Contacts of the strand formed by residues 37 - 48 (chain A) in PDB entry 4LOX


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with TRP 37 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  VAL*     3.9    23.3    -      -       +      -
     28A  ARG      3.1     7.0    -      -       -      -
     29A  LYS*     3.3    58.8    -      -       +      -
     30A  ASN      3.8     1.0    +      -       -      +
     33A  TYR*     3.7    15.2    -      -       -      +
     35A  THR*     3.1    32.0    +      -       -      +
     36A  GLY*     1.3    87.9    -      -       -      +
     38A  LEU*     1.3    59.6    +      -       -      +
     39A  VAL*     4.2     5.4    +      -       -      +
    122A  HIS      5.3     1.4    -      -       -      +
    123A  LEU*     6.0     1.6    -      -       -      +
    128A  LEU*     3.7    31.0    -      -       +      -
    145A  GLU*     4.4    12.6    -      -       +      -
    146A  LEU*     4.0    14.8    -      -       +      -
    149A  ALA*     3.4    32.2    -      -       +      +
    150A  PHE*     3.9    15.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ARG      3.6     1.9    -      -       -      +
     27A  VAL*     3.2     4.7    -      -       -      -
     28A  ARG*     2.6    67.3    +      -       +      +
     30A  ASN*     4.7     7.2    -      -       +      +
     33A  TYR*     3.7    45.9    -      -       +      +
     37A  TRP*     1.3    72.8    -      -       -      +
     39A  VAL*     1.3    79.6    +      -       -      +
     40A  VAL*     4.0     6.2    +      -       +      -
     21C    A      5.1     2.5    -      -       -      +
      4D    A      4.2     9.0    -      -       +      +
      5D    T      3.6    41.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  VAL*     4.8     1.3    -      -       +      -
     26A  ARG      3.5     6.1    -      -       -      +
     27A  VAL*     4.4     7.9    -      -       +      -
     37A  TRP      4.2     3.6    +      -       -      +
     38A  LEU*     1.3    89.5    -      -       -      +
     40A  VAL*     1.3    64.4    +      -       -      +
    113A  VAL*     4.6     3.6    -      -       +      -
    117A  MET*     3.4    35.8    -      -       +      +
    122A  HIS*     4.2    30.7    -      -       +      +
    128A  LEU*     4.1    25.8    -      -       +      -
    131A  ILE*     4.1    28.9    -      -       +      -
      4D    A      5.6     0.5    +      -       -      -
      5D    T      5.3     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  VAL*     3.2     8.4    -      -       -      +
     26A  ARG*     2.7    54.7    +      -       +      +
     28A  ARG*     4.8     6.7    -      -       -      +
     38A  LEU*     4.0    14.8    -      -       +      +
     39A  VAL*     1.3    80.2    -      -       -      +
     41A  ALA*     1.3    66.4    +      -       -      +
     42A  ILE*     3.6    23.4    -      -       +      +
     81A  GLU*     4.1    23.8    -      -       -      +
    117A  MET*     4.4     2.5    -      -       -      -
      5D    T      3.8    26.0    -      -       +      +
      6D    C      6.2     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  MET      3.5     4.9    -      -       -      +
     25A  VAL*     4.5     5.6    -      -       +      +
     40A  VAL*     1.3    73.1    -      -       -      +
     42A  ILE*     1.3    67.3    +      -       -      +
     81A  GLU*     3.4    15.3    +      -       -      +
     83A  SER*     5.2     0.8    +      -       -      +
     86A  LEU*     3.3    16.9    -      -       +      +
    110A  PHE*     3.8    17.3    -      -       +      -
    113A  VAL*     4.9     3.8    -      -       +      -
    114A  LEU*     3.5    32.1    -      -       +      -
    117A  MET*     4.3    13.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  SER      3.6     3.6    -      -       -      +
     23A  PHE*     3.7     1.4    -      -       -      -
     24A  MET*     2.8    67.4    +      -       +      +
     26A  ARG*     3.9    23.3    -      -       +      +
     40A  VAL*     3.6    30.1    -      -       +      +
     41A  ALA*     1.3    83.0    -      -       -      +
     43A  PHE*     1.3    74.5    +      -       -      +
     79A  ARG*     3.9    23.3    -      -       +      +
     80A  ILE      3.4     5.4    -      -       -      +
     81A  GLU*     3.8    18.2    -      -       +      +
    110A  PHE*     3.7     5.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ILE*     3.6    38.4    -      -       +      -
     22A  SER      3.6     5.8    -      -       -      -
     23A  PHE*     3.4    37.0    -      +       -      -
     42A  ILE*     1.3    73.0    -      -       -      +
     44A  SER*     1.3    69.4    +      -       -      +
     45A  VAL*     4.8     5.4    -      -       +      -
     58A  LEU*     6.4     0.2    -      -       +      -
     62A  PHE*     4.2    12.8    -      +       -      -
     78A  TYR*     3.8    16.9    -      +       -      +
     79A  ARG*     3.1     6.9    -      -       -      +
     80A  ILE*     2.8    44.3    +      -       +      +
     86A  LEU*     3.7    23.5    -      -       +      +
     90A  ILE*     4.0    28.5    -      -       +      -
     94A  PHE*     4.0     9.9    -      +       -      -
    110A  PHE*     4.7     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  GLY*     3.3     1.2    -      -       -      -
     22A  SER*     2.9    36.2    +      -       -      +
     24A  MET*     3.3    30.2    -      -       -      +
     43A  PHE*     1.3    77.1    -      -       -      +
     45A  VAL*     1.3    67.8    +      -       -      +
     46A  THR*     4.1     5.5    +      -       -      -
     77A  SER*     3.8     6.2    +      -       -      -
     78A  TYR      3.4     5.4    -      -       -      -
     79A  ARG*     2.9    31.1    +      -       -      +
     16C    G      5.0     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PHE*     3.8    33.4    -      -       +      -
     17A  ILE*     4.3    16.8    -      -       +      -
     20A  GLU*     4.1    19.7    -      -       +      +
     21A  GLY*     4.3     1.3    -      -       -      -
     43A  PHE*     4.8     4.5    -      -       +      -
     44A  SER*     1.3    77.2    +      -       -      +
     46A  THR*     1.3    66.6    +      -       -      +
     55A  LEU*     4.3     5.3    -      -       +      +
     58A  LEU*     3.8    22.9    -      -       +      -
     76A  PHE      4.3     0.2    -      -       -      +
     77A  SER*     3.5     1.6    -      -       -      -
     78A  TYR*     2.8    52.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLU*     4.3     8.3    +      -       -      +
     44A  SER*     4.1     5.5    +      -       -      -
     45A  VAL*     1.3    76.5    -      -       -      +
     47A  VAL*     1.3    71.7    +      -       -      +
     71A  SER*     4.2     5.5    +      -       -      -
     75A  THR*     3.7    25.8    -      -       +      +
     76A  PHE      3.4    15.7    -      -       -      +
     77A  SER*     3.2    17.7    +      -       -      -
     14B    A      3.7    25.4    -      -       +      +
     15C    T      3.2    35.7    -      -       +      -
     16C    G      5.1     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  PHE*     3.9    32.3    -      -       +      -
     20A  GLU*     5.7     0.2    -      -       +      -
     45A  VAL*     4.8     0.4    -      -       +      -
     46A  THR*     1.3    79.7    -      -       -      +
     48A  ASP*     1.3    72.7    +      -       -      +
     51A  ASP*     3.4    36.8    -      -       +      +
     52A  LEU*     4.3     0.9    -      -       -      +
     54A  LEU*     4.9     3.4    -      -       +      -
     55A  LEU*     3.5    30.7    -      -       +      +
     75A  THR*     3.2     2.9    -      -       -      -
     76A  PHE*     2.9    31.4    +      -       +      +
     14B    A      3.4    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  VAL*     1.3    85.1    -      -       -      +
     49A  LYS*     1.3    68.5    +      -       -      +
     50A  LYS*     3.0    56.4    +      -       +      +
     51A  ASP*     2.7    23.2    +      -       -      +
     74A  SER*     3.2    28.0    +      -       -      +
     13B    A      3.5    17.2    -      -       -      +
     14B    A      2.7    19.3    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il