Contacts of the strand formed by residues 560 - 566 (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 ALA 560 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  LEU*     3.6    13.5    -      -       -      +
    212A  TRP*     3.2    29.2    +      -       +      +
    523A  PRO*     5.1     0.9    -      -       -      -
    524A  VAL*     3.4     8.1    -      -       +      +
    527A  TYR*     4.0    22.7    -      -       +      -
    541A  PHE*     3.9    22.4    -      -       +      -
    558A  GLU*     3.6     4.0    -      -       -      +
    559A  PRO*     1.3    81.4    -      -       -      +
    561A  LYS*     1.3    61.6    +      -       -      +
    562A  GLN      4.5     2.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 561 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  LYS*     5.1     9.3    -      -       -      +
    209A  LEU*     4.7     5.4    -      -       -      +
    210A  ASP*     5.5     0.2    -      -       -      +
    211A  HIS*     3.6    19.4    +      -       +      +
    212A  TRP*     3.4    15.9    -      -       -      -
    523A  PRO*     3.7    31.4    -      -       +      -
    524A  VAL      2.7    19.4    +      -       -      +
    525A  ASP*     3.6    17.9    +      -       +      +
    560A  ALA*     1.3    72.7    -      -       -      +
    562A  GLN*     1.3    59.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 562 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  TYR*     4.8     4.9    +      -       -      -
    211A  HIS*     3.5    30.7    +      -       +      +
    212A  TRP*     4.3     2.7    -      -       -      -
    525A  ASP      2.9    18.2    +      -       -      +
    526A  ILE*     3.4    23.4    -      -       +      +
    527A  TYR*     2.9    30.9    +      -       -      +
    560A  ALA*     4.5     1.2    -      -       -      +
    561A  LYS*     1.3    75.1    -      -       +      +
    563A  LEU*     1.3    63.4    +      -       -      +
    564A  LEU*     5.7     0.8    -      -       -      +
    718A  ARG      4.8     2.4    +      -       -      -
    720A  GLN*     3.5    33.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 563 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  MET*     5.1     4.9    -      -       +      -
    211A  HIS      3.5     8.6    +      -       -      +
    212A  TRP*     3.5    46.7    -      -       +      -
    213A  PRO*     3.6    22.6    -      -       +      +
    216A  VAL*     3.8    15.7    -      -       +      -
    527A  TYR*     3.5    24.7    -      -       +      +
    529A  GLY      5.2     1.3    -      -       -      +
    538A  LEU*     3.5    37.5    -      -       +      -
    562A  GLN*     1.3    78.7    +      -       -      +
    564A  LEU*     1.3    62.6    +      -       -      +
    565A  CYS*     3.9    20.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 564 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ILE*     3.6    29.8    -      -       +      -
     62A  ILE*     4.0     9.9    -      -       +      -
    526A  ILE*     3.9    15.5    -      -       +      +
    527A  TYR      2.9    12.3    +      -       -      +
    528A  ILE*     3.6    12.2    -      -       +      +
    529A  GLY      3.4    18.3    +      -       -      +
    562A  GLN*     4.2     0.9    -      -       -      +
    563A  LEU*     1.3    72.8    -      -       -      +
    565A  CYS*     1.3    64.9    +      -       -      +
    566A  GLN*     3.2     8.4    +      -       +      +
    652A  ALA*     4.3    18.8    -      -       +      -
    653A  ASP*     5.1     8.3    -      -       +      +
    720A  GLN*     3.9    39.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 565 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  MET*     6.1     0.4    -      -       -      -
    213A  PRO*     5.1     6.4    -      -       +      +
    216A  VAL*     3.7    26.9    -      -       +      -
    529A  GLY      3.3     5.8    -      -       -      -
    530A  GLY      3.8    17.7    -      -       -      -
    531A  ILE*     3.5    29.8    -      -       +      +
    534A  ALA*     5.2     1.1    -      -       -      -
    538A  LEU*     4.6     5.6    -      -       -      -
    563A  LEU*     3.9    24.8    +      -       -      +
    564A  LEU*     1.3    71.2    -      -       -      +
    566A  GLN*     1.3    65.4    +      -       -      +
    653A  ASP*     3.8    20.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 566 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  ARG*     3.5    20.4    -      -       -      +
     55A  ASN*     2.8    53.5    +      -       -      +
     58A  ILE*     4.0    14.1    -      -       +      -
    528A  ILE*     4.7     5.2    -      -       +      -
    529A  GLY*     3.0    13.5    +      -       -      +
    530A  GLY*     3.9     6.6    -      -       -      +
    531A  ILE*     3.5    19.5    +      -       -      +
    564A  LEU*     3.2     7.0    +      -       +      +
    565A  CYS*     1.3    76.1    -      -       -      +
    567A  GLY*     1.3    62.9    +      -       -      +
    652A  ALA*     3.3    17.7    -      -       +      +
    901A  LSS      2.7    38.5    +      -       -      -
----------------------------------------------------------
 Back to top of page


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