
#######################################################
#                                                     #
#                        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   85 (   85),  selected   85 , name T0353TS393_2
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS393_2.T0353.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    Q       2      Y       6           #
LGA    I       3      D       7          3.074
LGA    H       4      T       8          4.721
LGA    V       5      Y       9           -
LGA    Y       6      V      10           -
LGA    D       7      K      11           -
LGA    T       8      A      12           -
LGA    Y       9      K      13           -
LGA    V      10      D      14           -
LGA    K      11      G      15           -
LGA    A      12      H      16           -
LGA    K      13      V      17           -
LGA    D      14      M      18           -
LGA    G      15      H      19           -
LGA    H      16      F      20           -
LGA    V      17      D      21           -
LGA    M      18      V      22           -
LGA    H      19      -       -           -
LGA    F      20      -       -           -
LGA    D      21      -       -           -
LGA    V      22      -       -           -
LGA    F      23      F      23           #
LGA    T      24      T      24          3.864
LGA    D      25      D      25          3.481
LGA    V      26      V      26          2.955
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    R      27      D      29          1.898
LGA    D      28      K      30          2.224
LGA    D      29      K      31          2.054
LGA    K      30      A      32          1.546
LGA    K      31      I      33          1.111
LGA    A      32      E      34          1.146
LGA    I      33      F      35          1.218
LGA    E      34      A      36          0.683
LGA    F      35      K      37          0.351
LGA    A      36      Q      38          1.107
LGA    K      37      W      39          1.909
LGA    Q      38      L      40          1.761
LGA    W      39      S      41          1.141
LGA    L      40      S      42          2.280
LGA    S      41      I      43          3.486
LGA    S      42      G      44          2.906
LGA    I      43      E      45           #
LGA    G      44      E      46           -
LGA    E      45      G      47           -
LGA    E      46      A      48           -
LGA    G      47      T      49           -
LGA    A      48      V      50           -
LGA    T      49      T      51           -
LGA    V      50      S      52           -
LGA    T      51      E      53           -
LGA    -       -      E      54           -
LGA    -       -      C      55           -
LGA    -       -      R      56           -
LGA    -       -      F      57           -
LGA    -       -      C      58           -
LGA    -       -      H      59           -
LGA    -       -      S      60           -
LGA    -       -      Q      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    S      52      E      66          3.310
LGA    E      53      V      67          2.753
LGA    -       -      I      68           -
LGA    E      54      E      69          2.284
LGA    C      55      A      70          3.021
LGA    R      56      I      71          3.928
LGA    F      57      K      72          2.470
LGA    -       -      Q      73           -
LGA    C      58      N      74          4.146
LGA    H      59      G      75          5.505
LGA    S      60      Y      76           #
LGA    Q      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      F      77          2.056
LGA    P      64      I      78          2.933
LGA    D      65      Y      79          3.493
LGA    E      66      -       -           -
LGA    V      67      -       -           -
LGA    I      68      -       -           -
LGA    E      69      K      80          3.007
LGA    A      70      M      81           -
LGA    I      71      E      82           -
LGA    K      72      G      83          4.663
LGA    Q      73      C      84           #
LGA    N      74      N      85           -
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      -       -           -
LGA    C      84      -       -           -
LGA    N      85      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   85    5.0     34    2.87    11.76     27.647     1.145

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.739635 * X  +   0.671255 * Y  +  -0.048545 * Z  +  -0.513357
  Y_new =  -0.652747 * X  +  -0.697933 * Y  +   0.294638 * Z  +  -7.035541
  Z_new =   0.163896 * X  +   0.249612 * Y  +   0.954375 * Z  +   0.861005 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.255815   -2.885778  [ DEG:    14.6571   -165.3429 ]
  Theta =  -0.164639   -2.976954  [ DEG:    -9.4331   -170.5669 ]
  Phi   =  -2.418516    0.723077  [ DEG:  -138.5708     41.4292 ]
 
# 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                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS393_2.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   85   5.0   34   2.87   11.76  27.647
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS393_2
PFRMAT TS
TARGET T0353
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      -0.152   9.291   8.122  1.00 25.00           C
ATOM      2  CA  GLN     2      -0.417   5.723   6.810  1.00 25.00           C
ATOM      3  CA  ILE     3      -0.489   2.858   4.386  1.00 25.00           C
ATOM      4  CA  HIS     4      -1.062   0.641   1.369  1.00 25.00           C
ATOM      5  CA  VAL     5      -0.865  -3.038   0.433  1.00 25.00           C
ATOM      6  CA  TYR     6      -0.579  -6.752  -0.389  1.00 25.00           C
ATOM      7  CA  ASP     7      -1.426  -9.814  -2.450  1.00 25.00           C
ATOM      8  CA  THR     8       2.040  -9.358  -3.947  1.00 25.00           C
ATOM      9  CA  TYR     9       2.964 -12.308  -1.791  1.00 25.00           C
ATOM     10  CA  VAL    10       0.052 -14.597  -1.004  1.00 25.00           C
ATOM     11  CA  LYS    11      -0.892 -15.695  -4.489  1.00 25.00           C
ATOM     12  CA  ALA    12      -3.706 -16.867  -6.824  1.00 25.00           C
ATOM     13  CA  LYS    13      -6.687 -19.251  -7.388  1.00 25.00           C
ATOM     14  CA  ASP    14      -7.484 -23.008  -7.223  1.00 25.00           C
ATOM     15  CA  GLY    15      -4.216 -24.813  -6.354  1.00 25.00           C
ATOM     16  CA  HIS    16      -3.832 -22.145  -3.700  1.00 25.00           C
ATOM     17  CA  VAL    17      -4.463 -20.278  -0.439  1.00 25.00           C
ATOM     18  CA  MET    18      -5.876 -17.093  -2.027  1.00 25.00           C
ATOM     19  CA  HIS    19      -5.262 -13.538  -3.217  1.00 25.00           C
ATOM     20  CA  PHE    20      -6.621 -10.097  -2.187  1.00 25.00           C
ATOM     21  CA  ASP    21      -5.371  -7.514  -4.706  1.00 25.00           C
ATOM     22  CA  VAL    22      -2.054  -6.774  -6.408  1.00 25.00           C
ATOM     23  CA  PHE    23      -0.377  -3.901  -4.659  1.00 25.00           C
ATOM     24  CA  THR    24       0.677  -1.608  -7.454  1.00 25.00           C
ATOM     25  CA  ASP    25       1.835   1.276  -9.652  1.00 25.00           C
ATOM     26  CA  VAL    26      -0.026   4.485  -8.805  1.00 25.00           C
ATOM     27  CA  ARG    27      -2.085   6.179  -6.055  1.00 25.00           C
ATOM     28  CA  ASP    28      -5.285   4.605  -7.450  1.00 25.00           C
ATOM     29  CA  ASP    29      -3.604   1.165  -7.497  1.00 25.00           C
ATOM     30  CA  LYS    30      -2.475   1.640  -3.868  1.00 25.00           C
ATOM     31  CA  LYS    31      -6.038   2.622  -2.863  1.00 25.00           C
ATOM     32  CA  ALA    32      -7.418  -0.488  -4.622  1.00 25.00           C
ATOM     33  CA  ILE    33      -4.864  -2.683  -2.797  1.00 25.00           C
ATOM     34  CA  GLU    34      -5.859  -1.105   0.547  1.00 25.00           C
ATOM     35  CA  PHE    35      -9.556  -1.751  -0.220  1.00 25.00           C
ATOM     36  CA  ALA    36      -8.765  -5.398  -1.080  1.00 25.00           C
ATOM     37  CA  LYS    37      -6.832  -5.779   2.204  1.00 25.00           C
ATOM     38  CA  GLN    38      -9.782  -4.293   4.142  1.00 25.00           C
ATOM     39  CA  TRP    39     -12.179  -6.722   2.403  1.00 25.00           C
ATOM     40  CA  LEU    40      -9.884  -9.658   3.289  1.00 25.00           C
ATOM     41  CA  SER    41      -9.773  -8.502   6.938  1.00 25.00           C
ATOM     42  CA  SER    42     -13.594  -8.261   7.003  1.00 25.00           C
ATOM     43  CA  ILE    43     -13.343 -12.006   7.164  1.00 25.00           C
ATOM     44  CA  GLY    44     -10.204 -13.364   8.924  1.00 25.00           C
ATOM     45  CA  GLU    45      -7.553 -15.236  10.957  1.00 25.00           C
ATOM     46  CA  GLU    46      -3.915 -14.937  12.173  1.00 25.00           C
ATOM     47  CA  GLY    47      -0.469 -14.909  10.632  1.00 25.00           C
ATOM     48  CA  ALA    48       0.437 -13.716   7.075  1.00 25.00           C
ATOM     49  CA  THR    49       4.137 -13.964   6.096  1.00 25.00           C
ATOM     50  CA  VAL    50       5.464 -13.399   2.637  1.00 25.00           C
ATOM     51  CA  THR    51       7.033 -10.470   0.698  1.00 25.00           C
ATOM     52  CA  SER    52       9.234  -8.433  -1.639  1.00 25.00           C
ATOM     53  CA  GLU    53      11.522  -7.576  -4.556  1.00 25.00           C
ATOM     54  CA  GLU    54      11.893 -10.608  -6.724  1.00 25.00           C
ATOM     55  CA  CYS    55       8.111 -10.760  -6.720  1.00 25.00           C
ATOM     56  CA  ARG    56       8.469  -7.511  -8.717  1.00 25.00           C
ATOM     57  CA  PHE    57       5.980  -5.320 -10.618  1.00 25.00           C
ATOM     58  CA  CYS    58       3.772  -6.006  -7.526  1.00 25.00           C
ATOM     59  CA  HIS    59       5.445  -2.923  -6.034  1.00 25.00           C
ATOM     60  CA  SER    60       7.696  -1.073  -3.586  1.00 25.00           C
ATOM     61  CA  GLN    61       5.464   1.977  -3.734  1.00 25.00           C
ATOM     62  CA  LYS    62       2.980  -0.035  -1.646  1.00 25.00           C
ATOM     63  CA  ALA    63       3.990  -3.665  -1.240  1.00 25.00           C
ATOM     64  CA  PRO    64       3.925  -2.765   2.472  1.00 25.00           C
ATOM     65  CA  ASP    65       2.965  -0.909   5.682  1.00 25.00           C
ATOM     66  CA  GLU    66      -0.642  -2.148   5.350  1.00 25.00           C
ATOM     67  CA  VAL    67       0.608  -5.736   4.864  1.00 25.00           C
ATOM     68  CA  ILE    68       2.821  -5.411   7.973  1.00 25.00           C
ATOM     69  CA  GLU    69      -0.159  -4.097   9.987  1.00 25.00           C
ATOM     70  CA  ALA    70      -2.298  -7.039   8.787  1.00 25.00           C
ATOM     71  CA  ILE    71       0.465  -9.492   9.798  1.00 25.00           C
ATOM     72  CA  LYS    72       0.683  -7.859  13.255  1.00 25.00           C
ATOM     73  CA  GLN    73      -3.116  -8.135  13.652  1.00 25.00           C
ATOM     74  CA  ASN    74      -6.330  -9.759  12.284  1.00 25.00           C
ATOM     75  CA  GLY    75      -5.707 -11.118   8.749  1.00 25.00           C
ATOM     76  CA  TYR    76      -5.063  -9.613   5.304  1.00 25.00           C
ATOM     77  CA  PHE    77      -2.790 -12.044   3.382  1.00 25.00           C
ATOM     78  CA  ILE    78       0.677 -10.618   2.736  1.00 25.00           C
ATOM     79  CA  TYR    79       3.613  -9.175   4.691  1.00 25.00           C
ATOM     80  CA  LYS    80       6.814  -7.865   6.206  1.00 25.00           C
ATOM     81  CA  MET    81       9.516  -7.195   3.675  1.00 25.00           C
ATOM     82  CA  GLU    82      11.983  -4.436   2.857  1.00 25.00           C
ATOM     83  CA  GLY    83      14.262  -3.833   5.800  1.00 25.00           C
ATOM     84  CA  CYS    84      12.973  -0.470   7.143  1.00 25.00           C
ATOM     85  CA  ASN    85      16.449  -0.258   8.647  1.00 25.00           C
TER
END
