
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS599_5.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          1.488
LGA    Q       2      Q       2          1.528
LGA    I       3      I       3          1.019
LGA    H       4      H       4          1.457
LGA    V       5      V       5          0.878
LGA    Y       6      Y       6          1.858
LGA    D       7      D       7          1.509
LGA    T       8      -       -           -
LGA    Y       9      -       -           -
LGA    V      10      T       8          1.656
LGA    K      11      Y       9          0.982
LGA    A      12      V      10          0.707
LGA    K      13      K      11          1.369
LGA    D      14      A      12          3.016
LGA    -       -      K      13           -
LGA    -       -      D      14           -
LGA    -       -      G      15           -
LGA    -       -      H      16           -
LGA    G      15      V      17          1.630
LGA    H      16      M      18          2.090
LGA    V      17      H      19          2.656
LGA    M      18      F      20          2.581
LGA    -       -      D      21           -
LGA    H      19      V      22          2.855
LGA    F      20      F      23          2.779
LGA    D      21      T      24          2.843
LGA    V      22      D      25          1.492
LGA    F      23      V      26          4.143
LGA    T      24      R      27           -
LGA    D      25      D      28           -
LGA    V      26      D      29           -
LGA    R      27      K      30           -
LGA    D      28      K      31           -
LGA    D      29      A      32           -
LGA    K      30      I      33           -
LGA    K      31      E      34           -
LGA    A      32      F      35           -
LGA    I      33      A      36           -
LGA    E      34      K      37           -
LGA    F      35      Q      38           -
LGA    A      36      W      39           -
LGA    K      37      L      40           -
LGA    Q      38      S      41           -
LGA    W      39      S      42           -
LGA    L      40      I      43           -
LGA    S      41      G      44           -
LGA    S      42      E      45           -
LGA    I      43      E      46           -
LGA    G      44      G      47           -
LGA    E      45      A      48           -
LGA    E      46      T      49           -
LGA    G      47      V      50           -
LGA    A      48      T      51           -
LGA    T      49      S      52           -
LGA    V      50      E      53           -
LGA    T      51      E      54           -
LGA    S      52      C      55           -
LGA    E      53      R      56           -
LGA    E      54      F      57           -
LGA    C      55      C      58           -
LGA    R      56      H      59           -
LGA    F      57      S      60           -
LGA    C      58      Q      61           -
LGA    H      59      K      62           -
LGA    -       -      A      63           -
LGA    S      60      P      64          5.652
LGA    Q      61      D      65          2.554
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    K      62      I      68          0.137
LGA    A      63      E      69          2.189
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    P      64      K      72          1.128
LGA    D      65      Q      73          1.576
LGA    E      66      N      74          5.382
LGA    V      67      G      75           #
LGA    I      68      Y      76          2.994
LGA    E      69      -       -           -
LGA    A      70      F      77          4.306
LGA    I      71      I      78          1.911
LGA    K      72      -       -           -
LGA    Q      73      Y      79           #
LGA    N      74      K      80          4.037
LGA    G      75      M      81           #
LGA    Y      76      E      82           -
LGA    F      77      G      83           -
LGA    I      78      C      84           -
LGA    Y      79      N      85           -
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     32    2.60    31.25     26.953     1.184

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.210614 * X  +   0.743538 * Y  +   0.634660 * Z  +   8.549803
  Y_new =  -0.954966 * X  +   0.295289 * Y  +  -0.029039 * Z  +  -5.507948
  Z_new =  -0.209000 * X  +  -0.599963 * Y  +   0.772246 * Z  +  -7.288208 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.660500    2.481093  [ DEG:   -37.8439    142.1561 ]
  Theta =   0.210552    2.931041  [ DEG:    12.0638    167.9362 ]
  Phi   =  -1.353726    1.787867  [ DEG:   -77.5628    102.4372 ]
 
# 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_5                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS599_5.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   32   2.60   31.25  26.953
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS599_5
PFRMAT TS                                                                       
TARGET T0353                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      12.336   1.044 -10.161  1.00  0.00              
ATOM      2  CA  GLN     2      10.469   3.587  -8.090  1.00  0.00              
ATOM      3  CA  ILE     3       9.001   2.581  -4.780  1.00  0.00              
ATOM      4  CA  HIS     4       6.707   4.943  -3.012  1.00  0.00              
ATOM      5  CA  VAL     5       5.438   4.240   0.471  1.00  0.00              
ATOM      6  CA  TYR     6       2.233   5.944   1.617  1.00  0.00              
ATOM      7  CA  ASP     7       1.288   6.115   5.175  1.00  0.00              
ATOM      8  CA  THR     8      -1.568   8.510   5.211  1.00  0.00              
ATOM      9  CA  TYR     9      -3.343   7.195   2.113  1.00  0.00              
ATOM     10  CA  VAL    10      -3.663   3.723   3.691  1.00  0.00              
ATOM     11  CA  LYS    11      -5.322   4.550   7.002  1.00  0.00              
ATOM     12  CA  ALA    12      -7.314   1.553   8.129  1.00  0.00              
ATOM     13  CA  LYS    13      -9.846   1.729  10.991  1.00  0.00              
ATOM     14  CA  ASP    14      -7.300   0.189  13.392  1.00  0.00              
ATOM     15  CA  GLY    15      -4.674   2.814  12.728  1.00  0.00              
ATOM     16  CA  HIS    16      -2.278   1.017  10.455  1.00  0.00              
ATOM     17  CA  VAL    17      -1.454   3.023   7.344  1.00  0.00              
ATOM     18  CA  MET    18       0.193   1.203   4.595  1.00  0.00              
ATOM     19  CA  HIS    19      -0.239   1.961   0.906  1.00  0.00              
ATOM     20  CA  PHE    20       2.439   0.748  -1.434  1.00  0.00              
ATOM     21  CA  ASP    21       2.853   2.296  -4.728  1.00  0.00              
ATOM     22  CA  VAL    22       5.001   0.656  -7.241  1.00  0.00              
ATOM     23  CA  PHE    23       6.032   2.535 -10.327  1.00  0.00              
ATOM     24  CA  THR    24       7.435   0.705 -13.277  1.00  0.00              
ATOM     25  CA  ASP    25       9.008   2.998 -15.937  1.00  0.00              
ATOM     26  CA  VAL    26       9.330   1.311 -19.265  1.00  0.00              
ATOM     27  CA  ARG    27      13.035   2.228 -19.680  1.00  0.00              
ATOM     28  CA  ASP    28      13.806   0.919 -16.186  1.00  0.00              
ATOM     29  CA  ASP    29      11.758  -2.285 -16.211  1.00  0.00              
ATOM     30  CA  LYS    30      13.375  -3.388 -19.481  1.00  0.00              
ATOM     31  CA  LYS    31      16.858  -2.741 -18.136  1.00  0.00              
ATOM     32  CA  ALA    32      16.314  -4.745 -14.940  1.00  0.00              
ATOM     33  CA  ILE    33      14.976  -7.702 -16.898  1.00  0.00              
ATOM     34  CA  GLU    34      17.998  -7.509 -19.260  1.00  0.00              
ATOM     35  CA  PHE    35      20.493  -7.631 -16.400  1.00  0.00              
ATOM     36  CA  ALA    36      18.633 -10.666 -14.982  1.00  0.00              
ATOM     37  CA  LYS    37      18.712 -12.384 -18.381  1.00  0.00              
ATOM     38  CA  GLN    38      22.464 -11.847 -18.772  1.00  0.00              
ATOM     39  CA  TRP    39      23.215 -13.220 -15.285  1.00  0.00              
ATOM     40  CA  LEU    40      20.946 -16.189 -15.682  1.00  0.00              
ATOM     41  CA  SER    41      22.551 -17.126 -19.043  1.00  0.00              
ATOM     42  CA  SER    42      26.031 -16.944 -17.598  1.00  0.00              
ATOM     43  CA  ILE    43      25.038 -19.397 -14.836  1.00  0.00              
ATOM     44  CA  GLY    44      23.329 -21.862 -17.186  1.00  0.00              
ATOM     45  CA  GLU    45      19.717 -20.984 -16.636  1.00  0.00              
ATOM     46  CA  GLU    46      17.360 -20.465 -19.505  1.00  0.00              
ATOM     47  CA  GLY    47      15.256 -17.373 -18.617  1.00  0.00              
ATOM     48  CA  ALA    48      12.110 -19.491 -18.271  1.00  0.00              
ATOM     49  CA  THR    49      13.553 -21.723 -15.586  1.00  0.00              
ATOM     50  CA  VAL    50      15.073 -19.113 -13.293  1.00  0.00              
ATOM     51  CA  THR    51      16.336 -20.810 -10.205  1.00  0.00              
ATOM     52  CA  SER    52      15.688 -19.086  -6.828  1.00  0.00              
ATOM     53  CA  GLU    53      19.345 -18.367  -6.227  1.00  0.00              
ATOM     54  CA  GLU    54      20.087 -16.830  -9.563  1.00  0.00              
ATOM     55  CA  CYS    55      17.210 -14.322  -9.748  1.00  0.00              
ATOM     56  CA  ARG    56      17.105 -13.161  -6.118  1.00  0.00              
ATOM     57  CA  PHE    57      20.650 -11.901  -6.299  1.00  0.00              
ATOM     58  CA  CYS    58      19.462  -8.817  -8.264  1.00  0.00              
ATOM     59  CA  HIS    59      15.776  -8.798  -7.768  1.00  0.00              
ATOM     60  CA  SER    60      15.374  -9.668  -4.139  1.00  0.00              
ATOM     61  CA  GLN    61      13.055  -6.885  -3.143  1.00  0.00              
ATOM     62  CA  LYS    62      11.143  -6.427  -6.309  1.00  0.00              
ATOM     63  CA  ALA    63       9.352  -8.783  -8.598  1.00  0.00              
ATOM     64  CA  PRO    64       5.821  -7.333  -9.087  1.00  0.00              
ATOM     65  CA  ASP    65       3.788 -10.240  -7.876  1.00  0.00              
ATOM     66  CA  GLU    66       6.023 -10.779  -4.826  1.00  0.00              
ATOM     67  CA  VAL    67       5.747  -7.153  -3.730  1.00  0.00              
ATOM     68  CA  ILE    68       1.967  -7.340  -4.058  1.00  0.00              
ATOM     69  CA  GLU    69       1.876 -10.540  -2.029  1.00  0.00              
ATOM     70  CA  ALA    70       3.998  -8.961   0.746  1.00  0.00              
ATOM     71  CA  ILE    71       1.783  -5.916   0.846  1.00  0.00              
ATOM     72  CA  LYS    72      -1.345  -7.983   1.090  1.00  0.00              
ATOM     73  CA  GLN    73       0.090 -10.165   3.902  1.00  0.00              
ATOM     74  CA  ASN    74       0.901  -7.066   5.934  1.00  0.00              
ATOM     75  CA  GLY    75      -2.538  -5.411   5.439  1.00  0.00              
ATOM     76  CA  TYR    76      -1.125  -3.058   2.830  1.00  0.00              
ATOM     77  CA  PHE    77      -2.651  -2.055  -0.452  1.00  0.00              
ATOM     78  CA  ILE    78      -0.376  -2.375  -3.454  1.00  0.00              
ATOM     79  CA  TYR    79      -0.743  -0.134  -6.365  1.00  0.00              
ATOM     80  CA  LYS    80       1.258  -0.732  -9.457  1.00  0.00              
ATOM     81  CA  MET    81       1.776   2.006 -11.922  1.00  0.00              
ATOM     82  CA  GLU    82       3.027   1.039 -15.309  1.00  0.00              
ATOM     83  CA  GLY    83       4.807   3.553 -17.142  1.00  0.00              
ATOM     84  CA  CYS    84       1.685   5.299 -16.753  1.00  0.00              
ATOM     85  CA  ASN    85       5.021   5.486 -19.320  1.00  0.00              
TER                                                                             
END
