Contacts of the strand formed by residues 589 - 593 (chain S) in PDB entry 1I84


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 LYS 589 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    471S  ILE*     3.9    12.6    -      -       -      +
    570S  GLN*     3.0    25.9    +      -       -      +
    573S  LYS*     3.3    21.5    -      -       -      +
    582S  CYS*     3.7    20.2    -      -       +      -
    583S  ILE      3.8     5.6    -      -       -      +
    584S  LEU*     3.6    27.3    -      -       +      +
    588S  GLY*     1.3    68.8    -      -       -      -
    590S  VAL*     1.3    78.4    +      -       -      +
    591S  THR*     4.6     2.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 590 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    469S  PHE*     4.0    11.4    -      -       +      -
    470S  GLU      5.8     0.4    -      -       -      +
    471S  ILE*     4.2    16.8    -      -       +      -
    475S  ASN*     2.9    39.0    -      -       +      +
    483S  ASN*     4.5     4.3    -      -       -      +
    581S  PHE      3.5     1.0    -      -       -      +
    582S  CYS*     3.1    25.9    -      -       -      -
    583S  ILE      3.5     7.7    +      -       -      +
    585S  HIS*     3.8    19.3    -      -       +      -
    588S  GLY      3.8    10.5    -      -       -      +
    589S  LYS*     1.3    85.0    -      -       -      +
    591S  THR*     1.3    60.3    +      -       -      +
    592S  TYR*     3.7    27.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 591 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473S  GLU      4.7     3.3    -      -       -      +
    475S  ASN*     3.1    25.6    +      -       -      +
    572S  SER*     4.3     6.5    -      -       -      -
    573S  LYS*     3.6    22.4    +      -       +      +
    580S  GLU*     4.0    30.0    -      -       +      +
    581S  PHE      3.3     5.2    -      -       -      +
    582S  CYS*     3.2    21.6    -      -       -      -
    589S  LYS*     4.6     2.4    -      -       -      +
    590S  VAL*     1.3    74.2    -      -       -      +
    592S  TYR*     1.3    62.6    +      -       -      +
    593S  ASN*     4.0     0.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 592 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    475S  ASN*     3.0    26.2    -      -       +      +
    476S  SER      3.6     5.6    -      -       -      -
    479S  GLN*     3.4    10.2    +      -       +      -
    480S  LEU*     3.2    37.8    -      -       +      -
    483S  ASN*     3.4    17.5    -      -       -      +
    580S  GLU*     2.9    23.7    -      -       -      +
    581S  PHE*     2.7    30.3    +      +       +      +
    583S  ILE*     3.4    42.6    -      -       +      -
    585S  HIS*     2.6    26.5    +      -       -      -
    590S  VAL*     3.8    23.8    -      -       +      -
    591S  THR*     1.3    73.7    -      -       -      +
    593S  ASN*     1.3    59.9    +      -       -      +
    594S  ALA      3.7     0.9    +      -       -      -
    597S  TRP*     4.1    12.1    -      +       +      -
----------------------------------------------------------
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Residues in contact with ASN 593 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    474S  ILE*     4.5    17.9    -      -       +      +
    475S  ASN      3.2    22.1    +      -       -      +
    476S  SER*     4.5     3.6    +      -       -      +
    578S  LYS*     2.8    57.8    +      -       -      +
    579S  THR      3.6     2.3    +      -       -      -
    580S  GLU*     4.3     6.8    +      -       +      +
    591S  THR      4.0     1.0    +      -       -      +
    592S  TYR*     1.3    69.8    -      -       -      +
    594S  ALA*     1.3    53.1    +      -       -      +
    595S  SER*     2.8    37.5    +      -       -      +
    597S  TRP*     3.0    16.4    +      -       -      -
----------------------------------------------------------
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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