Contacts of the strand formed by residues 342 - 346 (chain B) in PDB entry 4WGK


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 VAL 342 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  VAL*     4.0    20.0    -      -       +      +
    107B  GLY*     3.9    27.6    -      -       -      +
    108B  ARG*     3.7    15.0    -      -       +      +
    140B  ARG*     3.6    32.5    -      -       +      -
    142B  PHE*     3.8    16.4    -      -       +      -
    294B  LEU      3.3     6.5    +      -       -      -
    295B  GLY*     3.1     3.1    -      -       -      -
    296B  LEU      3.0    24.9    +      -       -      +
    327B  GLU*     3.7     4.3    -      -       -      +
    339B  GLY      5.0     0.4    -      -       -      +
    340B  PRO      3.5    11.4    -      -       -      +
    341B  PHE*     1.3    78.5    -      -       -      +
    343B  ALA*     1.3    63.0    +      -       -      +
    344B  ALA      4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 343 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  ARG*     3.3    11.0    +      -       -      -
    296B  LEU*     3.6    14.6    -      -       +      -
    323B  SER*     3.3    21.9    -      -       -      +
    326B  LEU*     3.7    24.2    -      -       +      -
    327B  GLU*     3.1    21.9    +      -       +      +
    341B  PHE*     3.6    20.9    -      -       +      -
    342B  VAL*     1.3    73.4    -      -       -      +
    344B  ALA*     1.3    59.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 344 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  ARG*     3.6    20.6    -      -       +      +
    142B  PHE*     3.6    26.2    -      -       +      -
    157B  SER*     3.8    22.0    -      -       -      +
    296B  LEU*     3.0     8.3    +      -       -      +
    297B  ILE*     3.3     7.3    -      -       +      +
    298B  SER*     2.9    23.6    +      -       -      -
    323B  SER*     4.1     0.7    -      -       -      -
    342B  VAL      4.1     0.4    -      -       -      -
    343B  ALA*     1.3    74.0    -      -       -      +
    345B  PHE*     1.3    62.4    +      -       -      +
    346B  ALA      3.7     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 345 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  ARG*     5.7     0.2    -      -       -      +
    157B  SER*     2.9    15.4    +      -       -      -
    193B  THR*     3.6    15.0    -      -       +      +
    281B  MET*     3.7    14.1    -      -       +      -
    298B  SER*     3.3    33.9    -      -       -      -
    300B  PHE*     4.8     7.9    -      -       +      -
    319B  VAL*     3.9    34.7    -      -       +      +
    322B  ALA*     3.5    23.3    -      -       +      -
    323B  SER*     3.3    26.7    +      -       -      +
    326B  LEU*     3.5    28.7    -      -       +      -
    344B  ALA*     1.3    72.4    -      -       -      +
    346B  ALA*     1.3    62.8    +      -       -      +
    404B  MET*     3.7    33.2    -      -       +      -
    408B  ALA*     3.8     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 346 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  PHE*     3.6    26.0    -      -       +      -
    157B  SER*     3.9     5.6    -      -       -      +
    191B  SER*     5.2     1.1    -      -       -      +
    297B  ILE*     4.0     5.4    -      -       +      -
    298B  SER      2.7    18.5    +      -       -      +
    299B  TRP*     3.4    33.8    -      -       +      +
    300B  PHE      3.5    16.5    +      -       -      +
    319B  VAL*     6.5     0.7    -      -       -      -
    344B  ALA      3.7     1.4    +      -       -      -
    345B  PHE*     1.3    74.7    -      -       -      +
    347B  SER*     1.3    65.2    +      -       -      +
    348B  SER      3.7     0.2    +      -       -      -
----------------------------------------------------------
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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