
#######################################################
#                                                     #
#                        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   77 (   77),  selected   77 , name T0303TS168_5-D2
# Molecule2: number of CA atoms   77 (  602),  selected   77 , name T0303_D2.pdb
# PARAMETERS: T0303TS168_5-D2.T0303_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      18      S      18           -
LGA    L      19      L      19          3.600
LGA    P      20      P      20          2.560
LGA    D      21      D      21          3.818
LGA    L      22      L      22          4.231
LGA    A      23      A      23          2.339
LGA    L      24      L      24           #
LGA    S      25      S      25           -
LGA    I      26      I      26           #
LGA    N      27      N      27           #
LGA    -       -      S      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      K      31           -
LGA    -       -      D      32           -
LGA    -       -      V      33           -
LGA    -       -      N      34           -
LGA    -       -      L      35           -
LGA    -       -      P      36           -
LGA    -       -      Q      37           -
LGA    -       -      A      38           -
LGA    -       -      S      39           -
LGA    -       -      E      40           -
LGA    -       -      N      41           -
LGA    -       -      L      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      T      45           -
LGA    -       -      W      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      N      49           -
LGA    -       -      G      50           -
LGA    S      28      A      51          3.226
LGA    A      29      D      52          4.786
LGA    L      30      V      53          5.329
LGA    K      31      L      54           #
LGA    D      32      S      55          4.453
LGA    V      33      -       -           -
LGA    N      34      -       -           -
LGA    L      35      Q      56          3.972
LGA    P      36      -       -           -
LGA    Q      37      -       -           -
LGA    A      38      R      57          3.202
LGA    S      39      A      58           #
LGA    E      40      V      59           #
LGA    -       -      D      60           -
LGA    N      41      W      61          3.346
LGA    L      42      A      62           #
LGA    V      43      -       -           -
LGA    M      44      -       -           -
LGA    T      45      -       -           -
LGA    W      46      -       -           -
LGA    I      47      -       -           -
LGA    G      48      -       -           -
LGA    N      49      -       -           -
LGA    G      50      -       -           -
LGA    A      51      -       -           -
LGA    D      52      -       -           -
LGA    V      53      -       -           -
LGA    L      54      -       -           -
LGA    S      55      -       -           -
LGA    Q      56      -       -           -
LGA    R      57      -       -           -
LGA    A      58      -       -           -
LGA    V      59      -       -           -
LGA    D      60      -       -           -
LGA    W      61      C      63          3.499
LGA    A      62      T      64          3.006
LGA    C      63      Q      65          4.279
LGA    -       -      A      66           -
LGA    T      64      E      67          2.523
LGA    Q      65      K      68          4.790
LGA    A      66      E      69          3.184
LGA    E      67      L      70           #
LGA    K      68      -       -           -
LGA    E      69      -       -           -
LGA    L      70      -       -           -
LGA    T      71      T      71          1.346
LGA    E      72      E      72          1.207
LGA    D      73      D      73          1.428
LGA    E      74      E      74          1.278
LGA    F      75      F      75          0.905
LGA    K      76      K      76          1.048
LGA    Y      77      Y      77          1.059
LGA    F      78      F      78          0.802
LGA    K      79      K      79          0.568
LGA    R      80      R      80          0.731
LGA    Q      81      Q      81          0.913
LGA    F      82      F      82          0.638
LGA    G      83      G      83          0.194
LGA    F      84      F      84          0.428
LGA    Y      85      Y      85          1.243
LGA    Y      86      Y      86          1.435
LGA    G      87      G      87          0.668
LGA    E      88      E      88          0.353
LGA    N      89      N      89          1.682
LGA    L      90      L      90          2.612
LGA    C      91      -       -           -
LGA    N      92      -       -           -
LGA    I      93      C      91          3.225
LGA    S      94      N      92          0.643
LGA    -       -      I      93           -
LGA    -       -      S      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77   77    5.0     40    2.71    62.50     37.724     1.426

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.782169 * X  +   0.405604 * Y  +  -0.472967 * Z  + -15.530282
  Y_new =   0.617607 * X  +  -0.604985 * Y  +   0.502549 * Z  +  90.775589
  Z_new =  -0.082302 * X  +  -0.685186 * Y  +  -0.723704 * Z  +  17.085077 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.383527    0.758066  [ DEG:  -136.5660     43.4340 ]
  Theta =   0.082395    3.059197  [ DEG:     4.7209    175.2791 ]
  Phi   =   0.668372   -2.473221  [ DEG:    38.2949   -141.7051 ]
 
# 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: T0303TS168_5-D2                               
REMARK     2: T0303_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS168_5-D2.T0303_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   77   77   5.0   40   2.71   62.50  37.724
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS168_5-D2
PFRMAT TS
TARGET T0303
MODEL 5
PARENT N/A
ATOM     18  CA  SER    18     -14.020  92.317  18.978  1.00 25.00           C
ATOM     19  CA  LEU    19     -13.949  88.787  20.489  1.00 25.00           C
ATOM     20  CA  PRO    20     -12.229  88.625  23.908  1.00 25.00           C
ATOM     21  CA  ASP    21     -10.973  85.090  23.136  1.00 25.00           C
ATOM     22  CA  LEU    22      -9.621  86.282  19.757  1.00 25.00           C
ATOM     23  CA  ALA    23      -7.839  89.206  21.473  1.00 25.00           C
ATOM     24  CA  LEU    24      -6.302  86.801  24.027  1.00 25.00           C
ATOM     25  CA  SER    25      -5.110  84.515  21.195  1.00 25.00           C
ATOM     26  CA  ILE    26      -3.553  87.516  19.395  1.00 25.00           C
ATOM     27  CA  ASN    27      -1.778  88.562  22.624  1.00 25.00           C
ATOM     28  CA  SER    28      -0.443  85.002  23.073  1.00 25.00           C
ATOM     29  CA  ALA    29       0.826  84.994  19.460  1.00 25.00           C
ATOM     30  CA  LEU    30       2.558  88.361  20.036  1.00 25.00           C
ATOM     31  CA  LYS    31       4.196  87.001  23.220  1.00 25.00           C
ATOM     32  CA  ASP    32       5.402  83.910  21.308  1.00 25.00           C
ATOM     33  CA  VAL    33       8.892  85.335  21.913  1.00 25.00           C
ATOM     34  CA  ASN    34       9.884  83.484  18.745  1.00 25.00           C
ATOM     35  CA  LEU    35       7.324  85.342  16.719  1.00 25.00           C
ATOM     36  CA  PRO    36       8.310  84.053  13.320  1.00 25.00           C
ATOM     37  CA  GLN    37       5.589  85.953  11.455  1.00 25.00           C
ATOM     38  CA  ALA    38       3.230  87.489  14.015  1.00 25.00           C
ATOM     39  CA  SER    39       2.482  90.707  12.230  1.00 25.00           C
ATOM     40  CA  GLU    40       0.217  91.469  15.243  1.00 25.00           C
ATOM     41  CA  ASN    41       1.177  94.848  16.770  1.00 25.00           C
ATOM     42  CA  LEU    42      -2.421  96.091  16.340  1.00 25.00           C
ATOM     43  CA  VAL    43      -3.744  92.917  18.027  1.00 25.00           C
ATOM     44  CA  MET    44      -1.300  93.414  20.934  1.00 25.00           C
ATOM     45  CA  THR    45      -2.440  97.053  21.301  1.00 25.00           C
ATOM     46  CA  TRP    46      -6.100  95.929  21.331  1.00 25.00           C
ATOM     47  CA  ILE    47      -5.304  93.319  24.018  1.00 25.00           C
ATOM     48  CA  GLY    48      -3.585  95.570  26.596  1.00 25.00           C
ATOM     49  CA  ASN    49      -4.940  99.129  27.146  1.00 25.00           C
ATOM     50  CA  GLY    50      -2.459  99.090  29.992  1.00 25.00           C
ATOM     51  CA  ALA    51      -3.108 102.894  29.908  1.00 25.00           C
ATOM     52  CA  ASP    52      -2.945 105.408  27.024  1.00 25.00           C
ATOM     53  CA  VAL    53       0.637 106.341  28.008  1.00 25.00           C
ATOM     54  CA  LEU    54       1.603 102.637  28.099  1.00 25.00           C
ATOM     55  CA  SER    55       0.060 102.124  24.632  1.00 25.00           C
ATOM     56  CA  GLN    56       2.003 105.141  23.293  1.00 25.00           C
ATOM     57  CA  ARG    57       5.245 103.740  24.774  1.00 25.00           C
ATOM     58  CA  ALA    58       4.550 100.344  23.146  1.00 25.00           C
ATOM     59  CA  VAL    59       3.923 102.058  19.779  1.00 25.00           C
ATOM     60  CA  ASP    60       7.210 103.993  20.124  1.00 25.00           C
ATOM     61  CA  TRP    61       9.069 100.741  20.919  1.00 25.00           C
ATOM     62  CA  ALA    62       7.511  99.070  17.846  1.00 25.00           C
ATOM     63  CA  CYS    63       8.790 101.667  15.330  1.00 25.00           C
ATOM     64  CA  THR    64      11.990 102.316  17.168  1.00 25.00           C
ATOM     65  CA  GLN    65      15.228 102.000  19.222  1.00 25.00           C
ATOM     66  CA  ALA    66      14.793 100.100  22.487  1.00 25.00           C
ATOM     67  CA  GLU    67      15.457 100.716  26.182  1.00 25.00           C
ATOM     68  CA  LYS    68      12.317 100.461  28.208  1.00 25.00           C
ATOM     69  CA  GLU    69      12.869  98.258  31.236  1.00 25.00           C
ATOM     70  CA  LEU    70      15.657  96.441  29.337  1.00 25.00           C
ATOM     71  CA  THR    71      13.777  95.745  26.074  1.00 25.00           C
ATOM     72  CA  GLU    72      13.853  91.986  26.805  1.00 25.00           C
ATOM     73  CA  ASP    73      12.504  92.619  30.332  1.00 25.00           C
ATOM     74  CA  GLU    74       9.694  94.789  28.895  1.00 25.00           C
ATOM     75  CA  PHE    75       8.817  92.032  26.385  1.00 25.00           C
ATOM     76  CA  LYS    76       8.729  89.451  29.212  1.00 25.00           C
ATOM     77  CA  TYR    77       6.434  91.735  31.259  1.00 25.00           C
ATOM     78  CA  PHE    78       4.117  92.154  28.239  1.00 25.00           C
ATOM     79  CA  LYS    79       4.014  88.355  27.759  1.00 25.00           C
ATOM     80  CA  ARG    80       3.165  87.886  31.464  1.00 25.00           C
ATOM     81  CA  GLN    81       0.361  90.478  31.176  1.00 25.00           C
ATOM     82  CA  PHE    82      -1.018  88.678  28.090  1.00 25.00           C
ATOM     83  CA  GLY    83      -0.937  85.342  29.968  1.00 25.00           C
ATOM     84  CA  PHE    84      -2.788  86.931  32.921  1.00 25.00           C
ATOM     85  CA  TYR    85      -5.429  88.347  30.535  1.00 25.00           C
ATOM     86  CA  TYR    86      -5.863  84.897  28.930  1.00 25.00           C
ATOM     87  CA  GLY    87      -6.274  83.311  32.392  1.00 25.00           C
ATOM     88  CA  GLU    88      -8.899  85.942  33.312  1.00 25.00           C
ATOM     89  CA  ASN    89     -10.779  85.245  30.049  1.00 25.00           C
ATOM     90  CA  LEU    90     -10.702  81.486  30.780  1.00 25.00           C
ATOM     91  CA  CYS    91     -12.051  82.120  34.307  1.00 25.00           C
ATOM     92  CA  ASN    92     -14.641  84.614  35.603  1.00 25.00           C
ATOM     93  CA  ILE    93     -15.675  84.737  31.885  1.00 25.00           C
ATOM     94  CA  SER    94     -15.745  87.808  29.627  1.00 25.00           C
TER
END
