Contacts of the strand formed by residues 448 - 453 (chain D) 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 ARG 448 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276C  ARG*     4.4     0.4    -      -       -      +
    446D  PRO*     4.0     8.5    +      -       +      +
    447D  GLN*     1.3    82.9    -      -       -      +
    449D  LYS*     1.3    61.4    +      -       -      +
    477D  GLU      4.3     1.0    +      -       -      -
    478D  PRO      3.1    28.0    +      -       -      +
    479D  ASN*     3.8     9.4    -      -       +      +
    480D  HIS*     2.7    45.7    +      -       -      +
    481D  ILE*     4.0    10.8    -      -       +      -
    571D  TYR*     3.2     5.5    -      -       -      -
    572D  GLY      2.8    38.3    +      -       -      +
    573D  THR*     4.6     5.8    -      -       -      +
    574D  ALA*     3.4    22.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 449 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269C  LEU*     4.2     7.0    +      -       -      +
    272C  GLU*     2.6    40.1    +      -       -      +
    273C  ALA      5.3     0.2    -      -       -      +
    276C  ARG*     4.0    28.3    -      -       -      +
    448D  ARG*     1.3    76.6    -      -       -      +
    450D  CYS*     1.3    60.1    +      -       -      +
    451D  ILE*     4.0    23.2    +      -       +      +
    479D  ASN*     3.2    24.5    -      -       -      +
    481D  ILE*     4.4     0.2    -      -       -      -
    569D  VAL*     3.7    21.3    -      -       +      -
    570D  LEU      3.3     4.0    -      -       -      +
    571D  TYR*     3.4    28.0    -      -       +      -
    602D  FMT      2.9    22.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 450 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    449D  LYS*     1.3    72.1    -      -       -      +
    451D  ILE*     1.3    60.7    +      -       -      +
    452D  ILE*     3.9    17.0    +      -       -      -
    473D  ALA*     3.4    10.3    -      -       -      -
    474D  CYS*     2.1    59.5    -      -       -      -
    479D  ASN*     3.8    11.4    -      -       -      +
    481D  ILE*     3.8    12.1    -      -       +      +
    568D  LEU      3.7     1.6    -      -       -      +
    569D  VAL*     3.6     2.5    -      -       -      -
    570D  LEU*     2.8    43.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 451 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234C  ALA*     4.1    13.9    -      -       +      -
    237C  ALA*     3.8    29.6    -      -       +      +
    238C  ARG*     3.7    35.8    +      -       +      +
    269C  LEU*     4.0    22.0    -      -       +      +
    449D  LYS*     4.0    28.4    +      -       +      +
    450D  CYS*     1.3    74.6    -      -       -      +
    452D  ILE*     1.3    69.2    +      -       -      +
    453D  ASP      4.8     0.2    -      -       -      +
    474D  CYS*     4.4     3.5    -      -       -      -
    479D  ASN*     5.6     0.2    +      -       -      -
    567D  THR*     3.8    22.9    -      -       +      -
    568D  LEU      3.8     2.9    -      -       -      +
    569D  VAL*     4.5     8.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 452 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    450D  CYS*     3.9    24.0    -      -       -      -
    451D  ILE*     1.3    80.4    -      -       -      +
    453D  ASP*     1.3    65.6    +      -       -      +
    454D  ILE*     3.4    23.8    +      -       +      +
    469D  LYS*     4.9     7.6    -      -       -      -
    471D  VAL*     3.9    34.3    -      -       +      -
    473D  ALA*     4.5     3.8    -      -       -      +
    474D  CYS      5.3     0.4    -      -       -      +
    567D  THR*     4.0     2.0    -      -       -      -
    568D  LEU*     2.8    42.9    +      -       +      +
    570D  LEU*     3.9    23.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 453 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232C  THR*     3.8    18.0    +      -       -      +
    234C  ALA*     3.7    25.5    -      -       +      +
    238C  ARG*     6.0     1.0    -      -       -      +
    451D  ILE*     4.2     2.4    +      -       -      +
    452D  ILE*     1.3    74.7    -      -       -      +
    454D  ILE*     1.3    63.0    +      -       -      +
    455D  LEU      3.9     8.8    +      -       -      +
    469D  LYS*     5.4     3.5    +      -       -      -
    565D  LYS*     4.1    12.3    -      -       -      +
    566D  PHE      3.4    10.2    +      -       -      +
    567D  THR*     2.7    27.8    +      -       -      +
----------------------------------------------------------
 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