Contacts of the strand formed by residues 528 - 535 (chain B) in PDB entry 4RYD


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 PHE 528 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263B  VAL*     3.9    31.6    -      -       +      -
    305B  CYS*     4.6     4.5    -      -       -      -
    491B  LEU      3.9    13.5    -      -       -      +
    492B  THR*     3.2     5.0    -      -       -      +
    493B  LEU*     2.9    56.9    +      -       +      +
    498B  ARG*     3.6    29.8    -      -       +      -
    501B  LEU*     4.7     4.5    -      -       +      -
    503B  ILE*     4.9     1.1    -      -       +      -
    516B  LEU*     3.8    29.2    -      -       +      -
    519B  ARG*     5.5     0.2    -      -       -      -
    522B  ASP*     5.4     0.9    -      -       -      -
    526B  ASP      4.8     1.3    -      -       -      -
    527B  GLY*     1.3    76.6    -      -       -      -
    529B  ASN*     1.3    60.4    +      -       -      +
    530B  ASP      3.8     0.9    -      -       -      -
    531B  TRP*     3.8    22.4    -      +       +      -
    533B  PHE*     3.6    29.4    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 529 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  ARG*     5.2     3.6    +      -       -      -
    492B  THR*     4.2    12.1    -      -       +      +
    526B  ASP      5.8     1.8    -      -       -      +
    528B  PHE*     1.3    72.5    -      -       -      +
    530B  ASP*     1.3    76.6    +      -       -      +
    531B  TRP*     3.2     6.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 530 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  ASP*     4.7     6.7    -      -       -      +
    267A  ALA*     5.6     1.7    -      -       -      +
    268A  ARG*     3.5    24.0    +      -       -      +
    490B  ARG*     3.1    46.6    +      -       -      +
    491B  LEU      3.0     6.6    +      -       -      -
    492B  THR*     2.9    23.5    +      -       -      +
    529B  ASN*     1.3    79.3    +      -       -      +
    531B  TRP*     1.3    62.9    +      -       -      +
    532B  ALA      3.6     1.9    +      -       -      -
    565B  LYS*     3.0    24.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 531 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263B  VAL*     3.7    25.6    -      -       +      -
    264B  ASP*     3.7    27.1    -      -       -      -
    265B  GLY*     4.5     2.5    -      -       -      -
    304B  ASN      2.9    29.7    +      -       -      -
    305B  CYS*     3.8    13.3    -      -       -      +
    306B  ASP      4.2     0.2    -      -       -      -
    307B  GLY*     3.8    19.3    -      -       -      -
    310B  ASN*     4.1    11.3    -      -       -      +
    489B  ALA      3.4     0.7    -      -       -      +
    490B  ARG*     4.2     0.4    -      -       -      -
    491B  LEU      2.9    25.6    +      -       -      -
    528B  PHE*     3.8    28.9    -      +       +      -
    529B  ASN      3.2     6.0    -      -       -      +
    530B  ASP*     1.3    76.6    -      -       -      +
    532B  ALA*     1.3    60.8    +      -       -      +
    533B  PHE*     3.3    42.7    +      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 532 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310B  ASN*     2.5    30.7    +      -       -      +
    488B  GLN*     3.9    18.7    +      -       -      +
    489B  ALA      4.0     4.5    -      -       -      -
    490B  ARG*     3.5    40.2    -      -       +      +
    530B  ASP      3.6     2.6    +      -       -      -
    531B  TRP*     1.3    75.8    -      -       -      +
    533B  PHE*     1.3    58.2    +      -       -      +
    534B  MET*     3.3     3.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 533 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304B  ASN*     4.2     9.4    -      -       +      +
    305B  CYS*     5.0     1.1    -      -       -      -
    310B  ASN*     4.0     4.9    -      -       -      +
    487B  ALA      4.0     0.2    -      -       -      +
    488B  GLN*     3.2     3.8    -      -       -      -
    489B  ALA*     2.8    43.6    +      -       -      +
    491B  LEU*     3.8    31.2    -      -       +      -
    503B  ILE*     4.5     6.5    -      -       +      -
    515B  LEU*     3.5    51.0    -      -       +      +
    516B  LEU*     4.0    15.5    -      -       +      -
    528B  PHE*     3.6    35.4    -      +       -      -
    531B  TRP*     3.3    37.9    +      +       +      -
    532B  ALA*     1.3    69.6    -      -       -      +
    534B  MET*     1.3    59.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 534 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304B  ASN*     3.5     3.9    +      -       -      +
    310B  ASN*     3.2    46.9    +      -       -      +
    311B  SER      3.6    18.2    -      -       -      +
    312B  ILE*     4.0    16.6    -      -       +      -
    314B  THR      5.4     0.7    -      -       -      +
    334B  SER*     2.9    15.8    +      -       -      -
    335B  SER*     3.3    37.8    +      -       -      +
    486B  HIS*     4.1    19.3    -      -       +      -
    487B  ALA      3.4    11.0    -      -       -      +
    488B  GLN*     4.2     7.0    -      -       +      +
    515B  LEU*     4.6     1.1    -      -       -      -
    532B  ALA      4.1     2.9    -      -       -      +
    533B  PHE*     1.3    76.0    -      -       -      +
    535B  THR*     1.3    90.1    +      -       -      +
    536B  THR*     3.6    13.7    -      -       +      -
    607B   NA      4.0     2.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 535 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334B  SER*     3.4    18.1    -      -       -      -
    485B  GLU      4.5     1.4    -      -       -      +
    486B  HIS*     3.9     2.6    -      -       -      -
    487B  ALA*     3.0    43.2    +      -       +      +
    505B  LEU*     4.6    10.8    -      -       +      -
    513B  SER*     2.6    34.2    +      -       -      +
    515B  LEU*     4.4     8.1    -      -       +      -
    534B  MET*     1.3    81.5    -      -       -      +
    536B  THR*     1.3    60.9    +      -       -      +
    537B  HIS*     3.1    12.4    +      -       -      +
    538B  SER*     5.1     8.0    +      -       -      +
    547B  TRP*     5.6     2.5    -      -       +      -
----------------------------------------------------------
 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