
#######################################################
#                                                     #
#                        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 T0353TS599_1
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS599_1.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.711
LGA    Q       2      Q       2          3.037
LGA    I       3      I       3          2.915
LGA    H       4      H       4          0.938
LGA    V       5      V       5          1.038
LGA    Y       6      Y       6          1.248
LGA    D       7      D       7          1.585
LGA    T       8      T       8          1.631
LGA    Y       9      Y       9          1.540
LGA    V      10      V      10          1.669
LGA    K      11      K      11          0.696
LGA    A      12      A      12          0.821
LGA    K      13      K      13          1.580
LGA    D      14      D      14          3.315
LGA    G      15      G      15           #
LGA    H      16      H      16          3.098
LGA    V      17      V      17          1.429
LGA    M      18      M      18          1.823
LGA    H      19      H      19          1.104
LGA    F      20      F      20          0.974
LGA    D      21      D      21          1.277
LGA    V      22      V      22          1.517
LGA    F      23      F      23          1.486
LGA    T      24      T      24          2.081
LGA    D      25      D      25          4.035
LGA    V      26      -       -           -
LGA    R      27      -       -           -
LGA    D      28      -       -           -
LGA    D      29      -       -           -
LGA    K      30      V      26           #
LGA    K      31      R      27           -
LGA    A      32      D      28           -
LGA    I      33      D      29           -
LGA    E      34      K      30           -
LGA    F      35      K      31           -
LGA    A      36      A      32           -
LGA    K      37      I      33           -
LGA    Q      38      E      34           -
LGA    W      39      -       -           -
LGA    L      40      -       -           -
LGA    S      41      -       -           -
LGA    S      42      -       -           -
LGA    I      43      -       -           -
LGA    G      44      -       -           -
LGA    E      45      -       -           -
LGA    E      46      -       -           -
LGA    G      47      -       -           -
LGA    A      48      -       -           -
LGA    T      49      -       -           -
LGA    V      50      -       -           -
LGA    T      51      -       -           -
LGA    S      52      -       -           -
LGA    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      F      35          3.223
LGA    P      64      A      36          2.924
LGA    D      65      K      37          4.019
LGA    E      66      Q      38          1.506
LGA    V      67      W      39          2.455
LGA    I      68      L      40          4.332
LGA    E      69      S      41          3.078
LGA    -       -      S      42           -
LGA    A      70      I      43          5.465
LGA    I      71      G      44           #
LGA    K      72      E      45           #
LGA    Q      73      E      46          4.397
LGA    N      74      -       -           -
LGA    G      75      G      47          3.032
LGA    Y      76      A      48          3.377
LGA    F      77      T      49          3.818
LGA    I      78      V      50          3.795
LGA    Y      79      T      51           #
LGA    -       -      S      52           -
LGA    -       -      E      53           -
LGA    K      80      E      54          3.746
LGA    M      81      C      55          2.403
LGA    E      82      R      56          2.969
LGA    G      83      F      57          1.030
LGA    C      84      C      58          2.859
LGA    -       -      H      59           -
LGA    -       -      S      60           -
LGA    -       -      Q      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    N      85      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     42    2.76    61.90     32.954     1.467

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.857337 * X  +  -0.165121 * Y  +   0.487554 * Z  +  -3.339821
  Y_new =   0.466535 * X  +   0.649506 * Y  +  -0.600406 * Z  +  -4.681440
  Z_new =  -0.217529 * X  +   0.742211 * Y  +   0.633880 * Z  +  -1.390411 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.863960   -2.277632  [ DEG:    49.5013   -130.4987 ]
  Theta =   0.219283    2.922310  [ DEG:    12.5640    167.4360 ]
  Phi   =   0.498355   -2.643238  [ DEG:    28.5536   -151.4464 ]
 
# 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: T0353TS599_1                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_1.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   42   2.76   61.90  32.954
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_1
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      14.145   4.254 -10.386  1.00  0.00              
ATOM      2  CA  GLN     2      10.722   4.798  -9.410  1.00  0.00              
ATOM      3  CA  ILE     3       9.694   4.136  -5.906  1.00  0.00              
ATOM      4  CA  HIS     4       6.126   4.627  -4.843  1.00  0.00              
ATOM      5  CA  VAL     5       5.131   4.464  -1.229  1.00  0.00              
ATOM      6  CA  TYR     6       1.592   3.682  -0.286  1.00  0.00              
ATOM      7  CA  ASP     7       0.470   4.207   3.142  1.00  0.00              
ATOM      8  CA  THR     8      -2.443   2.445   4.260  1.00  0.00              
ATOM      9  CA  TYR     9      -3.922   3.408   7.418  1.00  0.00              
ATOM     10  CA  VAL    10      -6.328   1.142   8.968  1.00  0.00              
ATOM     11  CA  LYS    11      -8.673   2.428  11.478  1.00  0.00              
ATOM     12  CA  ALA    12     -10.519  -0.047  13.571  1.00  0.00              
ATOM     13  CA  LYS    13     -13.945   0.889  15.018  1.00  0.00              
ATOM     14  CA  ASP    14     -12.447   1.400  18.463  1.00  0.00              
ATOM     15  CA  GLY    15      -9.839   3.883  17.313  1.00  0.00              
ATOM     16  CA  HIS    16      -6.852   1.656  17.061  1.00  0.00              
ATOM     17  CA  VAL    17      -4.720   2.759  14.318  1.00  0.00              
ATOM     18  CA  MET    18      -3.034   0.189  12.174  1.00  0.00              
ATOM     19  CA  HIS    19      -0.296   1.250   9.817  1.00  0.00              
ATOM     20  CA  PHE    20       0.265  -0.641   6.618  1.00  0.00              
ATOM     21  CA  ASP    21       3.063   0.282   4.427  1.00  0.00              
ATOM     22  CA  VAL    22       2.998  -0.783   0.817  1.00  0.00              
ATOM     23  CA  PHE    23       6.009  -0.132  -1.307  1.00  0.00              
ATOM     24  CA  THR    24       5.691  -0.047  -4.972  1.00  0.00              
ATOM     25  CA  ASP    25       8.702  -0.375  -7.141  1.00  0.00              
ATOM     26  CA  VAL    26       8.182   0.278 -10.792  1.00  0.00              
ATOM     27  CA  ARG    27      10.023  -2.570 -12.422  1.00  0.00              
ATOM     28  CA  ASP    28       8.923  -4.962  -9.648  1.00  0.00              
ATOM     29  CA  ASP    29       5.311  -3.775  -9.390  1.00  0.00              
ATOM     30  CA  LYS    30       4.535  -4.578 -13.013  1.00  0.00              
ATOM     31  CA  LYS    31       6.006  -8.085 -12.593  1.00  0.00              
ATOM     32  CA  ALA    32       4.020  -8.804  -9.453  1.00  0.00              
ATOM     33  CA  ILE    33       0.789  -7.703 -11.087  1.00  0.00              
ATOM     34  CA  GLU    34       1.408  -9.909 -14.099  1.00  0.00              
ATOM     35  CA  PHE    35       2.195 -12.979 -12.026  1.00  0.00              
ATOM     36  CA  ALA    36      -0.929 -12.422  -9.898  1.00  0.00              
ATOM     37  CA  LYS    37      -3.128 -12.020 -12.999  1.00  0.00              
ATOM     38  CA  GLN    38      -1.783 -15.239 -14.554  1.00  0.00              
ATOM     39  CA  TRP    39      -2.399 -17.207 -11.328  1.00  0.00              
ATOM     40  CA  LEU    40      -5.869 -15.928 -10.826  1.00  0.00              
ATOM     41  CA  SER    41      -6.834 -16.753 -14.439  1.00  0.00              
ATOM     42  CA  SER    42      -5.498 -20.255 -14.298  1.00  0.00              
ATOM     43  CA  ILE    43      -7.464 -21.001 -11.100  1.00  0.00              
ATOM     44  CA  GLY    44     -10.719 -19.594 -12.484  1.00  0.00              
ATOM     45  CA  GLU    45     -10.686 -16.336 -10.623  1.00  0.00              
ATOM     46  CA  GLU    46     -11.501 -13.128 -12.450  1.00  0.00              
ATOM     47  CA  GLY    47      -9.194 -10.400 -11.118  1.00  0.00              
ATOM     48  CA  ALA    48     -12.061  -8.504  -9.434  1.00  0.00              
ATOM     49  CA  THR    49     -13.291 -11.497  -7.533  1.00  0.00              
ATOM     50  CA  VAL    50     -10.001 -12.955  -6.362  1.00  0.00              
ATOM     51  CA  THR    51     -10.257 -15.340  -3.477  1.00  0.00              
ATOM     52  CA  SER    52      -7.972 -14.861  -0.480  1.00  0.00              
ATOM     53  CA  GLU    53      -5.962 -18.027  -1.223  1.00  0.00              
ATOM     54  CA  GLU    54      -5.392 -17.203  -4.868  1.00  0.00              
ATOM     55  CA  CYS    55      -4.180 -13.704  -4.220  1.00  0.00              
ATOM     56  CA  ARG    56      -1.919 -14.004  -1.198  1.00  0.00              
ATOM     57  CA  PHE    57       0.629 -16.157  -2.924  1.00  0.00              
ATOM     58  CA  CYS    58       1.798 -13.220  -5.124  1.00  0.00              
ATOM     59  CA  HIS    59       0.263 -10.279  -3.408  1.00  0.00              
ATOM     60  CA  SER    60       2.097  -9.945  -0.138  1.00  0.00              
ATOM     61  CA  GLN    61       1.279  -6.240   0.071  1.00  0.00              
ATOM     62  CA  LYS    62      -2.486  -6.691  -0.350  1.00  0.00              
ATOM     63  CA  ALA    63      -3.886  -4.893  -3.337  1.00  0.00              
ATOM     64  CA  PRO    64      -6.190  -1.972  -2.780  1.00  0.00              
ATOM     65  CA  ASP    65      -9.473  -3.525  -3.813  1.00  0.00              
ATOM     66  CA  GLU    66      -9.003  -6.562  -1.659  1.00  0.00              
ATOM     67  CA  VAL    67      -7.927  -4.664   1.387  1.00  0.00              
ATOM     68  CA  ILE    68     -10.856  -2.293   1.203  1.00  0.00              
ATOM     69  CA  GLU    69     -13.338  -5.090   0.896  1.00  0.00              
ATOM     70  CA  ALA    70     -11.845  -6.968   3.874  1.00  0.00              
ATOM     71  CA  ILE    71     -11.745  -3.932   6.085  1.00  0.00              
ATOM     72  CA  LYS    72     -15.316  -2.989   5.382  1.00  0.00              
ATOM     73  CA  GLN    73     -16.557  -6.471   6.071  1.00  0.00              
ATOM     74  CA  ASN    74     -14.680  -6.531   9.349  1.00  0.00              
ATOM     75  CA  GLY    75     -15.704  -3.087  10.641  1.00  0.00              
ATOM     76  CA  TYR    76     -12.338  -1.528   9.712  1.00  0.00              
ATOM     77  CA  PHE    77     -11.968   1.844   8.046  1.00  0.00              
ATOM     78  CA  ILE    78      -9.276   2.193   5.431  1.00  0.00              
ATOM     79  CA  TYR    79      -7.435   5.360   5.054  1.00  0.00              
ATOM     80  CA  LYS    80      -5.042   5.634   2.190  1.00  0.00              
ATOM     81  CA  MET    81      -2.161   8.070   2.289  1.00  0.00              
ATOM     82  CA  GLU    82      -0.431   8.753  -0.957  1.00  0.00              
ATOM     83  CA  GLY    83       2.912   9.873  -0.363  1.00  0.00              
ATOM     84  CA  CYS    84       3.541   7.946   3.287  1.00  0.00              
ATOM     85  CA  ASN    85       5.312   5.037   5.752  1.00  0.00              
TER                                                                             
END
