Contacts of the strand formed by residues 594 - 598 (chain A) in PDB entry 5I4E


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 594 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493A  LEU*     5.2     2.0    -      -       +      -
    550A  LEU*     4.6     9.2    -      -       +      -
    568A  PHE*     4.3    17.7    -      +       -      -
    569A  VAL*     5.1     5.6    -      -       +      -
    572A  VAL*     4.8     7.4    -      -       +      -
    582A  PHE*     3.4    42.2    -      +       +      -
    583A  GLN      3.6     6.7    -      -       -      +
    585A  PRO*     4.6     4.0    -      -       +      -
    592A  ALA*     3.5     2.8    -      -       -      +
    593A  ASP*     1.3    93.4    -      -       +      +
    595A  SER*     1.3    63.6    +      -       -      +
    596A  VAL*     4.2    11.7    -      -       +      -
    604A  ASP*     3.6     2.6    -      -       -      -
    605A  TYR*     2.8    55.3    +      +       +      -
    607A  ALA*     4.4     4.9    -      -       +      -
    610A  TRP*     3.4    37.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 595 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    581A  LYS      3.7     0.2    -      -       -      +
    582A  PHE*     3.5     7.6    -      -       -      -
    583A  GLN*     2.9    54.5    +      -       -      +
    584A  ARG      5.7     0.5    +      -       -      -
    585A  PRO*     6.0     1.4    -      -       -      +
    590A  ASP*     5.4     6.8    +      -       -      +
    592A  ALA*     5.6     0.5    -      -       -      +
    594A  PHE*     1.3    74.4    +      -       -      +
    596A  VAL*     1.3    66.7    +      -       -      +
    597A  LEU*     6.0     0.2    -      -       -      -
    602A  LYS*     3.9    17.8    +      -       -      +
    603A  VAL      3.4     5.6    -      -       -      -
    604A  ASP*     2.7    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 596 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493A  LEU*     4.7     2.7    -      -       +      -
    537A  CYS*     3.8    18.4    -      -       -      -
    540A  LEU*     4.3    10.3    -      -       +      -
    541A  ILE*     4.6     5.2    -      -       +      -
    550A  LEU*     4.0    24.7    -      -       +      -
    581A  LYS      3.4     6.1    -      -       -      +
    582A  PHE*     4.8     1.1    -      -       +      -
    594A  PHE*     4.2     7.2    -      -       +      -
    595A  SER*     1.3    78.6    -      -       -      +
    597A  LEU*     1.4    62.3    +      -       -      +
    598A  HIS*     3.2    40.7    +      -       +      +
    602A  LYS*     4.5     1.3    -      -       -      -
    603A  VAL      3.0    31.9    +      -       -      -
    605A  TYR*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 597 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    500A  GLU*     4.6     0.2    -      -       -      +
    537A  CYS*     3.9    10.9    -      -       -      +
    580A  PRO      3.4    24.2    -      -       -      +
    581A  LYS*     2.8    49.9    +      -       +      +
    582A  PHE      6.3     0.2    -      -       -      -
    583A  GLN*     4.8    15.0    -      -       +      +
    595A  SER      6.0     0.2    -      -       -      -
    596A  VAL*     1.4    69.4    -      -       -      +
    598A  HIS*     1.3    66.0    +      -       -      +
    601A  GLY      4.3     1.8    -      -       -      -
    602A  LYS*     3.7    35.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 598 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    482A  PHE*     3.7    20.4    -      +       +      -
    493A  LEU*     4.6     3.1    -      -       +      -
    496A  ASN*     3.9    15.3    +      -       +      +
    500A  GLU*     3.4    17.4    +      -       -      +
    537A  CYS*     4.1     3.4    -      -       -      -
    541A  ILE*     4.4    12.7    -      -       +      +
    596A  VAL*     3.2    33.0    +      -       +      +
    597A  LEU*     1.3    78.0    -      -       -      +
    599A  TYR*     1.3    66.7    +      -       +      +
    600A  ALA      3.1     2.0    -      -       -      +
    601A  GLY*     3.0    22.9    +      -       -      +
    603A  VAL*     2.9    32.8    -      -       +      -
    605A  TYR*     2.6    35.9    +      +       -      -
----------------------------------------------------------
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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