Contacts of the strand formed by residues 354 - 358 (chain B) in PDB entry 6ZGI


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 ASN 354 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348B  ALA*     4.1    12.5    -      -       +      +
    352B  ALA      3.8     0.4    +      -       -      -
    353B  TRP*     1.3    75.5    -      -       -      +
    355B  ARG*     1.3    73.4    +      -       -      +
    356B  LYS*     4.6     9.1    -      -       -      +
    397B  ALA      3.7     0.6    -      -       -      +
    398B  ASP*     3.0    10.0    -      -       -      +
    399B  SER*     2.9    48.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 355 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353B  TRP*     3.7    27.6    +      -       +      -
    354B  ASN*     1.3    83.2    +      -       -      +
    356B  LYS*     1.3    62.5    +      -       -      +
    357B  ARG      4.4     0.2    -      -       -      -
    396B  TYR*     3.9    30.1    -      -       +      +
    397B  ALA      3.5     3.1    -      -       -      +
    398B  ASP*     3.3    37.5    +      -       -      +
    464B  PHE*     4.0    21.9    -      -       -      +
    466B  ARG*     4.3    11.7    -      -       -      +
    514B  SER*     4.7     6.5    +      -       -      -
    200C  TYR*     3.0    34.1    +      -       -      -
    230C  PRO*     3.8    31.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 356 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337B  PRO*     4.2    16.8    -      -       -      +
    340B  GLU*     3.6    33.1    +      -       -      +
    341B  VAL*     4.3    19.2    -      -       +      +
    354B  ASN*     4.6     9.9    -      -       -      +
    355B  ARG*     1.3    76.2    -      -       -      +
    357B  ARG*     1.3    76.0    +      -       -      +
    358B  ILE*     4.1     6.6    -      -       +      +
    396B  TYR*     3.4     7.4    -      -       -      -
    397B  ALA*     2.9    39.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 357 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356B  LYS*     1.3    87.2    -      -       -      +
    358B  ILE*     1.3    76.8    +      -       -      +
    359B  SER*     4.7    13.5    +      -       -      +
    394B  ASN*     3.1    50.9    -      -       -      +
    395B  VAL      3.8     3.8    -      -       -      -
    396B  TYR*     3.5    45.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 358 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336B  CYS*     4.5     4.0    -      -       +      -
    337B  PRO*     4.4    16.4    -      -       +      -
    341B  VAL*     4.9    11.4    -      -       +      -
    356B  LYS*     4.1    11.4    -      -       +      +
    357B  ARG*     1.3    83.8    +      -       -      +
    359B  SER*     1.3    66.9    +      -       -      +
    361B  CYS*     3.6    25.8    -      -       -      -
    395B  VAL*     3.0    52.4    +      -       +      +
    397B  ALA*     3.9    26.9    -      -       +      +
    513B  LEU*     4.7     7.2    -      -       +      -
    523B  THR*     5.1     0.7    -      -       -      +
    524B  VAL*     4.2     6.5    -      -       +      +
----------------------------------------------------------
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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