           C
ATOM     71  CA  VAL    71      15.335   2.288 -23.442  1.00 25.00           C
ATOM     72  CA  LYS    72      16.569   5.645 -22.243  1.00 25.00           C
ATOM     73  CA  VAL    73      16.860   7.309 -18.804  1.00 25.00           C
ATOM     74  CA  ILE    74      16.654   7.394 -15.039  1.00 25.00           C
ATOM     75  CA  GLU    75      17.535   3.768 -14.395  1.00 25.00           C
ATOM     76  CA  ASP    76      18.525   4.774 -10.845  1.00 25.00           C
ATOM     77  CA  SER    77      21.890   3.123 -11.659  1.00 25.00           C
ATOM     78  CA  THR    78      22.602   6.464 -13.389  1.00 25.00           C
ATOM     79  CA  ASN    79      22.756   6.373 -17.192  1.00 25.00           C
ATOM     80  CA  GLU    80      20.790   3.755 -19.162  1.00 25.00           C
ATOM     81  CA  VAL    81      20.646   0.654 -16.866  1.00 25.00           C
ATOM     82  CA  ILE    82      17.607  -0.171 -19.028  1.00 25.00           C
ATOM     83  CA  ARG    83      15.094  -2.395 -20.861  1.00 25.00           C
ATOM     84  CA  GLU    84      12.321  -4.550 -22.318  1.00 25.00           C
ATOM     85  CA  ILE    85      10.740  -1.329 -23.579  1.00 25.00           C
ATOM     86  CA  PRO    86       9.208  -2.228 -26.909  1.00 25.00           C
ATOM     87  CA  PRO    87       6.599   0.156 -28.191  1.00 25.00           C
ATOM     88  CA  LYS    88       3.209  -1.532 -27.617  1.00 25.00           C
ATOM     89  CA  ARG    89       4.724  -3.687 -24.838  1.00 25.00           C
ATOM     90  CA  TRP    90       6.226  -0.567 -23.204  1.00 25.00           C
ATOM     91  CA  LEU    91       2.828   1.190 -23.376  1.00 25.00           C
ATOM     92  CA  ASP    92       1.144  -1.855 -21.777  1.00 25.00           C
ATOM     93  CA  PHE    93       3.766  -1.870 -18.986  1.00 25.00           C
ATOM     94  CA  TYR    94       3.177   1.866 -18.381  1.00 25.00           C
ATOM     95  CA  ALA    95      -0.601   1.267 -18.208  1.00 25.00           C
ATOM     96  CA  ALA    96      -0.062  -1.576 -15.699  1.00 25.00           C
ATOM     97  CA  MET    97       2.168   0.695 -13.568  1.00 25.00           C
ATOM     98  CA  THR    98      -0.508   3.434 -13.644  1.00 25.00           C
ATOM     99  CA  GLU    99      -3.170   0.898 -12.574  1.00 25.00           C
ATOM    100  CA  PHE   100      -0.931  -0.276  -9.697  1.00 25.00           C
ATOM    101  CA  LEU   101      -0.408   3.353  -8.592  1.00 25.00           C
ATOM    102  CA  GLY   102      -4.190   3.951  -8.679  1.00 25.00           C
ATOM    103  CA  LEU   103      -4.761   0.799  -6.580  1.00 25.00           C
ATOM    104  CA  PHE   104      -2.143   1.981  -4.048  1.00 25.00           C
ATOM    105  CA  VAL   105       1.255   0.383  -4.908  1.00 25.00           C
ATOM    106  CA  ASP   106       2.710  -3.076  -4.645  1.00 25.00           C
ATOM    107  CA  GLU   107       3.588  -5.475  -1.832  1.00 25.00           C
ATOM    108  CA  LYS   108       3.233  -9.096  -0.637  1.00 25.00           C
ATOM    109  CA  LYS   109       6.916  -9.754  -1.455  1.00 25.00           C
ATOM    110  CA  LEU   110       5.432 -12.609  -3.509  1.00 25.00           C
ATOM    111  CA  GLU   111       1.851 -12.229  -4.506  1.00 25.00           C
ATOM    112  CA  HIS   112       1.391 -15.785  -5.697  1.00 25.00           C
ATOM    113  CA  HIS   113      -0.525 -18.245  -3.557  1.00 25.00           C
ATOM    114  CA  HIS   114      -4.086 -17.154  -4.473  1.00 25.00           C
ATOM    115  CA  HIS   115      -6.815 -19.780  -4.679  1.00 25.00           C
ATOM    116  CA  HIS   116      -9.402 -17.821  -6.664  1.00 25.00           C
ATOM    117  CA  HIS   117      -9.278 -17.048 -10.436  1.00 25.00           C
TER
END
