Contacts of the strand formed by residues 239 - 243 (chain G) in PDB entry 5DK3


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 SER 239 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237G  GLY      3.6     7.0    +      -       -      -
    238G  PRO*     1.4    73.0    +      -       -      +
    240G  VAL*     1.4    63.9    +      -       -      +
    241G  PHE*     4.1    21.5    -      -       -      -
    263G  VAL*     3.4     4.2    -      -       -      +
    264G  VAL*     2.9    40.1    +      -       -      +
    265G  ASP*     4.0     8.6    +      -       -      -
    332G  ILE*     5.6     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 240 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238G  PRO*     5.4     0.7    -      -       +      -
    239G  SER*     1.4    79.4    -      -       -      +
    241G  PHE*     1.3    78.7    +      -       -      +
    242G  LEU      4.3     0.4    +      -       -      -
    261G  CYS*     3.8    29.2    -      -       -      -
    262G  VAL      3.5     4.9    -      -       -      +
    263G  VAL*     4.0    11.7    -      -       +      -
    321G  CYS*     5.0     2.5    -      -       -      +
    323G  VAL*     3.9    24.9    -      -       +      -
    332G  ILE*     3.6    36.6    -      -       +      +
    334G  LYS*     4.4    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 241 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239G  SER*     4.1    18.8    -      -       -      -
    240G  VAL*     1.3    82.8    -      -       -      +
    242G  LEU*     1.3    59.2    +      -       -      +
    243G  PHE*     3.6    30.3    -      +       +      -
    260G  THR      3.8     1.2    -      -       -      +
    261G  CYS*     3.5     1.7    -      -       -      -
    262G  VAL*     2.8    46.0    +      -       +      +
    264G  VAL*     3.7    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 242 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240G  VAL*     4.4     0.4    +      -       -      +
    241G  PHE*     1.3    74.0    -      -       -      +
    243G  PHE*     1.3    63.6    +      -       -      +
    244G  PRO*     4.2     0.7    -      -       -      +
    259G  VAL*     3.5    19.7    -      -       +      -
    260G  THR      3.4    14.1    -      -       -      +
    261G  CYS*     3.7    21.5    -      -       +      -
    277G  TRP*     3.7     7.0    -      -       +      -
    319G  TYR      3.4    24.9    -      -       -      +
    321G  CYS*     4.0     6.1    -      -       +      -
    334G  LYS*     3.4    39.0    -      -       +      +
    335G  THR      3.8     1.1    -      -       -      +
    336G  ILE*     3.6    36.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 243 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241G  PHE*     3.6    34.1    -      +       +      -
    242G  LEU*     1.3    75.5    -      -       -      +
    244G  PRO*     1.3    75.4    -      -       +      +
    259G  VAL*     3.4     7.2    -      -       -      +
    260G  THR*     2.7    54.2    +      -       +      +
    262G  VAL*     4.0    25.8    -      -       +      -
    301G  ARG*     6.0     0.7    -      -       -      -
    336G  ILE*     4.3     2.0    -      -       -      -
----------------------------------------------------------
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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