Contacts of the strand formed by residues 608 - 612 (chain E) in PDB entry 6Q2J


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 THR 608 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523E  LYS*     4.4    22.6    +      -       -      +
    543E  TRP*     4.6     9.2    -      -       +      -
    556E  SER*     3.3    26.0    -      -       -      +
    557E  THR*     6.0     0.2    -      -       -      -
    607E  GLY*     1.3    70.0    -      -       -      -
    609E  CYS*     1.3    60.6    +      -       -      +
    610E  ASN*     3.9     5.4    +      -       -      +
    619E  PHE      3.4     2.3    -      -       -      +
    620E  CYS*     3.3     1.7    -      -       -      -
    621E  GLU      2.6    42.9    +      -       -      +
    622E  PRO*     4.4    10.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 609 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555E  PHE*     3.8    19.1    -      -       +      -
    556E  SER      3.4     8.1    +      -       -      -
    557E  THR*     3.6     8.3    +      -       -      -
    583E  GLN*     3.3    20.8    -      -       -      +
    602E  ILE*     4.0    13.0    -      -       +      -
    605E  GLY*     3.8    19.5    -      -       -      -
    607E  GLY      3.5     7.6    +      -       -      -
    608E  THR*     1.3    73.4    -      -       -      +
    610E  ASN*     1.3    61.6    +      -       -      +
    611E  CYS*     4.6     1.5    -      -       -      -
    619E  PHE      3.1     4.7    -      -       -      -
    620E  CYS*     2.0    48.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 610 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520E  ALA*     3.6     9.2    -      -       -      +
    521E  VAL      4.2     6.0    +      -       -      +
    522E  SER      3.4    23.3    -      -       -      +
    523E  LYS*     3.3    32.8    -      -       -      +
    557E  THR*     5.5     0.2    -      -       -      -
    583E  GLN*     5.3     0.7    -      -       -      -
    608E  THR*     3.9     5.4    +      -       -      +
    609E  CYS*     1.3    74.4    -      -       -      +
    611E  CYS*     1.3    64.0    +      -       -      +
    612E  PHE*     4.3    16.5    -      -       -      -
    618E  CYS*     3.3     3.3    -      -       -      -
    619E  PHE*     2.9    55.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 611 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520E  ALA*     3.0    26.3    +      -       +      +
    521E  VAL*     3.9     6.1    -      -       -      -
    582E  PRO*     3.9    22.7    -      -       +      -
    583E  GLN*     4.0    25.4    -      -       -      -
    586E  LEU*     5.4     0.7    -      -       +      -
    602E  ILE*     4.1     5.8    -      -       -      -
    609E  CYS      4.6     1.1    -      -       -      -
    610E  ASN*     1.3    76.1    -      -       -      +
    612E  PHE*     1.3    65.6    +      -       -      +
    613E  PRO*     3.5     9.1    -      -       +      +
    617E  LYS      3.5     4.0    -      -       -      -
    618E  CYS*     2.0    47.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 612 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202B  HIS*     5.7    11.9    -      +       +      -
    247B  GLN      5.8     1.3    -      -       -      -
    249B  ARG*     5.7     6.5    -      -       +      -
    521E  VAL*     3.6    33.2    -      -       +      -
    523E  LYS*     6.2     1.6    -      -       +      -
    586E  LEU*     5.7     0.3    -      -       -      +
    610E  ASN*     4.3    16.6    -      -       -      -
    611E  CYS*     1.3    75.5    -      -       -      +
    613E  PRO*     1.3    63.8    -      -       +      +
    614E  GLU*     3.4    13.5    -      -       +      +
    615E  GLU*     4.8    17.5    -      -       +      +
    616E  GLU*     2.8    21.8    +      -       -      -
    617E  LYS*     2.9    22.8    +      -       +      +
    619E  PHE*     3.7    38.6    -      +       -      -
----------------------------------------------------------
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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