Contacts of the strand formed by residues 524 - 530 (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 VAL 524 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  TYR*     3.7    34.8    -      -       +      +
     38A  LEU*     3.8    28.0    -      -       +      -
    500A  TYR*     4.3    14.8    -      -       +      -
    522A  LEU*     4.3     1.3    -      -       +      -
    523A  PRO*     1.3    72.0    -      -       -      +
    525A  ASP*     1.3    57.8    +      -       -      +
    526A  ILE      3.2    29.6    -      -       -      +
    527A  TYR*     4.2     8.3    -      -       +      -
    541A  PHE*     5.2     2.2    -      -       +      -
    559A  PRO      2.7    20.4    +      -       -      +
    560A  ALA*     3.4     6.6    -      -       +      -
    561A  LYS*     2.7    34.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 525 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LYS*     2.9    34.6    +      -       -      +
     35A  TYR*     3.6    37.3    -      -       +      -
     36A  TYR      3.0    31.0    +      -       -      +
    523A  PRO      3.6     0.7    -      -       -      +
    524A  VAL*     1.3    71.9    -      -       -      +
    526A  ILE*     1.3    58.5    +      -       -      +
    561A  LYS*     3.6    18.6    +      -       +      +
    562A  GLN*     2.9    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 526 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  TYR*     3.3    36.6    -      -       +      +
     36A  TYR      3.4     0.6    +      -       -      -
     37A  CYS*     3.6    24.0    -      -       -      -
     38A  LEU      3.1    19.9    +      -       -      +
     62A  ILE*     4.0    12.3    -      -       +      -
    524A  VAL*     3.2     7.2    -      -       -      +
    525A  ASP*     1.3    77.7    -      -       -      +
    527A  TYR*     1.3    61.6    +      -       -      +
    528A  ILE*     3.8    18.8    -      -       +      -
    562A  GLN*     3.4    40.2    -      -       +      +
    564A  LEU*     3.9    24.2    -      -       +      -
    720A  GLN*     5.4     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 527 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  LEU*     3.5    36.1    -      -       +      -
     40A  MET*     3.6    21.4    -      -       +      +
    499A  TYR*     2.7    29.3    +      -       -      -
    524A  VAL*     4.2     3.6    -      -       +      -
    526A  ILE*     1.3    74.2    -      -       -      +
    528A  ILE*     1.3    60.9    +      -       -      +
    537A  HIS*     2.7    26.1    +      -       -      -
    538A  LEU*     3.6    22.2    -      -       +      -
    541A  PHE*     3.4    41.1    -      +       -      -
    560A  ALA*     4.0    13.9    -      -       +      -
    562A  GLN      2.9    15.1    +      -       -      +
    563A  LEU*     3.5    15.5    -      -       +      +
    564A  LEU      2.9    23.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 528 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  CYS*     4.3     9.6    -      -       -      -
     38A  LEU      2.9    13.7    +      -       -      +
     39A  SER*     3.5     4.6    -      -       -      +
     40A  MET*     3.1    28.9    +      -       -      +
     55A  ASN*     3.3    27.4    +      -       -      +
     58A  ILE*     4.0    18.4    -      -       +      -
     59A  GLY*     3.4    32.1    -      -       -      +
     62A  ILE*     3.9    19.3    -      -       +      -
    526A  ILE*     3.8    17.5    -      -       +      -
    527A  TYR*     1.3    77.1    -      -       -      +
    529A  GLY*     1.3    59.8    +      -       -      +
    564A  LEU*     3.6    19.7    -      -       +      +
    566A  GLN*     4.7     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 529 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  MET*     3.7    19.0    -      -       -      +
     55A  ASN*     3.4    14.8    -      -       -      -
    527A  TYR      4.1     1.6    +      -       -      -
    528A  ILE*     1.3    75.6    -      -       -      +
    530A  GLY*     1.3    64.8    +      -       -      -
    563A  LEU*     5.2     1.6    -      -       -      +
    564A  LEU      3.4     4.6    +      -       -      -
    565A  CYS*     3.3     5.6    -      -       -      +
    566A  GLN*     3.0    25.9    +      -       -      +
    901A  LSS      3.4     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 530 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  MET*     4.4     4.2    -      -       -      +
     55A  ASN*     3.9     0.2    +      -       -      -
    529A  GLY*     1.3    75.1    -      -       -      -
    531A  ILE*     1.3    63.6    +      -       -      -
    532A  GLU*     3.1     4.3    -      -       -      -
    533A  HIS*     3.3    17.0    +      -       -      +
    565A  CYS*     3.8    10.2    -      -       -      -
    566A  GLN*     3.9     5.8    -      -       -      -
    568A  MET*     3.4    17.9    -      -       -      -
    901A  LSS      2.8    25.2    +      -       -      -
----------------------------------------------------------
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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