Contacts of the strand formed by residues 616 - 620 (chain B) in PDB entry 6A5T


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 GLU 616 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373B  TYR*     2.8    33.5    +      -       +      -
    377B  ARG*     3.8     5.8    +      -       -      -
    571B  THR*     4.1     0.6    -      -       -      +
    572B  ARG*     4.3    13.5    -      -       -      +
    574B  PHE*     4.1    24.7    -      -       +      -
    610B  ARG*     4.3     3.5    +      -       -      +
    611B  ASP*     3.4    35.7    +      -       +      +
    614B  GLU*     2.9    32.4    -      -       +      +
    615B  ARG*     1.3    81.9    -      -       -      +
    617B  PHE*     1.3    64.1    +      -       -      +
    618B  LYS*     4.2    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 617 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551B  LEU*     4.6     4.5    -      -       +      -
    571B  THR*     3.4    19.0    -      -       +      +
    572B  ARG      4.1     4.4    +      -       -      -
    573B  ILE*     3.7    22.9    -      -       +      -
    574B  PHE*     3.4    20.0    +      -       -      +
    586B  PRO*     5.4     3.6    -      -       +      -
    589B  LEU*     3.6    30.3    -      -       +      -
    590B  VAL*     3.2    35.7    -      -       +      -
    593B  MET*     5.0     3.4    -      -       +      -
    608B  ILE*     4.0    17.9    -      -       +      -
    609B  ILE      3.3    18.8    -      -       -      -
    610B  ARG*     4.4     6.7    -      -       +      +
    611B  ASP      5.0     0.2    -      -       -      +
    616B  GLU*     1.3    78.8    -      -       -      +
    618B  LYS*     1.3    65.0    -      -       -      +
    619B  ILE*     4.0    24.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 618 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  ILE*     6.0     2.7    -      -       +      -
    396B  LYS*     4.9    13.2    -      -       -      +
    574B  PHE*     3.8    37.0    -      -       +      -
    609B  ILE*     2.9    53.3    +      -       +      +
    611B  ASP*     5.9     4.5    +      -       -      +
    616B  GLU*     4.2    18.6    -      -       +      +
    617B  PHE*     1.3    78.9    -      -       -      +
    619B  ILE*     1.3    65.8    +      -       -      +
    620B  PHE*     3.8    34.8    -      -       +      +
    693B  GLU*     4.3    22.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 619 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547B  ILE*     3.8    23.3    -      -       +      -
    551B  LEU*     3.7    40.8    -      -       +      -
    574B  PHE*     4.1    12.7    +      -       -      +
    575B  VAL*     3.8     8.9    -      -       +      +
    576B  ASN      3.7    13.7    +      -       -      -
    593B  MET*     5.2     4.5    -      -       +      -
    606B  VAL*     3.6    27.8    -      -       +      -
    607B  SER      4.3     4.0    -      -       -      -
    608B  ILE*     4.0    18.8    -      -       +      -
    617B  PHE*     4.0    19.2    +      -       +      -
    618B  LYS*     1.3    79.6    -      -       -      +
    620B  PHE*     1.3    64.6    +      -       -      +
    621B  THR*     3.5     4.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 620 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213B  ILE*     4.4    16.8    -      -       +      -
    395B  GLY      4.8     7.2    -      -       -      -
    396B  LYS*     5.1     8.1    -      -       +      -
    398B  ARG*     2.9    35.0    -      -       -      -
    574B  PHE*     6.1     0.2    -      -       +      -
    576B  ASN*     3.8    26.7    -      -       -      +
    606B  VAL*     3.3    18.5    -      -       -      +
    607B  SER*     3.5    18.7    +      -       -      -
    609B  ILE*     5.6     4.7    -      -       +      -
    618B  LYS*     3.8    38.3    -      -       +      -
    619B  ILE*     1.3    77.7    -      -       -      +
    621B  THR*     1.3    65.1    +      -       -      +
    622B  ASP*     3.7     3.4    -      -       +      +
    625B  ARG*     3.6    29.8    -      -       +      +
    691B  ASP*     4.8     5.8    -      -       -      -
    693B  GLU*     5.4     7.0    -      -       +      -
----------------------------------------------------------
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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