
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0359TS393_4
# Molecule2: number of CA atoms   93 (  690),  selected   93 , name T0359.pdb
# PARAMETERS: T0359TS393_4.T0359.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    S       3      S       3          4.905
LGA    E       4      E       4          3.607
LGA    T       5      T       5          2.204
LGA    F       6      F       6          1.176
LGA    D       7      D       7          2.638
LGA    V       8      V       8          1.232
LGA    E       9      E       9          0.849
LGA    L      10      L      10          3.015
LGA    T      11      -       -           -
LGA    K      12      T      11          1.410
LGA    N      13      K      12          3.452
LGA    V      14      N      13          1.830
LGA    Q      15      V      14          3.026
LGA    G      16      Q      15          4.126
LGA    L      17      G      16          2.825
LGA    G      18      L      17          2.435
LGA    -       -      G      18           -
LGA    I      19      I      19          1.007
LGA    T      20      T      20          1.324
LGA    I      21      I      21          2.490
LGA    A      22      A      22          0.618
LGA    G      23      G      23          0.827
LGA    -       -      Y      24           -
LGA    -       -      I      25           -
LGA    -       -      G      26           -
LGA    -       -      D      27           -
LGA    Y      24      P      32           #
LGA    I      25      S      33          2.037
LGA    G      26      G      34           #
LGA    D      27      -       -           -
LGA    K      28      -       -           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      -       -           -
LGA    P      32      -       -           -
LGA    S      33      -       -           -
LGA    G      34      -       -           -
LGA    I      35      I      35          1.866
LGA    F      36      F      36          1.761
LGA    V      37      V      37          1.077
LGA    K      38      K      38          1.193
LGA    S      39      S      39          1.314
LGA    I      40      I      40          1.012
LGA    T      41      T      41          2.108
LGA    K      42      K      42          2.054
LGA    S      43      S      43          3.432
LGA    S      44      S      44          1.976
LGA    A      45      A      45          1.885
LGA    V      46      V      46          1.612
LGA    E      47      E      47          1.548
LGA    H      48      H      48          1.769
LGA    D      49      D      49          0.540
LGA    G      50      G      50          1.348
LGA    R      51      R      51          1.864
LGA    I      52      I      52          1.862
LGA    Q      53      Q      53          1.387
LGA    I      54      I      54          1.044
LGA    G      55      G      55          1.360
LGA    D      56      D      56          1.373
LGA    Q      57      Q      57          1.107
LGA    I      58      I      58          0.714
LGA    I      59      I      59          0.745
LGA    A      60      A      60          1.028
LGA    V      61      V      61          1.037
LGA    D      62      D      62          1.785
LGA    G      63      G      63          0.960
LGA    T      64      T      64          0.558
LGA    N      65      N      65          2.440
LGA    L      66      L      66          2.135
LGA    Q      67      Q      67          1.986
LGA    G      68      G      68          2.592
LGA    F      69      F      69          2.637
LGA    T      70      T      70          2.994
LGA    N      71      N      71          2.775
LGA    Q      72      Q      72          1.901
LGA    Q      73      Q      73          1.625
LGA    A      74      A      74          2.098
LGA    V      75      V      75          1.965
LGA    E      76      E      76          1.363
LGA    V      77      V      77          1.271
LGA    L      78      L      78          1.172
LGA    R      79      R      79          1.988
LGA    H      80      H      80          2.527
LGA    T      81      T      81          2.029
LGA    G      82      G      82          1.695
LGA    Q      83      Q      83          2.362
LGA    T      84      T      84          1.976
LGA    V      85      V      85          1.330
LGA    L      86      L      86          1.419
LGA    L      87      L      87          1.029
LGA    T      88      T      88          1.148
LGA    L      89      L      89          1.129
LGA    M      90      M      90          0.811
LGA    R      91      R      91          1.703
LGA    R      92      R      92          2.442
LGA    G      93      G      93          1.607
LGA    E      94      E      94          3.290
LGA    T      95      -       -           -
LGA    S      96      T      95          6.250
LGA    V      97      S      96          3.353
LGA    -       -      V      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   93    5.0     83    2.13    87.95     70.706     3.718

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.340148 * X  +   0.576764 * Y  +  -0.742726 * Z  +  -4.468274
  Y_new =  -0.725367 * X  +  -0.663565 * Y  +  -0.183094 * Z  +  13.442204
  Z_new =  -0.598449 * X  +   0.476470 * Y  +   0.644077 * Z  +  -6.824340 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.636923   -2.504669  [ DEG:    36.4930   -143.5070 ]
  Theta =   0.641564    2.500029  [ DEG:    36.7589    143.2411 ]
  Phi   =  -2.009282    1.132310  [ DEG:  -115.1234     64.8766 ]
 
# 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: T0359TS393_4                                  
REMARK     2: T0359.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS393_4.T0359.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   93   5.0   83   2.13   87.95  70.706
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS393_4
PFRMAT TS
TARGET T0359
MODEL 4
PARENT N/A
ATOM      1  CA  SER     1       8.431  -1.828   1.037  1.00 25.00           C
ATOM      2  CA  MET     2       5.629   0.514   2.169  1.00 25.00           C
ATOM      3  CA  SER     3       5.216   2.796  -0.887  1.00 25.00           C
ATOM      4  CA  GLU     4       4.950   5.979   1.074  1.00 25.00           C
ATOM      5  CA  THR     5       1.208   6.727   0.589  1.00 25.00           C
ATOM      6  CA  PHE     6       1.916  10.414   1.191  1.00 25.00           C
ATOM      7  CA  ASP     7       0.473  13.669   2.535  1.00 25.00           C
ATOM      8  CA  VAL     8      -2.634  15.690   3.079  1.00 25.00           C
ATOM      9  CA  GLU     9      -5.387  18.019   4.230  1.00 25.00           C
ATOM     10  CA  LEU    10      -5.141  19.425   0.675  1.00 25.00           C
ATOM     11  CA  THR    11      -7.680  22.195   1.374  1.00 25.00           C
ATOM     12  CA  LYS    12     -10.927  24.273   1.160  1.00 25.00           C
ATOM     13  CA  ASN    13     -11.343  28.050   0.858  1.00 25.00           C
ATOM     14  CA  VAL    14     -11.780  30.781  -1.758  1.00 25.00           C
ATOM     15  CA  GLN    15     -13.861  28.220  -3.608  1.00 25.00           C
ATOM     16  CA  GLY    16     -12.948  25.826  -6.440  1.00 25.00           C
ATOM     17  CA  LEU    17     -10.995  22.924  -4.983  1.00 25.00           C
ATOM     18  CA  GLY    18      -7.970  23.816  -7.141  1.00 25.00           C
ATOM     19  CA  ILE    19      -6.155  21.354  -9.482  1.00 25.00           C
ATOM     20  CA  THR    20      -7.041  20.009 -12.967  1.00 25.00           C
ATOM     21  CA  ILE    21      -8.000  16.500 -14.115  1.00 25.00           C
ATOM     22  CA  ALA    22      -5.533  14.525 -16.301  1.00 25.00           C
ATOM     23  CA  GLY    23      -4.899  10.853 -17.063  1.00 25.00           C
ATOM     24  CA  TYR    24      -2.433   8.095 -16.147  1.00 25.00           C
ATOM     25  CA  ILE    25      -4.741   5.111 -16.290  1.00 25.00           C
ATOM     26  CA  GLY    26      -3.822   4.133 -19.806  1.00 25.00           C
ATOM     27  CA  ASP    27      -7.553   3.644 -20.257  1.00 25.00           C
ATOM     28  CA  LYS    28      -8.128   0.527 -18.215  1.00 25.00           C
ATOM     29  CA  LYS    29      -5.889  -2.337 -16.968  1.00 25.00           C
ATOM     30  CA  LEU    30      -3.237  -2.142 -14.201  1.00 25.00           C
ATOM     31  CA  GLU    31      -1.982   0.754 -16.324  1.00 25.00           C
ATOM     32  CA  PRO    32       0.079   3.694 -14.985  1.00 25.00           C
ATOM     33  CA  SER    33      -1.014   2.843 -11.434  1.00 25.00           C
ATOM     34  CA  GLY    34      -3.954   5.161 -10.946  1.00 25.00           C
ATOM     35  CA  ILE    35      -4.991   8.833 -11.492  1.00 25.00           C
ATOM     36  CA  PHE    36      -3.957  12.447 -12.028  1.00 25.00           C
ATOM     37  CA  VAL    37      -2.383  15.717 -10.877  1.00 25.00           C
ATOM     38  CA  LYS    38      -1.426  17.246 -14.284  1.00 25.00           C
ATOM     39  CA  SER    39      -1.586  20.983 -13.550  1.00 25.00           C
ATOM     40  CA  ILE    40      -1.696  23.495 -10.719  1.00 25.00           C
ATOM     41  CA  THR    41      -4.245  26.270 -11.128  1.00 25.00           C
ATOM     42  CA  LYS    42      -2.215  29.082  -9.598  1.00 25.00           C
ATOM     43  CA  SER    43      -4.679  30.712  -7.238  1.00 25.00           C
ATOM     44  CA  SER    44      -6.248  28.104  -4.942  1.00 25.00           C
ATOM     45  CA  ALA    45      -4.747  25.189  -3.068  1.00 25.00           C
ATOM     46  CA  VAL    46      -2.282  22.341  -3.878  1.00 25.00           C
ATOM     47  CA  GLU    47      -0.190  25.231  -5.268  1.00 25.00           C
ATOM     48  CA  HIS    48       0.439  26.518  -1.716  1.00 25.00           C
ATOM     49  CA  ASP    49       0.454  24.021   1.135  1.00 25.00           C
ATOM     50  CA  GLY    50       3.858  22.802  -0.164  1.00 25.00           C
ATOM     51  CA  ARG    51       3.318  19.853  -2.569  1.00 25.00           C
ATOM     52  CA  ILE    52       1.501  18.976  -5.755  1.00 25.00           C
ATOM     53  CA  GLN    53       4.335  18.225  -8.222  1.00 25.00           C
ATOM     54  CA  ILE    54       2.962  17.365 -11.627  1.00 25.00           C
ATOM     55  CA  GLY    55       2.461  13.741 -12.606  1.00 25.00           C
ATOM     56  CA  ASP    56       2.946  13.145  -8.864  1.00 25.00           C
ATOM     57  CA  GLN    57      -0.500  11.493  -8.541  1.00 25.00           C
ATOM     58  CA  ILE    58      -3.780  10.526  -6.818  1.00 25.00           C
ATOM     59  CA  ILE    59      -5.691   7.798  -4.971  1.00 25.00           C
ATOM     60  CA  ALA    60      -8.164   9.416  -2.551  1.00 25.00           C
ATOM     61  CA  VAL    61     -11.047  11.934  -2.040  1.00 25.00           C
ATOM     62  CA  ASP    62     -10.714  10.781   1.586  1.00 25.00           C
ATOM     63  CA  GLY    63     -11.429   7.066   2.141  1.00 25.00           C
ATOM     64  CA  THR    64     -12.983   6.317  -1.248  1.00 25.00           C
ATOM     65  CA  ASN    65     -11.273   5.146  -4.438  1.00 25.00           C
ATOM     66  CA  LEU    66     -10.050   7.187  -7.367  1.00 25.00           C
ATOM     67  CA  GLN    67      -8.453   3.900  -8.251  1.00 25.00           C
ATOM     68  CA  GLY    68      -9.917   1.775 -11.111  1.00 25.00           C
ATOM     69  CA  PHE    69     -11.705   4.603 -12.831  1.00 25.00           C
ATOM     70  CA  THR    70     -10.289   6.236 -15.955  1.00 25.00           C
ATOM     71  CA  ASN    71      -9.953  10.021 -15.566  1.00 25.00           C
ATOM     72  CA  GLN    72     -13.672  10.936 -15.496  1.00 25.00           C
ATOM     73  CA  GLN    73     -14.095   9.060 -12.184  1.00 25.00           C
ATOM     74  CA  ALA    74     -11.079  10.910 -10.721  1.00 25.00           C
ATOM     75  CA  VAL    75     -12.551  14.258 -11.856  1.00 25.00           C
ATOM     76  CA  GLU    76     -15.905  13.359 -10.241  1.00 25.00           C
ATOM     77  CA  VAL    77     -14.117  12.438  -6.983  1.00 25.00           C
ATOM     78  CA  LEU    78     -12.232  15.772  -7.045  1.00 25.00           C
ATOM     79  CA  ARG    79     -15.524  17.650  -7.597  1.00 25.00           C
ATOM     80  CA  HIS    80     -17.114  15.778  -4.659  1.00 25.00           C
ATOM     81  CA  THR    81     -15.597  17.964  -2.037  1.00 25.00           C
ATOM     82  CA  GLY    82     -17.119  21.207  -0.833  1.00 25.00           C
ATOM     83  CA  GLN    83     -14.689  21.010   2.059  1.00 25.00           C
ATOM     84  CA  THR    84     -11.460  19.376   3.325  1.00 25.00           C
ATOM     85  CA  VAL    85     -10.930  18.206  -0.243  1.00 25.00           C
ATOM     86  CA  LEU    86      -8.521  15.461   0.822  1.00 25.00           C
ATOM     87  CA  LEU    87      -6.229  14.039  -1.782  1.00 25.00           C
ATOM     88  CA  THR    88      -3.653  11.858  -0.135  1.00 25.00           C
ATOM     89  CA  LEU    89      -0.854  11.934  -2.706  1.00 25.00           C
ATOM     90  CA  MET    90       0.883   8.813  -4.010  1.00 25.00           C
ATOM     91  CA  ARG    91       4.521   8.649  -5.145  1.00 25.00           C
ATOM     92  CA  ARG    92       8.160   8.560  -6.032  1.00 25.00           C
ATOM     93  CA  GLY    93      11.800   8.930  -7.038  1.00 25.00           C
ATOM     94  CA  GLU    94      12.758   5.366  -5.973  1.00 25.00           C
ATOM     95  CA  THR    95      16.194   3.820  -6.757  1.00 25.00           C
ATOM     96  CA  SER    96      16.200   1.502  -9.771  1.00 25.00           C
ATOM     97  CA  VAL    97      13.327   1.460 -12.312  1.00 25.00           C
TER
END
