Contacts of the strand formed by residues 493 - 497 (chain X) in PDB entry 3F6B


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 GLN 493 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491X  GLY      4.1     2.0    +      -       -      -
    492X  VAL*     1.3    75.5    -      -       -      +
    494X  ALA*     1.3    64.5    +      -       -      +
    495X  LEU*     4.4     7.4    -      -       +      +
    509X  GLU*     2.9    36.2    +      -       -      +
    513X  ALA*     4.0    11.0    -      -       -      +
    515X  GLY      6.0     0.2    -      -       -      -
    516X  PRO      3.8    12.2    +      -       -      +
    517X  VAL*     3.5    24.8    -      -       +      +
    518X  LEU*     2.9    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 494 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484X  ARG*     3.8    33.1    +      -       +      +
    487X  ALA*     3.7    23.6    -      -       +      -
    488X  LYS*     5.0     0.9    -      -       +      +
    492X  VAL      3.4     1.8    +      -       -      +
    493X  GLN*     1.3    79.2    -      -       -      +
    495X  LEU*     1.3    71.7    +      -       -      +
    518X  LEU*     3.2     7.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 495 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484X  ARG*     4.0    10.3    -      -       -      +
    493X  GLN*     4.4     7.6    -      -       -      +
    494X  ALA*     1.3    83.0    -      -       -      +
    496X  LYS*     1.3    61.9    +      -       -      +
    506X  SER*     3.5    46.2    -      -       -      +
    509X  GLU*     3.9    37.5    -      -       +      +
    510X  ALA      4.4     0.7    -      -       -      +
    517X  VAL*     3.9    23.3    -      -       +      -
    518X  LEU      2.8     8.6    +      -       -      +
    519X  ILE*     3.3     5.9    -      -       +      -
    520X  GLU*     2.9    23.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 496 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484X  ARG*     3.4    48.6    -      -       -      +
    495X  LEU*     1.3    73.8    -      -       -      +
    497X  ALA*     1.3    61.2    +      -       -      +
    498X  ASP*     3.3    32.1    +      -       -      +
    502X  GLN*     3.8    12.2    -      -       -      +
    506X  SER*     3.6    11.3    +      -       -      -
    519X  ILE*     4.8     0.4    -      -       -      -
    520X  GLU*     3.4    33.2    +      -       +      +
    522X  SER*     4.0     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 497 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353X  LEU*     4.6     0.3    -      -       -      +
    496X  LYS*     1.3    73.0    -      -       -      +
    498X  ASP*     1.3    62.9    +      -       -      +
    499X  ASN      3.4     1.3    +      -       -      +
    502X  GLN*     3.8     7.6    -      -       -      +
    503X  LEU*     3.5    46.9    -      -       +      +
    519X  ILE*     4.3    10.2    -      -       +      +
    520X  GLU      2.8    12.9    +      -       -      +
    521X  VAL*     3.4     7.7    -      -       +      +
    522X  SER      2.9    24.9    +      -       -      +
----------------------------------------------------------
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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