Contacts of the strand formed by residues 552 - 556 (chain J) in PDB entry 6C6S


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 ILE 552 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    530J  PRO*     4.7     6.7    -      -       +      -
    550J  VAL*     3.7    23.9    +      -       +      -
    551J  ARG*     1.3    72.3    -      -       -      +
    553J  THR*     1.3    66.6    +      -       -      +
    554J  GLU*     3.9    20.2    -      -       +      +
    567J  THR*     3.0     5.5    +      -       -      -
    568J  SER      2.9    34.7    +      -       -      +
    570J  LYS*     3.6    37.0    -      -       +      +
    577J  ALA*     5.3     1.1    -      -       +      -
    580J  TRP*     4.4    15.5    -      -       +      +
    589J  TYR*     3.6    54.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 553 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551J  ARG*     4.6     3.6    +      -       -      +
    552J  ILE*     1.3    78.7    -      -       -      +
    554J  GLU*     1.3    59.5    +      -       -      +
    555J  TYR*     3.6    33.4    +      -       +      +
    565J  ALA*     5.2     1.3    -      -       +      -
    566J  LYS      3.2    15.7    -      -       -      +
    567J  THR*     3.2    20.0    +      -       +      -
    580J  TRP*     3.6    19.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 554 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552J  ILE*     3.9    12.4    -      -       +      +
    553J  THR*     1.3    75.3    -      -       -      +
    555J  TYR*     1.3    61.5    +      -       -      +
    556J  GLU*     5.3     3.8    -      -       +      +
    565J  ALA      3.8     0.2    -      -       -      -
    566J  LYS*     2.9    66.0    +      -       +      +
    570J  LYS*     4.3    10.7    +      -       -      +
    580J  TRP*     3.9    21.1    -      -       +      -
    587J  LEU      4.4     3.4    -      -       -      +
    588J  PRO*     3.3     9.9    -      -       +      +
    589J  TYR*     2.5    43.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 555 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553J  THR*     3.6    32.8    +      -       +      +
    554J  GLU*     1.3    78.5    -      -       -      +
    556J  GLU*     1.3    64.0    +      -       -      +
    557J  LYS*     3.6     0.9    +      -       -      +
    563J  LEU*     4.1    22.2    -      -       +      +
    564J  VAL      3.5     5.2    -      -       -      +
    565J  ALA*     3.6    25.6    -      -       +      -
    585J  LYS*     3.1    72.9    +      -       +      +
    586J  GLY*     3.2    17.2    -      -       -      +
    587J  LEU      4.8     1.1    +      -       -      -
    588J  PRO*     6.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 556 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554J  GLU*     3.9     5.6    +      -       +      +
    555J  TYR*     1.3    73.1    -      -       -      +
    557J  LYS*     1.3    59.6    +      -       -      +
    558J  ASP*     3.2    26.6    +      -       +      +
    564J  VAL*     2.9    41.4    +      -       +      +
    566J  LYS*     5.4    12.5    -      -       +      +
    586J  GLY      4.5     4.5    -      -       -      +
    588J  PRO*     6.5     1.3    -      -       +      -
----------------------------------------------------------
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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