Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 5ON2


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 LYS 34 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LYS      3.9     2.2    +      -       -      -
     33A  GLU*     1.3    84.8    -      -       +      +
     35A  TYR*     1.3    64.7    +      -       -      +
     36A  TYR      4.4     2.0    -      -       -      +
     71A  LYS*     4.9     1.3    -      -       -      +
     72A  ASN      3.5     6.1    -      -       -      -
    520A  TYR*     3.5    34.4    +      -       +      +
    521A  TRP*     2.8    49.0    +      -       +      +
    522A  LEU      4.9     2.2    -      -       -      -
    523A  PRO*     2.8    27.3    +      -       -      +
    525A  ASP*     2.9    26.7    +      -       -      +
    561A  LYS*     5.1     6.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LYS*     1.3    76.4    -      -       -      +
     36A  TYR*     1.3    61.1    +      -       -      +
     37A  CYS*     3.4    15.9    +      -       +      -
     62A  ILE*     3.8     7.8    -      -       +      +
     66A  GLN*     3.2    52.3    +      -       +      -
     71A  LYS*     4.4    16.6    -      -       +      -
     72A  ASN      3.1     8.3    +      -       -      -
     73A  VAL*     3.4    19.5    -      -       +      +
     74A  LEU      3.1    22.5    +      -       -      -
    521A  TRP*     4.6     1.8    -      -       -      -
    525A  ASP*     3.6    32.0    -      -       +      +
    526A  ILE*     3.3    38.4    +      -       +      +
    562A  GLN*     4.8     5.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LYS*     4.3     2.2    -      -       -      +
     35A  TYR*     1.3    70.3    -      -       -      +
     37A  CYS*     1.3    61.9    +      -       -      +
     38A  LEU*     3.8    19.6    -      -       +      +
     74A  LEU*     3.8    28.0    -      -       +      -
     76A  PRO*     3.7    22.2    -      -       +      -
    500A  TYR*     2.6    32.1    +      -       -      -
    503A  TYR*     3.4    21.8    -      -       -      +
    504A  THR*     4.4     7.0    -      -       +      -
    521A  TRP*     4.0    33.2    -      -       +      +
    522A  LEU*     4.1     8.1    -      -       +      -
    524A  VAL*     3.7    30.0    -      -       +      +
    525A  ASP*     3.0    35.2    +      -       -      +
    526A  ILE      3.4    10.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  TYR*     3.4    13.1    +      -       +      -
     36A  TYR*     1.3    71.8    -      -       -      +
     38A  LEU*     1.3    58.3    +      -       -      +
     39A  SER*     4.1     0.4    +      -       -      -
     59A  GLY*     3.3    35.9    -      -       -      -
     62A  ILE*     4.1     4.9    -      -       -      -
     63A  ALA*     4.0    21.3    -      -       +      -
     73A  VAL*     4.4     2.5    -      -       +      -
     74A  LEU      3.0    20.0    +      -       -      +
     75A  GLN*     3.5    21.0    -      -       +      +
     76A  PRO*     3.6     1.9    -      -       -      +
    526A  ILE*     3.6    25.1    -      -       +      -
    528A  ILE*     4.3     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  TYR*     3.8    11.9    -      -       +      +
     37A  CYS*     1.3    72.2    -      -       -      +
     39A  SER*     1.3    74.1    +      -       -      +
     76A  PRO*     3.7    26.9    -      -       +      +
    499A  TYR*     4.0     4.9    -      -       +      +
    500A  TYR*     3.4    30.1    -      -       +      -
    503A  TYR*     3.7    17.7    -      -       +      -
    524A  VAL*     3.8    23.6    -      -       +      -
    526A  ILE      3.1     8.0    +      -       -      +
    527A  TYR*     3.4    32.3    -      -       +      -
    528A  ILE*     2.9    29.3    +      -       -      +
    541A  PHE*     5.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  CYS*     4.1     2.4    +      -       -      -
     38A  LEU*     1.3    92.9    -      -       -      +
     40A  MET*     1.3    64.3    +      -       -      +
     41A  LEU*     3.5     2.9    +      -       -      -
     55A  ASN*     3.5    28.1    +      -       -      -
     56A  TYR*     3.6    21.1    -      -       -      -
     59A  GLY*     4.0    16.1    -      -       -      -
     75A  GLN*     4.6     6.7    +      -       -      +
     76A  PRO      5.1     7.8    +      -       -      +
     77A  ILE*     6.4     0.4    -      -       -      -
    119A  TYR*     4.8     6.7    -      -       -      -
    499A  TYR*     4.0     1.4    +      -       -      -
    503A  TYR*     5.3     1.0    +      -       -      -
    528A  ILE*     3.5     8.3    -      -       -      +
----------------------------------------------------------
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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