Contacts of the strand formed by residues 204 - 208 (chain D) in PDB entry 2WLM


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 ARG 204 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177C  HIS*     5.3    15.0    +      -       +      -
    197C  ASP*     5.8     2.5    -      -       -      +
    173D  GLU*     3.6    45.1    +      -       -      +
    174D  ALA      3.4    13.2    -      -       -      -
    175D  ASP*     2.8    31.6    +      -       -      +
    202D  ARG*     2.9    32.8    +      -       -      +
    203D  SER*     1.3    80.9    +      -       -      +
    205D  SER*     1.3    64.9    +      -       -      +
    206D  PRO*     4.1    10.1    -      -       +      -
    212D  TRP*     3.9     2.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 205 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195C  PHE*     5.5     5.8    -      -       -      -
    174D  ALA*     3.0    27.1    +      -       -      +
    202D  ARG*     3.4     9.1    +      -       -      +
    204D  ARG*     1.3    74.6    -      -       -      +
    206D  PRO*     1.3    69.2    -      -       -      +
    207D  ILE      3.1     5.9    +      -       -      -
    208D  PHE*     3.4    27.2    +      -       -      +
    212D  TRP*     3.8    32.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 206 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177C  HIS*     3.6    38.6    -      -       +      +
    179C  VAL*     4.7     8.5    -      -       +      -
    197C  ASP*     4.5     4.5    -      -       -      +
    242C  LEU*     3.1    41.6    -      -       +      +
    172D  ILE*     3.3     6.4    -      -       -      -
    173D  GLU*     3.0    27.9    +      -       -      +
    202D  ARG*     3.4    15.9    -      -       -      +
    204D  ARG*     4.1     6.7    -      -       +      -
    205D  SER*     1.3    85.1    -      -       -      +
    207D  ILE*     1.3    61.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 207 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  LEU*     6.2     0.7    -      -       +      -
     19C  GLY      4.2     8.7    -      -       -      +
    195C  PHE*     5.1     9.4    -      -       -      -
    240C  LEU*     4.0    32.7    -      -       +      +
    241C  VAL      4.5     0.2    -      -       -      +
    242C  LEU*     4.0    20.4    -      -       +      -
    257C  ARG*     3.5    40.4    -      -       +      -
    170D  GLN*     3.6    22.2    -      -       +      +
    171D  ILE      3.8     2.7    -      -       -      -
    172D  ILE*     4.9     6.1    -      -       +      -
    205D  SER*     3.1     6.7    +      -       -      -
    206D  PRO*     1.3    86.0    -      -       +      +
    208D  PHE*     1.3    58.4    +      -       -      +
    209D  SER*     3.4    19.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 208 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  VAL*     4.3    10.3    -      -       +      -
    163D  LEU*     3.8    18.2    -      -       +      -
    164D  ALA      3.9     1.6    -      -       -      -
    165D  ASN*     3.4    36.3    +      -       +      -
    170D  GLN*     3.7     1.2    -      -       -      -
    171D  ILE*     2.8    51.2    +      -       +      +
    174D  ALA*     3.7    16.2    -      -       +      -
    205D  SER*     3.4    13.5    +      -       -      +
    207D  ILE*     1.3    71.6    -      -       -      +
    209D  SER*     1.3    61.1    +      -       -      +
    210D  LEU      4.0     4.3    -      -       -      -
    211D  SER*     3.8    10.3    -      -       -      -
    212D  TRP*     3.6    40.4    -      +       +      -
    243D  PHE*     3.8    31.4    -      +       -      -
----------------------------------------------------------
 Back to top of page


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