Contacts of the strand formed by residues 611 - 615 (chain B) in PDB entry 5IY8


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 GLU 611 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367B  TYR*     3.9    11.2    +      -       -      -
    371B  ARG*     4.9     0.2    +      -       -      -
    380B  ARG*     5.1     0.3    +      -       -      -
    565B  THR*     3.7     1.6    -      -       -      -
    566B  LYS*     3.6    18.4    -      -       +      +
    568B  PHE*     2.9    34.8    -      -       +      -
    605B  ARG*     3.4    10.3    -      -       -      +
    606B  ASP*     3.1    36.7    +      -       +      +
    607B  ILE*     5.3     0.2    -      -       -      +
    609B  GLU*     3.4    28.3    -      -       +      +
    610B  ARG*     1.3    78.4    -      -       -      +
    612B  ILE*     1.3    66.1    -      -       -      +
    613B  ARG*     3.4    31.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 612 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    565B  THR*     3.7    10.5    -      -       +      -
    566B  LYS      2.8    13.8    +      -       -      +
    567B  ILE*     3.2    23.2    -      -       +      +
    568B  PHE*     3.0    24.1    +      -       -      -
    577B  HIS*     5.7     2.0    -      -       +      -
    580B  PRO*     3.7    35.7    -      -       +      +
    583B  LEU*     4.4    18.2    -      -       +      -
    584B  MET*     4.9    15.9    -      -       +      +
    587B  LEU*     5.5     4.5    -      -       +      -
    603B  MET*     6.3     0.4    -      -       +      -
    604B  ILE      4.0     5.4    -      -       -      +
    605B  ARG*     4.0    17.3    -      -       +      -
    611B  GLU*     1.3    79.2    -      -       -      +
    613B  ARG*     1.3    62.4    +      -       -      +
    614B  ILE*     4.4    13.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 613 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  THR*     3.9    18.2    -      -       -      +
    205B  VAL      5.5     0.8    -      -       -      +
    367B  TYR*     3.9    12.9    +      -       -      -
    371B  ARG*     4.1    17.2    -      -       -      +
    380B  ARG*     4.8     4.0    -      -       -      +
    390B  ASN*     5.8     1.2    +      -       -      -
    568B  PHE*     3.9    21.6    -      -       +      -
    571B  GLY*     5.6     2.0    -      -       -      +
    604B  ILE*     2.9    44.8    +      -       +      +
    606B  ASP      5.6     0.2    -      -       -      +
    611B  GLU*     3.4    32.1    +      -       -      +
    612B  ILE*     1.3    75.9    -      -       -      +
    614B  ILE*     1.3    67.3    +      -       -      +
    615B  TYR*     3.1    44.6    +      -       +      -
    668B  LEU*     4.6     9.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 614 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541B  ILE*     4.7    11.7    -      -       +      -
    545B  LEU*     4.5    11.2    -      -       +      -
    567B  ILE*     4.1    25.8    -      -       +      -
    568B  PHE      2.9    16.5    +      -       -      +
    569B  VAL*     4.5    13.5    -      -       +      -
    570B  ASN      2.9    22.2    +      -       -      -
    571B  GLY      4.4     0.5    +      -       -      -
    587B  LEU*     4.2    21.1    -      -       +      -
    601B  VAL*     4.1    20.4    -      -       +      -
    602B  SER      3.6     8.7    -      -       -      +
    603B  MET*     4.2    15.0    -      -       +      -
    612B  ILE*     4.4     8.5    -      -       +      -
    613B  ARG*     1.3    80.4    -      -       -      +
    615B  TYR*     1.3    75.1    +      -       -      +
    616B  THR*     5.7     1.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 615 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202B  THR      5.5     2.0    -      -       -      -
    203B  ASN      4.9     1.7    +      -       -      -
    204B  THR*     3.7    22.2    +      -       -      +
    389B  GLY      6.1     0.4    -      -       -      -
    392B  ARG*     3.8    24.7    -      -       -      -
    570B  ASN*     3.3    13.0    -      -       -      -
    571B  GLY*     3.8    19.5    +      -       -      -
    600B  GLU      3.6     0.3    -      -       -      +
    601B  VAL*     3.6     3.5    -      -       -      +
    602B  SER*     3.0    34.1    +      -       -      +
    604B  ILE*     4.0    15.3    -      -       +      -
    613B  ARG*     3.1    47.9    +      -       +      -
    614B  ILE*     1.3    82.0    -      -       -      +
    616B  THR*     1.3    63.5    +      -       -      +
    617B  ASP*     3.8     7.4    -      -       -      +
    620B  ARG*     3.8    22.7    +      -       -      +
    666B  ASP*     5.5     1.6    -      -       -      -
    668B  LEU*     3.6    18.6    -      -       +      +
----------------------------------------------------------
 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