Contacts of the strand formed by residues 890 - 893 (chain O) in PDB entry 6IY3


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 HIS 890 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    782O  PHE*     5.0     8.0    -      +       +      -
    805O  LEU*     3.6    26.5    -      -       +      -
    806O  LEU*     5.1     0.4    -      -       -      +
    809O  LEU*     3.5    28.2    -      -       +      +
    818O  PRO      3.6     2.9    +      -       -      +
    819O  TYR*     3.4    31.9    -      -       +      +
    820O  LEU      3.4     2.1    +      -       -      +
    888O  TRP*     4.4     2.2    -      -       -      +
    889O  VAL*     1.3    90.1    -      -       +      +
    891O  MET*     1.3    78.6    +      -       -      +
    892O  ILE*     3.4    18.6    -      -       +      +
    918O  TYR*     3.4    32.9    -      +       +      +
    920O  LEU*     3.4    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 891 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    820O  LEU*     3.3    33.2    -      -       +      -
    822O  ILE*     5.6     0.2    -      -       -      -
    888O  TRP*     5.2    11.6    -      -       +      +
    890O  HIS*     1.3    89.7    -      -       -      +
    892O  ILE*     1.3    62.7    +      -       -      +
    893O  ILE*     4.4    15.3    -      -       +      -
    910O  LEU*     4.9    11.4    -      -       -      -
    913O  HIS*     4.3    26.0    -      -       +      +
    915O  HIS*     4.2    31.2    -      -       +      +
    916O  ALA*     4.6     7.2    -      -       +      +
    918O  TYR      3.3    15.5    +      -       -      +
    919O  ARG*     3.3    28.9    -      -       +      -
    940O  PHE*     5.8     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 892 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    802O  THR*     3.7    20.0    -      -       +      +
    805O  LEU*     4.6     5.6    -      -       +      -
    806O  LEU*     3.8    28.5    -      -       +      -
    819O  TYR*     5.7     0.2    -      -       +      -
    820O  LEU      3.0     9.5    +      -       -      +
    821O  VAL*     3.3    28.9    -      -       +      +
    822O  ILE      3.6     0.9    +      -       -      +
    823O  VAL*     6.0     0.2    -      -       -      +
    831O  TRP*     6.0     0.6    -      -       +      -
    890O  HIS*     3.4    39.5    -      -       +      +
    891O  MET*     1.3    76.9    -      -       -      +
    893O  ILE*     1.3    63.3    +      -       -      +
    920O  LEU*     3.9    26.7    -      -       +      +
    922O  LEU*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 893 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    820O  LEU*     4.7     1.3    -      -       +      -
    822O  ILE*     3.7    39.3    -      -       +      +
    873O  PHE*     5.4     5.6    -      -       +      -
    891O  MET*     4.4    22.2    -      -       +      -
    892O  ILE*     1.3    79.9    -      -       -      +
    894O  ASP*     1.3    84.5    +      -       -      +
    899O  MET*     4.6    16.8    -      -       +      -
    906O  LEU*     6.1     2.0    -      -       +      -
    910O  LEU*     5.4     7.2    -      -       +      -
    919O  ARG*     5.5     4.0    -      -       +      -
    920O  LEU      3.0    25.8    +      -       -      +
    921O  ILE*     3.6    27.4    -      -       +      -
    922O  LEU*     3.5    18.1    +      -       -      +
    940O  PHE*     5.6     7.2    -      -       +      -
----------------------------------------------------------
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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