
#######################################################
#                                                     #
#                        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   83 (   83),  selected   83 , name T0353TS393_2-D1
# Molecule2: number of CA atoms   83 ( 1315),  selected   83 , name T0353_D1.pdb
# PARAMETERS: T0353TS393_2-D1.T0353_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    Q       2      -       -           -
LGA    I       3      -       -           -
LGA    H       4      -       -           -
LGA    V       5      -       -           -
LGA    Y       6      -       -           -
LGA    D       7      -       -           -
LGA    T       8      -       -           -
LGA    Y       9      -       -           -
LGA    V      10      -       -           -
LGA    K      11      -       -           -
LGA    A      12      -       -           -
LGA    K      13      -       -           -
LGA    D      14      -       -           -
LGA    G      15      Q       2          4.640
LGA    H      16      I       3          3.016
LGA    V      17      H       4          2.844
LGA    -       -      V       5           -
LGA    M      18      Y       6          2.375
LGA    H      19      D       7          1.614
LGA    F      20      T       8          3.240
LGA    D      21      Y       9          3.883
LGA    V      22      V      10          4.765
LGA    F      23      K      11          4.591
LGA    T      24      A      12          4.233
LGA    D      25      -       -           -
LGA    V      26      -       -           -
LGA    R      27      K      13          2.026
LGA    D      28      D      14          2.524
LGA    D      29      G      15          3.311
LGA    K      30      H      16           #
LGA    K      31      -       -           -
LGA    A      32      V      17          2.406
LGA    I      33      M      18          4.453
LGA    E      34      -       -           -
LGA    F      35      -       -           -
LGA    A      36      H      19           #
LGA    K      37      F      20           -
LGA    Q      38      D      21           -
LGA    W      39      V      22           -
LGA    L      40      F      23           -
LGA    S      41      T      24           -
LGA    S      42      D      25           -
LGA    I      43      V      26           -
LGA    G      44      R      27           -
LGA    E      45      D      28           -
LGA    E      46      D      29           #
LGA    G      47      K      30           #
LGA    A      48      K      31           #
LGA    -       -      A      32           -
LGA    T      49      I      33          4.089
LGA    V      50      E      34          1.841
LGA    -       -      F      35           -
LGA    T      51      A      36          4.450
LGA    S      52      K      37          2.626
LGA    E      53      Q      38          3.723
LGA    E      54      W      39          4.723
LGA    C      55      L      40          4.571
LGA    -       -      S      41           -
LGA    R      56      S      42          2.077
LGA    F      57      I      43          2.064
LGA    C      58      G      44           #
LGA    H      59      E      45          1.489
LGA    S      60      E      46          1.631
LGA    Q      61      G      47          1.594
LGA    K      62      A      48          1.398
LGA    A      63      -       -           -
LGA    P      64      T      49          1.562
LGA    D      65      -       -           -
LGA    E      66      -       -           -
LGA    V      67      V      50          1.751
LGA    I      68      T      51          3.136
LGA    E      69      -       -           -
LGA    A      70      S      52          2.732
LGA    I      71      -       -           -
LGA    K      72      -       -           -
LGA    Q      73      -       -           -
LGA    N      74      -       -           -
LGA    G      75      E      53          3.921
LGA    Y      76      E      54          3.182
LGA    F      77      C      55          0.906
LGA    I      78      R      56           -
LGA    Y      79      F      57           -
LGA    K      80      C      58           -
LGA    M      81      H      59           -
LGA    E      82      S      60           -
LGA    G      83      E      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    -       -      I      78           -
LGA    -       -      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   83   83    5.0     35    3.17     8.57     24.571     1.070

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.804526 * X  +   0.001910 * Y  +  -0.593914 * Z  +  -7.397629
  Y_new =   0.584374 * X  +  -0.181092 * Y  +   0.791020 * Z  +   4.032750
  Z_new =  -0.106043 * X  +  -0.983464 * Y  +  -0.146809 * Z  +   4.317622 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.718980    1.422613  [ DEG:   -98.4903     81.5097 ]
  Theta =   0.106242    3.035350  [ DEG:     6.0872    173.9128 ]
  Phi   =   0.628198   -2.513395  [ DEG:    35.9931   -144.0069 ]
 
# 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: T0353TS393_2-D1                               
REMARK     2: T0353_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS393_2-D1.T0353_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   83   83   5.0   35   3.17    8.57  24.571
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS393_2-D1
PFRMAT TS
TARGET T0353
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1     -22.209   9.309  12.814  1.00 25.00           C
ATOM      2  CA  GLN     2     -18.986   8.487  10.954  1.00 25.00           C
ATOM      3  CA  ILE     3     -15.883   6.640   9.931  1.00 25.00           C
ATOM      4  CA  HIS     4     -12.693   4.598   9.896  1.00 25.00           C
ATOM      5  CA  VAL     5      -9.817   3.808   7.540  1.00 25.00           C
ATOM      6  CA  TYR     6      -7.016   3.059   5.061  1.00 25.00           C
ATOM      7  CA  ASP     7      -3.495   1.968   4.197  1.00 25.00           C
ATOM      8  CA  THR     8      -5.122  -1.301   3.133  1.00 25.00           C
ATOM      9  CA  TYR     9      -4.512  -0.046  -0.368  1.00 25.00           C
ATOM     10  CA  VAL    10      -1.603   2.362  -0.643  1.00 25.00           C
ATOM     11  CA  LYS    11       1.215   0.138   0.523  1.00 25.00           C
ATOM     12  CA  ALA    12       4.641  -0.051   2.246  1.00 25.00           C
ATOM     13  CA  LYS    13       8.243   1.313   2.487  1.00 25.00           C
ATOM     14  CA  ASP    14      11.257   2.000   0.202  1.00 25.00           C
ATOM     15  CA  GLY    15      10.299   0.805  -3.311  1.00 25.00           C
ATOM     16  CA  HIS    16       7.058   2.656  -2.701  1.00 25.00           C
ATOM     17  CA  VAL    17       4.688   5.615  -2.322  1.00 25.00           C
ATOM     18  CA  MET    18       3.942   5.103   1.398  1.00 25.00           C
ATOM     19  CA  HIS    19       1.619   3.704   4.057  1.00 25.00           C
ATOM     20  CA  PHE    20      -0.476   5.262   6.875  1.00 25.00           C
ATOM     21  CA  ASP    21      -1.899   2.436   9.011  1.00 25.00           C
ATOM     22  CA  VAL    22      -3.553  -0.916   8.318  1.00 25.00           C
ATOM     23  CA  PHE    23      -7.275  -0.563   8.696  1.00 25.00           C
ATOM     24  CA  THR    24      -8.265  -3.489  10.851  1.00 25.00           C
ATOM     25  CA  ASP    25      -9.987  -6.008  13.126  1.00 25.00           C
ATOM     26  CA  VAL    26     -11.555  -4.295  16.139  1.00 25.00           C
ATOM     27  CA  ARG    27     -12.774  -0.898  17.421  1.00 25.00           C
ATOM     28  CA  ASP    28      -9.257  -0.092  18.701  1.00 25.00           C
ATOM     29  CA  ASP    29      -7.773  -1.050  15.303  1.00 25.00           C
ATOM     30  CA  LYS    30     -10.320   1.194  13.530  1.00 25.00           C
ATOM     31  CA  LYS    31      -9.433   4.093  15.872  1.00 25.00           C
ATOM     32  CA  ALA    32      -5.708   3.561  15.159  1.00 25.00           C
ATOM     33  CA  ILE    33      -6.404   3.566  11.392  1.00 25.00           C
ATOM     34  CA  GLU    34      -8.401   6.815  11.741  1.00 25.00           C
ATOM     35  CA  PHE    35      -5.527   8.400  13.714  1.00 25.00           C
ATOM     36  CA  ALA    36      -3.042   7.320  11.007  1.00 25.00           C
ATOM     37  CA  LYS    37      -5.293   8.829   8.302  1.00 25.00           C
ATOM     38  CA  GLN    38      -5.511  12.104  10.275  1.00 25.00           C
ATOM     39  CA  TRP    39      -1.697  12.176  10.623  1.00 25.00           C
ATOM     40  CA  LEU    40      -1.319  11.595   6.856  1.00 25.00           C
ATOM     41  CA  SER    41      -3.778  14.443   6.144  1.00 25.00           C
ATOM     42  CA  SER    42      -1.817  16.754   8.486  1.00 25.00           C
ATOM     43  CA  ILE    43       0.599  16.817   5.609  1.00 25.00           C
ATOM     44  CA  GLY    44      -0.987  16.406   2.129  1.00 25.00           C
ATOM     45  CA  GLU    45      -2.055  16.514  -1.547  1.00 25.00           C
ATOM     46  CA  GLU    46      -4.848  15.333  -3.915  1.00 25.00           C
ATOM     47  CA  GLY    47      -6.145  12.050  -5.254  1.00 25.00           C
ATOM     48  CA  ALA    48      -5.948   8.622  -3.491  1.00 25.00           C
ATOM     49  CA  THR    49      -7.439   5.648  -5.400  1.00 25.00           C
ATOM     50  CA  VAL    50      -7.082   2.064  -4.366  1.00 25.00           C
ATOM     51  CA  THR    51      -9.180  -0.492  -2.400  1.00 25.00           C
ATOM     52  CA  SER    52     -10.838  -3.723  -1.271  1.00 25.00           C
ATOM     53  CA  GLU    53     -11.465  -7.446  -0.800  1.00 25.00           C
ATOM     54  CA  GLU    54      -8.605  -9.345  -2.299  1.00 25.00           C
ATOM     55  CA  CYS    55      -6.363  -7.099  -0.236  1.00 25.00           C
ATOM     56  CA  ARG    56      -7.977  -8.991   2.678  1.00 25.00           C
ATOM     57  CA  PHE    57      -7.282  -9.097   6.434  1.00 25.00           C
ATOM     58  CA  CYS    58      -6.897  -5.283   5.968  1.00 25.00           C
ATOM     59  CA  HIS    59     -10.653  -5.140   6.602  1.00 25.00           C
ATOM     60  CA  SER    60     -14.286  -4.542   5.640  1.00 25.00           C
ATOM     61  CA  GLN    61     -15.100  -3.406   9.155  1.00 25.00           C
ATOM     62  CA  LYS    62     -13.192  -0.209   8.308  1.00 25.00           C
ATOM     63  CA  ALA    63     -11.394  -0.401   4.978  1.00 25.00           C
ATOM     64  CA  PRO    64     -13.600   2.608   4.160  1.00 25.00           C
ATOM     65  CA  ASP    65     -15.755   5.721   4.741  1.00 25.00           C
ATOM     66  CA  GLU    66     -12.703   7.617   6.064  1.00 25.00           C
ATOM     67  CA  VAL    67     -10.682   6.564   2.986  1.00 25.00           C
ATOM     68  CA  ILE    68     -13.511   7.751   0.693  1.00 25.00           C
ATOM     69  CA  GLU    69     -13.624  11.109   2.530  1.00 25.00           C
ATOM     70  CA  ALA    70      -9.831  11.474   2.147  1.00 25.00           C
ATOM     71  CA  ILE    71     -10.110  10.706  -1.596  1.00 25.00           C
ATOM     72  CA  LYS    72     -12.881  13.326  -1.951  1.00 25.00           C
ATOM     73  CA  GLN    73     -10.714  15.901  -0.125  1.00 25.00           C
ATOM     74  CA  ASN    74      -7.164  16.738   1.116  1.00 25.00           C
ATOM     75  CA  GLY    75      -5.027  13.552   1.215  1.00 25.00           C
ATOM     76  CA  TYR    76      -4.950  10.363   3.305  1.00 25.00           C
ATOM     77  CA  PHE    77      -3.694   7.522   1.042  1.00 25.00           C
ATOM     78  CA  ILE    78      -6.372   4.917   0.327  1.00 25.00           C
ATOM     79  CA  TYR    79      -9.893   4.722  -1.121  1.00 25.00           C
ATOM     80  CA  LYS    80     -13.278   4.017  -2.637  1.00 25.00           C
ATOM     81  CA  MET    81     -14.175   0.364  -2.693  1.00 25.00           C
ATOM     82  CA  GLU    82     -17.148  -1.817  -1.815  1.00 25.00           C
ATOM     83  CA  GLY    83     -20.137  -0.809  -3.882  1.00 25.00           C
TER
END
