
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0311TS168_4-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS168_4-D1.T0311_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      R       8           -
LGA    -       -      P       9           -
LGA    P       9      G      10           #
LGA    G      10      D      11          2.672
LGA    D      11      -       -           -
LGA    I      12      -       -           -
LGA    I      13      I      12          2.386
LGA    Q      14      I      13          2.735
LGA    E      15      Q      14          3.500
LGA    S      16      E      15          3.527
LGA    L      17      S      16          3.413
LGA    D      18      L      17          3.445
LGA    -       -      D      18           -
LGA    E      19      E      19          4.681
LGA    L      20      L      20          1.122
LGA    N      21      N      21          2.541
LGA    V      22      V      22          3.417
LGA    S      23      S      23          4.714
LGA    L      24      L      24          3.041
LGA    R      25      R      25          2.775
LGA    E      26      E      26          2.434
LGA    F      27      F      27          1.449
LGA    A      28      A      28          0.754
LGA    R      29      R      29          1.769
LGA    A      30      A      30          0.912
LGA    M      31      M      31          1.567
LGA    E      32      E      32          1.549
LGA    I      33      I      33          2.068
LGA    A      34      A      34          2.302
LGA    P      35      P      35          1.094
LGA    S      36      S      36          1.199
LGA    T      37      T      37          0.773
LGA    A      38      A      38          0.483
LGA    S      39      S      39          0.763
LGA    R      40      R      40          0.911
LGA    L      41      L      41          0.804
LGA    L      42      L      42          1.581
LGA    T      43      T      43          2.140
LGA    G      44      G      44          3.194
LGA    K      45      K      45          2.598
LGA    A      46      A      46          2.037
LGA    A      47      A      47          3.760
LGA    L      48      -       -           -
LGA    T      49      -       -           -
LGA    P      50      -       -           -
LGA    E      51      -       -           -
LGA    M      52      -       -           -
LGA    A      53      -       -           -
LGA    I      54      L      48          2.482
LGA    K      55      T      49           -
LGA    -       -      P      50           -
LGA    -       -      E      51           -
LGA    L      56      M      52          4.527
LGA    S      57      A      53          4.331
LGA    V      58      -       -           -
LGA    V      59      -       -           -
LGA    I      60      -       -           -
LGA    G      61      -       -           -
LGA    S      62      -       -           -
LGA    S      63      I      54          0.877
LGA    P      64      K      55          2.980
LGA    Q      65      -       -           -
LGA    M      66      -       -           -
LGA    W      67      L      56          2.264
LGA    L      68      S      57          2.078
LGA    N      69      V      58           #
LGA    L      70      V      59           -
LGA    -       -      I      60           -
LGA    -       -      G      61           -
LGA    -       -      S      62           -
LGA    -       -      S      63           -
LGA    -       -      P      64           -
LGA    -       -      Q      65           -
LGA    Q      71      M      66          4.191
LGA    -       -      W      67           -
LGA    -       -      L      68           -
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      Q      71           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   64    5.0     44    2.64    68.18     47.983     1.608

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.080012 * X  +   0.995902 * Y  +  -0.042151 * Z  +  32.992271
  Y_new =   0.407626 * X  +   0.005899 * Y  +   0.913130 * Z  +   2.549353
  Z_new =   0.909637 * X  +  -0.090243 * Y  +  -0.405483 * Z  +  14.700200 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.922605    0.218988  [ DEG:  -167.4529     12.5471 ]
  Theta =  -1.142409   -1.999183  [ DEG:   -65.4552   -114.5448 ]
  Phi   =   1.376973   -1.764620  [ DEG:    78.8947   -101.1053 ]
 
# 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: T0311TS168_4-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS168_4-D1.T0311_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   64   64   5.0   44   2.64   68.18  47.983
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS168_4-D1
PFRMAT TS
TARGET T0311
MODEL 4
PARENT N/A
ATOM      8  CA  ARG     8      39.099  -0.349  22.753  1.00 25.00           C
ATOM      9  CA  PRO     9      37.691   1.729  19.894  1.00 25.00           C
ATOM     10  CA  GLY    10      35.883  -0.394  17.268  1.00 25.00           C
ATOM     11  CA  ASP    11      32.675  -0.289  19.356  1.00 25.00           C
ATOM     12  CA  ILE    12      32.969   3.518  19.663  1.00 25.00           C
ATOM     13  CA  ILE    13      33.449   3.809  15.874  1.00 25.00           C
ATOM     14  CA  GLN    14      30.361   1.621  15.290  1.00 25.00           C
ATOM     15  CA  GLU    15      28.327   3.808  17.687  1.00 25.00           C
ATOM     16  CA  SER    16      29.495   6.956  15.845  1.00 25.00           C
ATOM     17  CA  LEU    17      28.496   5.395  12.493  1.00 25.00           C
ATOM     18  CA  ASP    18      25.048   4.508  13.905  1.00 25.00           C
ATOM     19  CA  GLU    19      24.618   8.097  15.173  1.00 25.00           C
ATOM     20  CA  LEU    20      23.794   6.419  18.431  1.00 25.00           C
ATOM     21  CA  ASN    21      21.715   3.217  18.890  1.00 25.00           C
ATOM     22  CA  VAL    22      24.624   1.333  20.520  1.00 25.00           C
ATOM     23  CA  SER    23      27.693  -0.880  19.818  1.00 25.00           C
ATOM     24  CA  LEU    24      27.130  -2.252  16.346  1.00 25.00           C
ATOM     25  CA  ARG    25      23.878  -4.208  16.865  1.00 25.00           C
ATOM     26  CA  GLU    26      21.853  -1.237  15.549  1.00 25.00           C
ATOM     27  CA  PHE    27      24.126  -1.017  12.474  1.00 25.00           C
ATOM     28  CA  ALA    28      23.681  -4.768  11.846  1.00 25.00           C
ATOM     29  CA  ARG    29      19.880  -4.389  12.126  1.00 25.00           C
ATOM     30  CA  ALA    30      19.963  -1.473   9.645  1.00 25.00           C
ATOM     31  CA  MET    31      22.053  -3.568   7.215  1.00 25.00           C
ATOM     32  CA  GLU    32      20.723  -7.128   6.536  1.00 25.00           C
ATOM     33  CA  ILE    33      24.130  -8.496   5.427  1.00 25.00           C
ATOM     34  CA  ALA    34      24.698  -8.938   9.105  1.00 25.00           C
ATOM     35  CA  PRO    35      25.204  -9.452  12.883  1.00 25.00           C
ATOM     36  CA  SER    36      28.096 -11.949  12.620  1.00 25.00           C
ATOM     37  CA  THR    37      29.700  -9.837   9.857  1.00 25.00           C
ATOM     38  CA  ALA    38      29.351  -6.697  12.021  1.00 25.00           C
ATOM     39  CA  SER    39      30.969  -8.522  14.974  1.00 25.00           C
ATOM     40  CA  ARG    40      33.857  -9.651  12.726  1.00 25.00           C
ATOM     41  CA  LEU    41      34.336  -6.055  11.494  1.00 25.00           C
ATOM     42  CA  LEU    42      34.382  -4.797  15.112  1.00 25.00           C
ATOM     43  CA  THR    43      36.987  -7.452  16.027  1.00 25.00           C
ATOM     44  CA  GLY    44      40.514  -7.337  14.611  1.00 25.00           C
ATOM     45  CA  LYS    45      40.905  -9.992  11.915  1.00 25.00           C
ATOM     46  CA  ALA    46      39.241  -7.814   9.360  1.00 25.00           C
ATOM     47  CA  ALA    47      42.025  -5.420   8.440  1.00 25.00           C
ATOM     48  CA  LEU    48      40.630  -1.871   8.068  1.00 25.00           C
ATOM     49  CA  THR    49      39.770   0.582   5.266  1.00 25.00           C
ATOM     50  CA  PRO    50      39.071   2.938   8.244  1.00 25.00           C
ATOM     51  CA  GLU    51      37.508   0.765  10.982  1.00 25.00           C
ATOM     52  CA  MET    52      34.156   2.561  10.528  1.00 25.00           C
ATOM     53  CA  ALA    53      34.338   1.996   6.745  1.00 25.00           C
ATOM     54  CA  ILE    54      35.081  -1.718   7.310  1.00 25.00           C
ATOM     55  CA  LYS    55      32.096  -1.978   9.694  1.00 25.00           C
ATOM     56  CA  LEU    56      29.844  -0.288   7.097  1.00 25.00           C
ATOM     57  CA  SER    57      31.066  -2.729   4.412  1.00 25.00           C
ATOM     58  CA  VAL    58      30.348  -5.686   6.737  1.00 25.00           C
ATOM     59  CA  VAL    59      26.830  -4.332   7.413  1.00 25.00           C
ATOM     60  CA  ILE    60      26.225  -3.960   3.650  1.00 25.00           C
ATOM     61  CA  GLY    61      25.630  -2.689   0.105  1.00 25.00           C
ATOM     62  CA  SER    62      29.247  -1.667  -0.492  1.00 25.00           C
ATOM     63  CA  SER    63      28.297   1.829   0.595  1.00 25.00           C
ATOM     64  CA  PRO    64      24.867   2.402   2.172  1.00 25.00           C
ATOM     65  CA  GLN    65      25.212   6.112   1.283  1.00 25.00           C
ATOM     66  CA  MET    66      24.903   7.052   4.983  1.00 25.00           C
ATOM     67  CA  TRP    67      27.592   4.480   5.887  1.00 25.00           C
ATOM     68  CA  LEU    68      29.894   5.896   3.174  1.00 25.00           C
ATOM     69  CA  ASN    69      29.332   9.440   4.511  1.00 25.00           C
ATOM     70  CA  LEU    70      30.152   8.256   8.061  1.00 25.00           C
ATOM     71  CA  GLN    71      33.356   6.587   6.790  1.00 25.00           C
TER
END
