Contacts of the strand formed by residues 41 - 46 (chain G) in PDB entry 4WFN


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 41 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39G  GLN*     3.3    25.5    +      -       -      +
     40G  ASN*     1.3    74.1    +      -       -      +
     42G  VAL*     1.3    63.0    +      -       -      +
     43G  VAL*     6.0     0.7    -      -       +      -
     79G  PHE*     3.1    62.6    -      +       +      -
     81G  VAL*     4.1    22.9    -      -       +      +
    149G  LYS*     4.9    14.1    -      -       +      +
    161G  GLN*     4.4    11.6    -      -       +      +
    163G  PRO*     4.1    30.3    -      -       +      +
    164G  GLN*     3.4    43.5    +      -       +      +
    166G  LEU*     3.5    17.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 42 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40G  ASN*     4.6     5.6    -      -       -      +
     41G  TRP*     1.3    82.0    -      -       -      +
     43G  VAL*     1.3    64.0    +      -       -      +
     44G  VAL*     4.0     4.7    +      -       +      -
     61G  ARG*     5.0     6.1    -      -       +      -
     78G  ASP*     3.8    31.0    -      -       +      +
     79G  PHE      2.9    16.6    +      -       -      +
     80G  VAL*     3.5     6.1    -      -       +      -
     81G  VAL*     2.8    33.4    +      -       -      +
    166G  LEU*     3.1    12.8    -      -       +      +
    167G  LYS      4.4     0.4    -      -       -      -
    168G  THR*     3.5    43.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 43 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41G  TRP*     6.0     0.2    -      -       +      -
     42G  VAL*     1.3    75.7    -      -       -      +
     44G  VAL*     1.3    62.6    +      -       -      +
     81G  VAL*     3.4    19.5    -      -       +      +
     83G  ILE*     3.5    34.3    -      -       +      -
    158G  HIS*     3.4    22.4    -      -       +      +
    161G  GLN*     4.9     3.6    -      -       -      +
    164G  GLN      5.0     1.8    -      -       -      +
    165G  VAL*     3.2    29.6    -      -       -      +
    166G  LEU      2.6    11.7    +      -       -      +
    167G  LYS*     3.2    36.2    -      -       +      -
    168G  THR      3.3     6.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 44 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42G  VAL*     4.5     4.9    -      -       +      -
     43G  VAL*     1.3    75.5    -      -       -      +
     45G  ASP*     1.3    64.2    +      -       -      +
     54G  LEU*     3.6    30.5    -      -       +      -
     57G  LEU*     4.1    18.4    -      -       +      -
     58G  ILE*     4.2    13.7    -      -       +      -
     61G  ARG*     6.4     1.6    -      -       +      -
     80G  VAL*     3.8    28.5    -      -       +      -
     81G  VAL      2.9     9.8    +      -       -      +
     82G  VAL*     3.3     6.1    -      -       -      +
     83G  ILE*     3.0    25.3    +      -       -      -
    167G  LYS*     4.3     1.3    -      -       -      -
    168G  THR*     3.7    25.6    -      -       -      +
    170G  PRO*     5.4     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 45 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44G  VAL*     1.3    75.6    -      -       -      +
     46G  ALA*     1.3    62.0    +      -       -      +
     47G  SER*     3.1    21.8    +      -       -      -
     49G  VAL*     4.3     0.2    -      -       -      +
     54G  LEU*     4.0     5.9    -      -       -      +
     83G  ILE*     4.4     7.5    -      -       +      +
     84G  ASN*     2.9    26.2    -      -       -      +
    167G  LYS*     3.4    28.6    -      -       +      +
    168G  THR      4.8     2.2    +      -       -      -
    170G  PRO*     3.7    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 46 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44G  VAL      3.8     3.2    +      -       -      -
     45G  ASP*     1.3    73.6    +      -       -      +
     47G  SER*     1.3    63.9    +      -       -      +
     48G  GLY      4.2     0.7    -      -       -      -
     49G  VAL*     4.0     4.7    -      -       +      -
     54G  LEU*     3.4    36.6    -      -       +      -
     82G  VAL*     4.4     8.1    -      -       +      -
     83G  ILE      3.9     6.8    +      -       -      +
     84G  ASN*     3.6    15.9    -      -       -      +
     85G  ALA*     3.8     9.4    +      -       +      +
     87G  GLN      4.3     0.7    -      -       -      -
     88G  VAL*     4.1    23.6    +      -       +      -
----------------------------------------------------------
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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