
#######################################################
#                                                     #
#                        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 T0353TS599_2-D1
# Molecule2: number of CA atoms   83 ( 1315),  selected   83 , name T0353_D1.pdb
# PARAMETERS: T0353TS599_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          4.718
LGA    Q       2      Q       2          3.009
LGA    I       3      I       3          2.883
LGA    H       4      H       4          0.885
LGA    V       5      V       5          0.992
LGA    Y       6      Y       6          1.252
LGA    D       7      D       7          1.591
LGA    T       8      T       8          1.682
LGA    Y       9      Y       9          1.563
LGA    V      10      V      10          1.695
LGA    K      11      K      11          0.714
LGA    A      12      A      12          0.853
LGA    K      13      K      13          1.601
LGA    D      14      D      14          3.262
LGA    G      15      G      15           #
LGA    H      16      H      16          3.052
LGA    V      17      V      17          1.364
LGA    M      18      M      18          1.812
LGA    H      19      H      19          1.115
LGA    F      20      F      20          1.021
LGA    D      21      D      21          1.317
LGA    V      22      V      22          1.513
LGA    F      23      F      23          1.457
LGA    T      24      T      24          2.059
LGA    D      25      D      25          4.044
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          3.216
LGA    P      64      A      36          2.909
LGA    D      65      K      37          4.006
LGA    E      66      Q      38          1.514
LGA    V      67      W      39          2.475
LGA    I      68      L      40          4.331
LGA    E      69      S      41          3.098
LGA    -       -      S      42           -
LGA    A      70      I      43          5.472
LGA    I      71      G      44           #
LGA    K      72      E      45           #
LGA    Q      73      E      46          4.455
LGA    N      74      -       -           -
LGA    G      75      G      47          3.054
LGA    Y      76      A      48          3.407
LGA    F      77      T      49          3.838
LGA    I      78      V      50          3.823
LGA    Y      79      T      51           #
LGA    -       -      S      52           -
LGA    -       -      E      53           -
LGA    K      80      E      54          3.709
LGA    M      81      C      55          2.377
LGA    E      82      R      56          2.884
LGA    G      83      F      57          0.980
LGA    -       -      C      58           -
LGA    -       -      H      59           -
LGA    -       -      S      60           -
LGA    -       -      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     41    2.76    60.98     33.258     1.434

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.291264 * X  +  -0.665068 * Y  +   0.687641 * Z  +  -3.379059
  Y_new =   0.110150 * X  +   0.737341 * Y  +   0.666480 * Z  +  -4.693837
  Z_new =  -0.950280 * X  +  -0.118378 * Y  +   0.288019 * Z  +  -1.370237 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.389959    2.751633  [ DEG:   -22.3430    157.6570 ]
  Theta =   1.254133    1.887459  [ DEG:    71.8566    108.1434 ]
  Phi   =   0.361556   -2.780037  [ DEG:    20.7156   -159.2844 ]
 
# 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_2-D1                               
REMARK     2: T0353_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_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   41   2.76   60.98  33.258
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_2-D1
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      14.118   4.284 -10.302  1.00  0.00              
ATOM      2  CA  GLN     2      10.695   4.825  -9.326  1.00  0.00              
ATOM      3  CA  ILE     3       9.665   4.143  -5.828  1.00  0.00              
ATOM      4  CA  HIS     4       6.096   4.628  -4.767  1.00  0.00              
ATOM      5  CA  VAL     5       5.082   4.448  -1.149  1.00  0.00              
ATOM      6  CA  TYR     6       1.568   3.664  -0.235  1.00  0.00              
ATOM      7  CA  ASP     7       0.427   4.181   3.221  1.00  0.00              
ATOM      8  CA  THR     8      -2.499   2.397   4.302  1.00  0.00              
ATOM      9  CA  TYR     9      -3.968   3.369   7.472  1.00  0.00              
ATOM     10  CA  VAL    10      -6.387   1.093   9.004  1.00  0.00              
ATOM     11  CA  LYS    11      -8.728   2.373  11.504  1.00  0.00              
ATOM     12  CA  ALA    12     -10.592  -0.127  13.600  1.00  0.00              
ATOM     13  CA  LYS    13     -14.027   0.811  15.039  1.00  0.00              
ATOM     14  CA  ASP    14     -12.529   1.310  18.483  1.00  0.00              
ATOM     15  CA  GLY    15      -9.928   3.799  17.355  1.00  0.00              
ATOM     16  CA  HIS    16      -6.920   1.569  17.094  1.00  0.00              
ATOM     17  CA  VAL    17      -4.803   2.685  14.375  1.00  0.00              
ATOM     18  CA  MET    18      -3.099   0.121  12.213  1.00  0.00              
ATOM     19  CA  HIS    19      -0.352   1.187   9.865  1.00  0.00              
ATOM     20  CA  PHE    20       0.211  -0.688   6.664  1.00  0.00              
ATOM     21  CA  ASP    21       3.009   0.221   4.453  1.00  0.00              
ATOM     22  CA  VAL    22       2.966  -0.802   0.868  1.00  0.00              
ATOM     23  CA  PHE    23       5.958  -0.148  -1.242  1.00  0.00              
ATOM     24  CA  THR    24       5.654  -0.045  -4.904  1.00  0.00              
ATOM     25  CA  ASP    25       8.688  -0.370  -7.083  1.00  0.00              
ATOM     26  CA  VAL    26       8.166   0.298 -10.725  1.00  0.00              
ATOM     27  CA  ARG    27      10.005  -2.536 -12.357  1.00  0.00              
ATOM     28  CA  ASP    28       8.901  -4.942  -9.596  1.00  0.00              
ATOM     29  CA  ASP    29       5.288  -3.757  -9.348  1.00  0.00              
ATOM     30  CA  LYS    30       4.528  -4.567 -12.968  1.00  0.00              
ATOM     31  CA  LYS    31       5.977  -8.038 -12.563  1.00  0.00              
ATOM     32  CA  ALA    32       3.995  -8.783  -9.424  1.00  0.00              
ATOM     33  CA  ILE    33       0.768  -7.677 -11.069  1.00  0.00              
ATOM     34  CA  GLU    34       1.391  -9.873 -14.094  1.00  0.00              
ATOM     35  CA  PHE    35       2.184 -12.966 -12.010  1.00  0.00              
ATOM     36  CA  ALA    36      -0.958 -12.399  -9.909  1.00  0.00              
ATOM     37  CA  LYS    37      -3.154 -11.987 -12.995  1.00  0.00              
ATOM     38  CA  GLN    38      -1.797 -15.189 -14.563  1.00  0.00              
ATOM     39  CA  TRP    39      -2.396 -17.197 -11.368  1.00  0.00              
ATOM     40  CA  LEU    40      -5.897 -15.904 -10.864  1.00  0.00              
ATOM     41  CA  SER    41      -6.846 -16.710 -14.462  1.00  0.00              
ATOM     42  CA  SER    42      -5.506 -20.219 -14.346  1.00  0.00              
ATOM     43  CA  ILE    43      -7.489 -20.979 -11.151  1.00  0.00              
ATOM     44  CA  GLY    44     -10.737 -19.565 -12.541  1.00  0.00              
ATOM     45  CA  GLU    45     -10.705 -16.317 -10.668  1.00  0.00              
ATOM     46  CA  GLU    46     -11.518 -13.091 -12.483  1.00  0.00              
ATOM     47  CA  GLY    47      -9.217 -10.370 -11.135  1.00  0.00              
ATOM     48  CA  ALA    48     -12.089  -8.482  -9.456  1.00  0.00              
ATOM     49  CA  THR    49     -13.326 -11.488  -7.557  1.00  0.00              
ATOM     50  CA  VAL    50     -10.051 -12.937  -6.386  1.00  0.00              
ATOM     51  CA  THR    51     -10.292 -15.354  -3.500  1.00  0.00              
ATOM     52  CA  SER    52      -8.004 -14.870  -0.511  1.00  0.00              
ATOM     53  CA  GLU    53      -6.013 -18.036  -1.258  1.00  0.00              
ATOM     54  CA  GLU    54      -5.425 -17.197  -4.895  1.00  0.00              
ATOM     55  CA  CYS    55      -4.217 -13.705  -4.234  1.00  0.00              
ATOM     56  CA  ARG    56      -1.968 -14.023  -1.212  1.00  0.00              
ATOM     57  CA  PHE    57       0.589 -16.169  -2.936  1.00  0.00              
ATOM     58  CA  CYS    58       1.764 -13.219  -5.127  1.00  0.00              
ATOM     59  CA  HIS    59       0.231 -10.277  -3.387  1.00  0.00              
ATOM     60  CA  SER    60       2.057  -9.981  -0.132  1.00  0.00              
ATOM     61  CA  GLN    61       1.238  -6.216   0.114  1.00  0.00              
ATOM     62  CA  LYS    62      -2.531  -6.697  -0.343  1.00  0.00              
ATOM     63  CA  ALA    63      -3.920  -4.897  -3.315  1.00  0.00              
ATOM     64  CA  PRO    64      -6.216  -1.988  -2.753  1.00  0.00              
ATOM     65  CA  ASP    65      -9.500  -3.520  -3.799  1.00  0.00              
ATOM     66  CA  GLU    66      -9.037  -6.567  -1.662  1.00  0.00              
ATOM     67  CA  VAL    67      -7.976  -4.688   1.394  1.00  0.00              
ATOM     68  CA  ILE    68     -10.889  -2.306   1.222  1.00  0.00              
ATOM     69  CA  GLU    69     -13.392  -5.112   0.886  1.00  0.00              
ATOM     70  CA  ALA    70     -11.885  -7.007   3.870  1.00  0.00              
ATOM     71  CA  ILE    71     -11.805  -3.969   6.088  1.00  0.00              
ATOM     72  CA  LYS    72     -15.361  -3.026   5.376  1.00  0.00              
ATOM     73  CA  GLN    73     -16.611  -6.508   6.042  1.00  0.00              
ATOM     74  CA  ASN    74     -14.744  -6.599   9.322  1.00  0.00              
ATOM     75  CA  GLY    75     -15.778  -3.133  10.628  1.00  0.00              
ATOM     76  CA  TYR    76     -12.401  -1.581   9.720  1.00  0.00              
ATOM     77  CA  PHE    77     -12.026   1.797   8.070  1.00  0.00              
ATOM     78  CA  ILE    78      -9.327   2.156   5.459  1.00  0.00              
ATOM     79  CA  TYR    79      -7.486   5.320   5.105  1.00  0.00              
ATOM     80  CA  LYS    80      -5.084   5.606   2.248  1.00  0.00              
ATOM     81  CA  MET    81      -2.204   8.039   2.363  1.00  0.00              
ATOM     82  CA  GLU    82      -0.467   8.736  -0.875  1.00  0.00              
ATOM     83  CA  GLY    83       2.876   9.857  -0.274  1.00  0.00              
TER                                                                             
END
