Contacts of the strand formed by residues 607 - 611 (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 SER 607 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597B  ARG*     4.5     5.9    +      -       -      +
    605B  GLU      4.1     0.7    +      -       -      -
    606B  VAL*     1.3    80.8    +      -       -      +
    608B  ILE*     1.3    65.7    +      -       -      +
    609B  ILE*     3.3    15.5    +      -       -      +
    618B  LYS      4.2     0.3    -      -       -      +
    620B  PHE*     3.5    25.9    +      -       -      +
    625B  ARG*     2.3    30.0    +      -       -      +
    627B  TYR*     5.9     0.2    -      -       -      -
    691B  ASP*     2.7    36.2    +      -       -      +
    694B  GLU*     4.9     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 608 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547B  ILE*     6.3     2.0    -      -       +      -
    590B  VAL*     5.1     6.3    -      -       +      +
    593B  MET*     3.4    48.2    -      -       +      +
    594B  ARG*     4.0    23.1    -      -       +      +
    597B  ARG*     4.7    17.9    -      -       +      +
    602B  ILE*     5.4     4.5    -      -       +      -
    606B  VAL*     3.8    13.8    +      -       +      -
    607B  SER*     1.3    74.4    -      -       -      +
    609B  ILE*     1.3    68.1    +      -       -      +
    617B  PHE*     4.0    22.0    -      -       +      -
    618B  LYS      3.8     5.2    -      -       -      -
    619B  ILE*     4.0    18.8    -      -       +      +
    694B  GLU*     3.2    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 609 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    594B  ARG*     5.9     0.7    -      -       -      +
    607B  SER*     3.3    15.3    -      -       -      +
    608B  ILE*     1.3    82.1    -      -       -      +
    610B  ARG*     1.3    72.7    +      -       -      +
    611B  ASP*     4.7     5.8    -      -       +      +
    617B  PHE*     3.3     7.4    -      -       -      -
    618B  LYS*     2.9    60.9    +      -       +      +
    620B  PHE*     5.6     7.6    -      -       +      -
    691B  ASP*     4.5     3.6    -      -       -      +
    693B  GLU*     3.4    36.1    -      -       +      +
    694B  GLU*     3.4    25.6    -      -       +      +
    697B  THR*     4.4    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 610 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    571B  THR*     4.9     2.6    +      -       -      -
    586B  PRO*     3.2    30.1    +      -       -      +
    587B  SER*     3.4    34.8    -      -       -      +
    590B  VAL*     4.1    24.3    -      -       +      +
    594B  ARG*     5.1    10.8    -      -       -      +
    608B  ILE*     5.1     0.8    -      -       +      +
    609B  ILE*     1.3    75.0    -      -       -      +
    611B  ASP*     1.3    64.5    +      -       -      +
    612B  ILE*     3.4    40.3    +      -       +      +
    616B  GLU      4.3     8.0    +      -       -      +
    617B  PHE*     4.4    10.2    -      -       +      +
    697B  THR*     3.5    26.9    +      -       -      +
     59I  VAL*     5.9     0.4    -      -       -      +
     61I  ASP*     4.3    17.1    +      -       -      +
     64I  GLN*     5.4     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 611 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    609B  ILE*     4.2     9.4    -      -       +      -
    610B  ARG*     1.3    78.4    -      -       -      +
    612B  ILE*     1.3    58.6    +      -       -      +
    613B  ARG*     3.8    19.0    +      -       -      +
    614B  GLU*     3.1    26.4    +      -       -      +
    615B  ARG      3.7     2.8    +      -       -      -
    616B  GLU*     3.4    33.2    +      -       +      +
    618B  LYS*     5.9     4.1    +      -       -      +
    693B  GLU*     5.2     5.7    -      -       -      +
    696B  GLU*     5.6     4.2    -      -       -      +
    697B  THR*     4.7    11.3    -      -       -      +
----------------------------------------------------------
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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