Contacts of the strand formed by residues 492 - 497 (chain A) in PDB entry 6AN8


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 GLU 492 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  ILE*     3.7    13.4    -      -       +      +
    435A  VAL      4.8     4.2    -      -       -      +
    436A  GLY      5.5     1.2    -      -       -      -
    437A  ALA*     3.5    24.7    +      -       +      +
    438A  GLU*     4.3     4.0    +      -       -      +
    489A  SER*     5.1     0.2    -      -       -      -
    490A  GLY*     3.2     9.4    +      -       -      +
    491A  LEU*     1.3    84.4    -      -       +      +
    493A  VAL*     1.3    63.7    +      -       -      +
    529A  GLU*     4.2    15.8    -      -       +      +
    530A  LYS*     3.2    46.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 493 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  ILE*     3.4     4.1    -      -       -      +
    437A  ALA*     3.8     2.7    -      -       -      +
    438A  GLU*     3.7     4.9    -      -       +      +
    440A  PHE*     3.5    31.2    -      -       +      -
    485A  ALA      4.6     0.4    -      -       -      +
    486A  LEU*     4.4     8.5    -      -       +      -
    489A  SER*     3.7    26.7    -      -       -      +
    492A  GLU*     1.3    76.1    -      -       -      +
    494A  ASN*     1.3    70.3    +      -       -      +
    495A  ILE*     3.7    14.8    +      -       +      -
    528A  LYS*     4.3    11.4    -      -       +      -
    530A  LYS      3.0    10.5    +      -       -      +
    531A  VAL*     3.4    16.1    -      -       +      +
    532A  TYR      3.1    22.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 494 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    433A  PRO*     3.6     2.9    -      -       -      +
    434A  ILE*     2.7    44.6    +      -       -      +
    437A  ALA*     3.0    30.5    +      -       -      +
    438A  GLU      3.2     6.2    +      -       -      +
    439A  THR*     3.3    13.6    +      -       -      +
    440A  PHE*     2.7    32.2    +      -       -      -
    493A  VAL*     1.3    75.9    -      -       -      +
    495A  ILE*     1.3    56.3    +      -       -      +
    496A  VAL      4.3     0.2    -      -       -      -
    532A  TYR*     3.4    18.5    -      -       -      +
    289B  LEU*     3.7    26.4    -      -       +      +
    290B  THR*     5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 495 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440A  PHE*     3.3     3.1    -      -       +      -
    442A  VAL*     3.9    33.0    -      -       +      -
    482A  ILE*     4.5    13.2    -      -       +      -
    485A  ALA*     4.0    16.2    -      -       +      -
    486A  LEU*     3.7    36.1    -      -       +      +
    493A  VAL*     3.7    19.3    -      -       +      +
    494A  ASN*     1.3    78.8    -      -       -      +
    496A  VAL*     1.3    65.6    +      -       -      +
    497A  THR*     4.1     1.5    +      -       -      +
    531A  VAL*     4.6     2.2    -      -       +      -
    532A  TYR      2.8    11.5    +      -       -      +
    533A  LEU*     3.4    29.4    -      -       +      +
    534A  ALA*     2.9    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 496 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439A  THR*     4.2     6.7    -      -       +      -
    440A  PHE      2.7     9.0    +      -       -      +
    441A  TYR*     3.6    35.7    -      -       +      -
    442A  VAL*     3.0    30.5    +      -       -      +
    495A  ILE*     1.3    75.9    -      -       -      +
    497A  THR*     1.3    62.2    +      -       -      +
    534A  ALA*     3.5    11.2    -      -       +      +
    536A  VAL*     3.9    34.3    -      -       +      -
    545A  ASN*     5.0     3.1    +      -       +      +
    258B  GLN*     4.1     4.0    -      -       -      +
    289B  LEU*     3.8    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 497 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442A  VAL*     3.7    20.5    -      -       -      +
    478A  GLU*     3.8     7.8    +      -       -      -
    482A  ILE*     4.4    19.3    -      -       +      +
    495A  ILE*     5.1     4.7    -      -       +      +
    496A  VAL*     1.3    75.9    -      -       -      +
    498A  ASP*     1.3    67.0    +      -       -      +
    499A  SER*     2.9    32.4    +      -       -      +
    503A  LEU*     4.6    16.4    -      -       +      -
    533A  LEU*     5.4     3.4    -      -       +      -
    534A  ALA      3.0    11.1    +      -       -      +
    535A  TRP*     3.2    10.7    -      -       +      -
    536A  VAL*     3.1    25.6    +      -       -      +
    545A  ASN*     4.7     1.1    -      -       -      +
----------------------------------------------------------
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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