
#######################################################
#                                                     #
#                        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 T0360TS168_2-D1
# Molecule2: number of CA atoms   97 (  785),  selected   97 , name T0360_D1.pdb
# PARAMETERS: T0360TS168_2-D1.T0360_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    K      20      K      20           -
LGA    K      21      K      21           -
LGA    K      22      K      22           -
LGA    Q      23      Q      23           -
LGA    T      24      T      24           -
LGA    E      25      E      25           -
LGA    M      26      -       -           -
LGA    I      27      -       -           -
LGA    A      28      -       -           -
LGA    D      29      -       -           -
LGA    H      30      -       -           -
LGA    I      31      -       -           -
LGA    Y      32      -       -           -
LGA    G      33      -       -           -
LGA    K      34      -       -           -
LGA    Y      35      -       -           -
LGA    D      36      -       -           -
LGA    V      37      -       -           -
LGA    F      38      -       -           -
LGA    K      39      -       -           -
LGA    R      40      -       -           -
LGA    F      41      -       -           -
LGA    K      42      -       -           -
LGA    P      43      M      26           #
LGA    L      44      I      27           -
LGA    A      45      A      28           -
LGA    L      46      D      29           #
LGA    G      47      H      30          4.373
LGA    -       -      I      31           -
LGA    I      48      Y      32          2.990
LGA    D      49      G      33           -
LGA    -       -      K      34           -
LGA    -       -      Y      35           -
LGA    -       -      D      36           -
LGA    -       -      V      37           -
LGA    Q      50      F      38           #
LGA    D      51      K      39           -
LGA    L      52      R      40           -
LGA    -       -      F      41           -
LGA    -       -      K      42           -
LGA    -       -      P      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      G      47           -
LGA    -       -      I      48           -
LGA    I      53      D      49          3.337
LGA    -       -      Q      50           -
LGA    A      54      D      51          3.522
LGA    A      55      L      52          4.124
LGA    L      56      I      53          2.916
LGA    P      57      A      54           #
LGA    Q      58      A      55           -
LGA    Y      59      L      56           -
LGA    D      60      P      57           -
LGA    -       -      Q      58           -
LGA    -       -      Y      59           -
LGA    -       -      D      60           -
LGA    A      61      A      61          2.232
LGA    A      62      A      62          1.824
LGA    L      63      L      63          0.597
LGA    I      64      I      64          1.429
LGA    A      65      A      65          1.480
LGA    R      66      R      66          0.566
LGA    V      67      V      67          0.816
LGA    L      68      L      68          1.311
LGA    A      69      A      69          0.500
LGA    N      70      N      70          0.860
LGA    H      71      H      71          1.379
LGA    C      72      C      72          0.649
LGA    R      73      R      73          0.906
LGA    R      74      R      74          2.137
LGA    P      75      -       -           -
LGA    R      76      P      75          4.376
LGA    Y      77      R      76          3.592
LGA    L      78      Y      77          4.248
LGA    K      79      L      78          3.740
LGA    A      80      K      79          4.066
LGA    L      81      -       -           -
LGA    A      82      -       -           -
LGA    R      83      -       -           -
LGA    G      84      -       -           -
LGA    G      85      A      80          4.999
LGA    -       -      L      81           -
LGA    -       -      A      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    K      86      G      85           #
LGA    R      87      K      86           #
LGA    -       -      R      87           -
LGA    F      88      F      88           #
LGA    -       -      D      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    D      89      N      92          4.332
LGA    L      90      -       -           -
LGA    N      91      -       -           -
LGA    N      92      -       -           -
LGA    R      93      R      93          4.908
LGA    F      94      F      94          3.497
LGA    K      95      K      95          4.363
LGA    G      96      G      96          4.565
LGA    E      97      E      97          3.001
LGA    V      98      V      98          2.480
LGA    T      99      T      99          4.887
LGA    -       -      P     100           -
LGA    P     100      E     101          3.383
LGA    E     101      E     102          2.475
LGA    E     102      Q     103          4.261
LGA    Q     103      A     104          3.902
LGA    A     104      I     105          3.696
LGA    I     105      -       -           -
LGA    A     106      A     106          3.590
LGA    Q     107      Q     107           -
LGA    N     108      N     108           -
LGA    H     109      H     109          4.847
LGA    P     110      P     110           #
LGA    F     111      F     111           -
LGA    V     112      V     112           -
LGA    Q     113      Q     113           -
LGA    Q     114      Q     114           -
LGA    A     115      A     115           -
LGA    L     116      L     116           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     41    3.28    58.54     26.521     1.212

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.219541 * X  +  -0.952153 * Y  +  -0.212618 * Z  + -79.593964
  Y_new =   0.724632 * X  +   0.013224 * Y  +   0.689009 * Z  +   1.738375
  Z_new =  -0.653230 * X  +  -0.305335 * Y  +   0.692864 * Z  + -14.238061 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.415081    2.726511  [ DEG:   -23.7824    156.2176 ]
  Theta =   0.711843    2.429749  [ DEG:    40.7856    139.2144 ]
  Phi   =   1.276618   -1.864975  [ DEG:    73.1448   -106.8552 ]
 
# 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: T0360TS168_2-D1                               
REMARK     2: T0360_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0360TS168_2-D1.T0360_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   97   5.0   41   3.28   58.54  26.521
REMARK  ---------------------------------------------------------- 
MOLECULE T0360TS168_2-D1
PFRMAT TS
TARGET T0360
MODEL 2
PARENT N/A
ATOM     20  CA  LYS    20    -100.053  -9.156 -17.321  1.00 25.00           C
ATOM     21  CA  LYS    21     -99.074 -12.826 -17.804  1.00 25.00           C
ATOM     22  CA  LYS    22     -98.153 -12.125 -21.455  1.00 25.00           C
ATOM     23  CA  GLN    23     -96.022  -9.134 -20.369  1.00 25.00           C
ATOM     24  CA  THR    24     -94.253 -11.309 -17.761  1.00 25.00           C
ATOM     25  CA  GLU    25     -93.568 -13.982 -20.417  1.00 25.00           C
ATOM     26  CA  MET    26     -92.145 -11.314 -22.769  1.00 25.00           C
ATOM     27  CA  ILE    27     -89.894 -10.005 -19.960  1.00 25.00           C
ATOM     28  CA  ALA    28     -88.669 -13.562 -19.250  1.00 25.00           C
ATOM     29  CA  ASP    29     -87.915 -14.072 -22.969  1.00 25.00           C
ATOM     30  CA  HIS    30     -85.973 -10.773 -23.054  1.00 25.00           C
ATOM     31  CA  ILE    31     -83.971 -11.845 -19.970  1.00 25.00           C
ATOM     32  CA  TYR    32     -83.179 -15.208 -21.622  1.00 25.00           C
ATOM     33  CA  GLY    33     -83.838 -18.787 -22.608  1.00 25.00           C
ATOM     34  CA  LYS    34     -82.987 -20.357 -19.262  1.00 25.00           C
ATOM     35  CA  TYR    35     -85.519 -19.148 -16.654  1.00 25.00           C
ATOM     36  CA  ASP    36     -83.821 -21.294 -13.975  1.00 25.00           C
ATOM     37  CA  VAL    37     -80.410 -19.850 -14.945  1.00 25.00           C
ATOM     38  CA  PHE    38     -81.821 -16.297 -14.719  1.00 25.00           C
ATOM     39  CA  LYS    39     -83.273 -17.068 -11.260  1.00 25.00           C
ATOM     40  CA  ARG    40     -79.887 -18.445 -10.118  1.00 25.00           C
ATOM     41  CA  PHE    41     -78.142 -15.289 -11.405  1.00 25.00           C
ATOM     42  CA  LYS    42     -80.402 -12.764  -9.566  1.00 25.00           C
ATOM     43  CA  PRO    43     -82.769 -10.258  -7.888  1.00 25.00           C
ATOM     44  CA  LEU    44     -79.969  -8.481  -6.099  1.00 25.00           C
ATOM     45  CA  ALA    45     -76.188  -8.639  -5.624  1.00 25.00           C
ATOM     46  CA  LEU    46     -74.331  -8.463  -8.931  1.00 25.00           C
ATOM     47  CA  GLY    47     -76.594  -5.999 -10.785  1.00 25.00           C
ATOM     48  CA  ILE    48     -76.240  -4.095 -13.985  1.00 25.00           C
ATOM     49  CA  ASP    49     -75.685  -0.559 -15.347  1.00 25.00           C
ATOM     50  CA  GLN    50     -75.356  -1.952 -18.899  1.00 25.00           C
ATOM     51  CA  ASP    51     -78.603  -3.933 -18.449  1.00 25.00           C
ATOM     52  CA  LEU    52     -80.382  -0.779 -17.199  1.00 25.00           C
ATOM     53  CA  ILE    53     -79.094   1.177 -20.229  1.00 25.00           C
ATOM     54  CA  ALA    54     -80.340  -1.583 -22.573  1.00 25.00           C
ATOM     55  CA  ALA    55     -83.771  -1.510 -20.876  1.00 25.00           C
ATOM     56  CA  LEU    56     -84.538   1.955 -22.100  1.00 25.00           C
ATOM     57  CA  PRO    57     -85.647   2.826 -25.615  1.00 25.00           C
ATOM     58  CA  GLN    58     -84.328   6.377 -25.942  1.00 25.00           C
ATOM     59  CA  TYR    59     -82.734   8.499 -23.202  1.00 25.00           C
ATOM     60  CA  ASP    60     -86.328   9.281 -22.303  1.00 25.00           C
ATOM     61  CA  ALA    61     -86.410   6.264 -19.988  1.00 25.00           C
ATOM     62  CA  ALA    62     -85.464   8.708 -17.196  1.00 25.00           C
ATOM     63  CA  LEU    63     -84.684   5.776 -14.859  1.00 25.00           C
ATOM     64  CA  ILE    64     -82.501   4.168 -17.564  1.00 25.00           C
ATOM     65  CA  ALA    65     -80.639   7.477 -18.063  1.00 25.00           C
ATOM     66  CA  ARG    66     -80.070   7.754 -14.286  1.00 25.00           C
ATOM     67  CA  VAL    67     -78.730   4.168 -14.200  1.00 25.00           C
ATOM     68  CA  LEU    68     -76.366   4.954 -17.108  1.00 25.00           C
ATOM     69  CA  ALA    69     -75.127   8.086 -15.284  1.00 25.00           C
ATOM     70  CA  ASN    70     -74.523   6.031 -12.111  1.00 25.00           C
ATOM     71  CA  HIS    71     -72.571   3.431 -14.137  1.00 25.00           C
ATOM     72  CA  CYS    72     -70.455   6.208 -15.708  1.00 25.00           C
ATOM     73  CA  ARG    73     -69.741   7.662 -12.237  1.00 25.00           C
ATOM     74  CA  ARG    74     -68.707   4.197 -10.973  1.00 25.00           C
ATOM     75  CA  PRO    75     -66.380   3.766 -13.983  1.00 25.00           C
ATOM     76  CA  ARG    76     -64.823   7.199 -13.304  1.00 25.00           C
ATOM     77  CA  TYR    77     -64.291   6.256  -9.630  1.00 25.00           C
ATOM     78  CA  LEU    78     -62.634   2.970 -10.687  1.00 25.00           C
ATOM     79  CA  LYS    79     -60.342   4.872 -13.094  1.00 25.00           C
ATOM     80  CA  ALA    80     -59.396   7.316 -10.302  1.00 25.00           C
ATOM     81  CA  LEU    81     -58.617   4.384  -7.965  1.00 25.00           C
ATOM     82  CA  ALA    82     -56.434   2.776 -10.670  1.00 25.00           C
ATOM     83  CA  ARG    83     -56.360   2.105 -14.378  1.00 25.00           C
ATOM     84  CA  GLY    84     -56.167  -1.563 -15.301  1.00 25.00           C
ATOM     85  CA  GLY    85     -59.620  -2.595 -16.425  1.00 25.00           C
ATOM     86  CA  LYS    86     -58.620  -5.142 -19.117  1.00 25.00           C
ATOM     87  CA  ARG    87     -62.212  -5.487 -20.486  1.00 25.00           C
ATOM     88  CA  PHE    88     -64.730  -8.391 -20.453  1.00 25.00           C
ATOM     89  CA  ASP    89     -65.311 -12.161 -20.823  1.00 25.00           C
ATOM     90  CA  LEU    90     -65.850 -12.027 -24.564  1.00 25.00           C
ATOM     91  CA  ASN    91     -66.672 -13.469 -27.993  1.00 25.00           C
ATOM     92  CA  ASN    92     -67.673 -11.923 -31.349  1.00 25.00           C
ATOM     93  CA  ARG    93     -65.268  -9.098 -30.530  1.00 25.00           C
ATOM     94  CA  PHE    94     -66.482  -5.468 -30.836  1.00 25.00           C
ATOM     95  CA  LYS    95     -63.813  -2.993 -31.990  1.00 25.00           C
ATOM     96  CA  GLY    96     -61.151  -0.295 -32.276  1.00 25.00           C
ATOM     97  CA  GLU    97     -59.862   1.355 -29.157  1.00 25.00           C
ATOM     98  CA  VAL    98     -59.735   2.616 -25.610  1.00 25.00           C
ATOM     99  CA  THR    99     -58.190   5.182 -23.262  1.00 25.00           C
ATOM    100  CA  PRO   100     -59.331   8.615 -24.440  1.00 25.00           C
ATOM    101  CA  GLU   101     -63.123   8.235 -24.062  1.00 25.00           C
ATOM    102  CA  GLU   102     -62.705   7.557 -20.316  1.00 25.00           C
ATOM    103  CA  GLN   103     -60.499  10.668 -19.973  1.00 25.00           C
ATOM    104  CA  ALA   104     -63.124  12.763 -21.815  1.00 25.00           C
ATOM    105  CA  ILE   105     -65.860  11.420 -19.495  1.00 25.00           C
ATOM    106  CA  ALA   106     -63.725  12.288 -16.436  1.00 25.00           C
ATOM    107  CA  GLN   107     -63.172  15.825 -17.796  1.00 25.00           C
ATOM    108  CA  ASN   108     -65.106  18.383 -15.841  1.00 25.00           C
ATOM    109  CA  HIS   109     -64.237  16.270 -12.746  1.00 25.00           C
ATOM    110  CA  PRO   110     -63.299  19.374 -10.708  1.00 25.00           C
ATOM    111  CA  PHE   111     -64.239  20.007  -7.050  1.00 25.00           C
ATOM    112  CA  VAL   112     -67.532  21.625  -8.152  1.00 25.00           C
ATOM    113  CA  GLN   113     -68.286  18.616 -10.400  1.00 25.00           C
ATOM    114  CA  GLN   114     -67.569  16.232  -7.490  1.00 25.00           C
ATOM    115  CA  ALA   115     -69.903  18.255  -5.226  1.00 25.00           C
ATOM    116  CA  LEU   116     -72.647  18.125  -7.894  1.00 25.00           C
TER
END
