
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS168_1-D1.T0311_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      -       -           -
LGA    P       9      -       -           -
LGA    G      10      -       -           -
LGA    D      11      -       -           -
LGA    I      12      R       8          2.382
LGA    I      13      P       9          2.262
LGA    Q      14      G      10          2.440
LGA    E      15      D      11          2.249
LGA    S      16      I      12          2.028
LGA    L      17      I      13          2.087
LGA    D      18      Q      14          2.063
LGA    E      19      E      15          2.791
LGA    L      20      S      16          3.780
LGA    -       -      L      17           -
LGA    N      21      D      18          1.791
LGA    -       -      E      19           -
LGA    -       -      L      20           -
LGA    -       -      N      21           -
LGA    V      22      V      22          2.454
LGA    S      23      S      23          3.319
LGA    L      24      L      24          3.008
LGA    R      25      R      25          2.858
LGA    E      26      E      26          3.451
LGA    F      27      F      27          2.717
LGA    A      28      A      28          1.393
LGA    R      29      R      29          2.221
LGA    A      30      A      30          2.171
LGA    M      31      M      31          1.397
LGA    E      32      E      32          0.495
LGA    I      33      I      33          0.891
LGA    A      34      A      34          2.270
LGA    P      35      P      35          1.797
LGA    S      36      S      36          3.688
LGA    T      37      T      37          3.512
LGA    A      38      A      38          1.510
LGA    S      39      S      39          2.209
LGA    R      40      R      40          2.761
LGA    L      41      L      41          1.328
LGA    L      42      L      42          2.772
LGA    -       -      T      43           -
LGA    T      43      G      44          2.946
LGA    G      44      K      45          2.279
LGA    K      45      A      46          3.710
LGA    A      46      A      47          2.618
LGA    A      47      L      48          5.109
LGA    L      48      T      49          1.064
LGA    T      49      P      50          3.899
LGA    P      50      E      51           #
LGA    E      51      M      52          4.659
LGA    M      52      A      53          2.611
LGA    A      53      I      54          4.734
LGA    I      54      K      55           #
LGA    K      55      L      56          3.749
LGA    L      56      S      57          2.579
LGA    S      57      V      58          4.975
LGA    V      58      V      59          5.612
LGA    V      59      I      60          3.195
LGA    I      60      G      61          2.620
LGA    G      61      S      62           #
LGA    S      62      S      63          4.841
LGA    S      63      P      64          3.586
LGA    P      64      -       -           -
LGA    Q      65      Q      65          0.742
LGA    M      66      M      66          3.745
LGA    W      67      W      67          3.331
LGA    L      68      L      68          3.988
LGA    N      69      N      69           #
LGA    L      70      -       -           -
LGA    Q      71      L      70           #
LGA    -       -      Q      71           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   64    5.0     53    3.03    54.72     53.360     1.694

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.279766 * X  +   0.871347 * Y  +  -0.403096 * Z  +  35.453224
  Y_new =   0.725957 * X  +   0.082760 * Y  +   0.682743 * Z  +   0.842196
  Z_new =   0.628266 * X  +  -0.483638 * Y  +  -0.609406 * Z  +  13.565622 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.470753    0.670840  [ DEG:  -141.5637     38.4363 ]
  Theta =  -0.679322   -2.462270  [ DEG:   -38.9223   -141.0777 ]
  Phi   =   1.202961   -1.938632  [ DEG:    68.9246   -111.0754 ]
 
# 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_1-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS168_1-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   53   3.03   54.72  53.360
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS168_1-D1
PFRMAT TS
TARGET T0311
MODEL 1
PARENT N/A
ATOM      8  CA  ARG     8      45.808  -1.600  11.869  1.00 25.00           C
ATOM      9  CA  PRO     9      42.276  -0.088  12.247  1.00 25.00           C
ATOM     10  CA  GLY    10      39.668  -2.654  13.377  1.00 25.00           C
ATOM     11  CA  ASP    11      39.300  -0.840  16.730  1.00 25.00           C
ATOM     12  CA  ILE    12      38.840   2.495  14.903  1.00 25.00           C
ATOM     13  CA  ILE    13      36.170   0.922  12.654  1.00 25.00           C
ATOM     14  CA  GLN    14      34.361  -0.467  15.730  1.00 25.00           C
ATOM     15  CA  GLU    15      34.462   2.987  17.381  1.00 25.00           C
ATOM     16  CA  SER    16      33.039   4.576  14.199  1.00 25.00           C
ATOM     17  CA  LEU    17      30.235   1.969  14.122  1.00 25.00           C
ATOM     18  CA  ASP    18      29.435   2.685  17.798  1.00 25.00           C
ATOM     19  CA  GLU    19      29.320   6.443  17.067  1.00 25.00           C
ATOM     20  CA  LEU    20      25.526   6.884  16.648  1.00 25.00           C
ATOM     21  CA  ASN    21      25.522   5.497  20.221  1.00 25.00           C
ATOM     22  CA  VAL    22      24.529   2.070  18.962  1.00 25.00           C
ATOM     23  CA  SER    23      26.367  -1.248  19.323  1.00 25.00           C
ATOM     24  CA  LEU    24      26.808  -2.441  15.713  1.00 25.00           C
ATOM     25  CA  ARG    25      23.166  -3.623  15.616  1.00 25.00           C
ATOM     26  CA  GLU    26      22.123  -0.346  13.928  1.00 25.00           C
ATOM     27  CA  PHE    27      24.913  -0.761  11.339  1.00 25.00           C
ATOM     28  CA  ALA    28      23.774  -4.353  10.651  1.00 25.00           C
ATOM     29  CA  ARG    29      20.166  -3.150  10.208  1.00 25.00           C
ATOM     30  CA  ALA    30      21.344  -0.436   7.776  1.00 25.00           C
ATOM     31  CA  MET    31      23.329  -3.041   5.792  1.00 25.00           C
ATOM     32  CA  GLU    32      21.755  -6.496   5.670  1.00 25.00           C
ATOM     33  CA  ILE    33      25.090  -8.111   6.682  1.00 25.00           C
ATOM     34  CA  ALA    34      23.281  -9.339   9.812  1.00 25.00           C
ATOM     35  CA  PRO    35      25.858  -8.844  12.561  1.00 25.00           C
ATOM     36  CA  SER    36      28.501 -10.476  10.320  1.00 25.00           C
ATOM     37  CA  THR    37      29.544  -7.034   9.002  1.00 25.00           C
ATOM     38  CA  ALA    38      29.831  -5.721  12.588  1.00 25.00           C
ATOM     39  CA  SER    39      31.981  -8.742  13.548  1.00 25.00           C
ATOM     40  CA  ARG    40      34.240  -8.129  10.516  1.00 25.00           C
ATOM     41  CA  LEU    41      34.598  -4.445  11.497  1.00 25.00           C
ATOM     42  CA  LEU    42      35.508  -5.460  15.076  1.00 25.00           C
ATOM     43  CA  THR    43      38.126  -7.915  13.739  1.00 25.00           C
ATOM     44  CA  GLY    44      39.674 -10.093  11.098  1.00 25.00           C
ATOM     45  CA  LYS    45      38.009 -11.654   8.101  1.00 25.00           C
ATOM     46  CA  ALA    46      38.508  -8.288   6.396  1.00 25.00           C
ATOM     47  CA  ALA    47      38.108  -6.921   2.868  1.00 25.00           C
ATOM     48  CA  LEU    48      36.723  -3.590   1.825  1.00 25.00           C
ATOM     49  CA  THR    49      33.048  -4.581   1.273  1.00 25.00           C
ATOM     50  CA  PRO    50      31.725  -5.736   4.676  1.00 25.00           C
ATOM     51  CA  GLU    51      33.769  -3.378   6.896  1.00 25.00           C
ATOM     52  CA  MET    52      33.396  -0.580   4.308  1.00 25.00           C
ATOM     53  CA  ALA    53      29.615  -1.172   4.177  1.00 25.00           C
ATOM     54  CA  ILE    54      29.435  -1.026   8.000  1.00 25.00           C
ATOM     55  CA  LYS    55      31.413   2.253   7.993  1.00 25.00           C
ATOM     56  CA  LEU    56      29.039   3.708   5.362  1.00 25.00           C
ATOM     57  CA  SER    57      26.019   2.661   7.472  1.00 25.00           C
ATOM     58  CA  VAL    58      27.574   4.308  10.560  1.00 25.00           C
ATOM     59  CA  VAL    59      28.188   7.522   8.567  1.00 25.00           C
ATOM     60  CA  ILE    60      24.553   7.496   7.361  1.00 25.00           C
ATOM     61  CA  GLY    61      24.387   6.502   3.648  1.00 25.00           C
ATOM     62  CA  SER    62      27.331   6.207   1.304  1.00 25.00           C
ATOM     63  CA  SER    63      29.642   3.276   0.325  1.00 25.00           C
ATOM     64  CA  PRO    64      33.349   4.241   0.114  1.00 25.00           C
ATOM     65  CA  GLN    65      35.723   7.244   0.031  1.00 25.00           C
ATOM     66  CA  MET    66      33.175   9.343   1.974  1.00 25.00           C
ATOM     67  CA  TRP    67      32.826   6.555   4.576  1.00 25.00           C
ATOM     68  CA  LEU    68      36.635   6.370   4.925  1.00 25.00           C
ATOM     69  CA  ASN    69      36.802  10.166   5.396  1.00 25.00           C
ATOM     70  CA  LEU    70      34.075   9.978   8.078  1.00 25.00           C
ATOM     71  CA  GLN    71      35.995   7.191   9.870  1.00 25.00           C
TER
END
