Contacts of the strand formed by residues 298 - 303 (chain B) in PDB entry 6QNW


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 LEU 298 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    677A  GLU*     4.3     2.5    -      -       -      +
    297B  GLU*     1.3    73.6    -      -       -      +
    299B  SER*     1.3    60.5    +      -       -      +
    300B  PHE*     3.5    33.0    -      -       +      -
    452B  ASN*     3.3     2.2    -      -       -      +
    453B  ALA      3.2    27.5    +      -       -      +
    454B  PRO      4.9     1.8    -      -       -      +
    455B  ASN*     4.8     7.0    -      -       -      +
    456B  HIS*     3.9    33.7    -      -       +      +
    459B  ILE*     3.2    41.3    -      -       +      +
    486B  ARG*     3.8    30.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289B  MET      3.6    12.0    +      -       -      -
    290B  MET*     4.5     7.7    -      -       -      +
    297B  GLU*     3.6    17.6    +      -       -      +
    298B  LEU*     1.3    73.0    -      -       -      +
    300B  PHE*     1.3    64.2    +      -       -      +
    450B  ILE*     4.6     2.2    -      -       -      -
    452B  ASN*     2.9    36.5    +      -       -      +
    486B  ARG*     3.5     8.1    +      -       -      +
    487B  THR*     2.7    44.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    677A  GLU*     3.4    49.8    -      -       +      -
    298B  LEU*     3.5    21.9    +      -       +      -
    299B  SER*     1.3    85.2    -      -       -      +
    301B  THR*     1.3    61.8    +      -       -      +
    450B  ILE*     3.5     1.0    -      -       -      -
    451B  VAL*     2.9    39.0    +      -       +      +
    456B  HIS*     3.6    17.7    -      +       -      -
    459B  ILE*     4.1    26.9    -      -       +      -
    484B  ILE*     4.1    19.3    -      -       +      -
    485B  ASN      3.4     6.1    -      -       -      +
    486B  ARG*     3.5    27.8    -      -       +      -
    487B  THR*     3.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300B  PHE*     1.3    70.8    -      -       -      +
    302B  ILE*     1.3    64.4    +      -       -      +
    448B  ALA*     5.5     0.2    -      -       +      -
    449B  LEU      3.2    16.6    -      -       -      +
    450B  ILE*     3.5    18.3    -      -       +      +
    484B  ILE*     3.5     0.3    -      -       -      -
    485B  ASN*     2.9    43.8    +      -       -      +
    486B  ARG      4.6     0.7    -      -       -      -
    487B  THR*     3.0    34.3    +      -       -      +
    488B  GLY      4.5     0.6    +      -       -      -
    489B  THR      5.0     0.2    -      -       -      -
    490B  PHE*     3.7    42.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 302 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681A  PHE*     4.9    13.2    -      -       +      -
    300B  PHE      4.8     4.0    -      -       -      +
    301B  THR*     1.3    77.0    -      -       -      +
    303B  THR*     1.3    63.1    +      -       -      +
    304B  GLY*     5.1     2.7    -      -       -      -
    447B  PHE*     3.9    27.1    -      -       +      -
    448B  ALA*     3.6     4.3    -      -       -      +
    449B  LEU*     2.9    53.7    +      -       +      +
    451B  VAL*     5.0     4.9    -      -       +      -
    463B  VAL*     5.0    19.3    -      -       +      -
    466B  PHE*     4.9     4.7    -      -       +      -
    477B  MET*     5.1     7.9    -      -       +      -
    482B  SER*     6.1     0.4    -      -       -      -
    483B  TYR      3.2    11.7    -      -       -      +
    484B  ILE*     3.5    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 303 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  THR      4.2     0.6    +      -       -      -
    302B  ILE*     1.3    71.6    -      -       -      +
    304B  GLY*     1.3    64.6    +      -       -      +
    447B  PHE      4.3     1.6    -      -       -      -
    448B  ALA*     4.9     0.2    -      -       -      +
    481B  LYS      5.3     0.2    -      -       -      -
    482B  SER*     3.3     5.8    -      -       -      -
    483B  TYR*     2.9    57.8    +      -       +      +
    485B  ASN*     5.4     0.4    +      -       -      -
    490B  PHE*     3.2    14.8    -      -       -      +
    491B  GLU*     3.0    67.0    +      -       +      +
----------------------------------------------------------
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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