Contacts of the strand formed by residues 662 - 667 (chain D) in PDB entry 5ZX2


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 TRP 662 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    635D  VAL      3.7     0.2    -      -       -      +
    636D  ARG*     3.4     4.3    -      -       -      -
    637D  LEU*     2.9    77.8    +      -       +      +
    640D  LEU      2.8    25.1    +      -       -      -
    641D  ARG      4.0     4.3    -      -       -      -
    642D  PRO*     3.5    47.7    -      -       +      +
    643D  PRO*     4.0    12.6    -      -       +      -
    646D  ILE*     4.1    16.6    -      -       +      -
    650D  LEU*     4.7    11.2    -      -       +      -
    651D  PHE*     4.2    13.7    -      -       +      -
    656D  TRP*     3.9     3.1    -      +       -      -
    660D  ASP      3.8     9.0    -      -       -      -
    661D  ALA*     1.3    75.4    -      -       -      +
    663D  MET*     1.3    82.5    +      -       -      +
    664D  ALA*     3.5    26.2    +      -       +      -
    683D  PHE*     4.2    13.9    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 663 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  GLU*     5.1    10.8    -      -       +      +
     78B  LEU*     3.8    32.1    -      -       +      -
    611D  VAL*     5.9     1.1    -      -       -      -
    634D  LYS*     4.6    22.2    -      -       +      +
    635D  VAL*     3.7    21.3    -      -       -      +
    636D  ARG*     4.0    24.0    -      -       +      +
    646D  ILE*     5.3     4.0    -      -       -      +
    650D  LEU*     5.3     8.8    -      -       +      +
    662D  TRP*     1.3    85.1    -      -       -      +
    664D  ALA*     1.3    60.7    +      -       -      +
    665D  GLU      4.4     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 664 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    633D  ILE      3.7     0.3    -      -       -      +
    634D  LYS*     3.0     8.7    -      -       -      -
    635D  VAL      2.9    33.3    +      -       -      +
    637D  LEU*     3.8    18.6    -      -       +      -
    646D  ILE*     6.2     0.4    -      -       -      -
    662D  TRP*     3.5    30.5    -      -       +      -
    663D  MET*     1.3    74.1    -      -       -      +
    665D  GLU*     1.3    59.7    +      -       -      +
    666D  THR*     3.8    15.5    +      -       +      +
    683D  PHE*     5.5     2.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 665 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599D  TYR*     4.7     7.0    -      -       +      -
    632D  LYS*     3.3    42.9    +      -       +      +
    633D  ILE      3.3    10.3    -      -       -      +
    634D  LYS*     4.3    27.4    +      -       +      -
    663D  MET      4.4     0.2    +      -       -      -
    664D  ALA*     1.3    70.8    -      -       -      +
    666D  THR*     1.3    64.8    +      -       -      +
    685D  ASN*     3.7    15.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 666 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    591D  GLU*     6.6     0.2    -      -       -      -
    632D  LYS*     4.4     4.9    -      -       -      +
    633D  ILE*     2.9    37.3    +      -       -      +
    635D  VAL*     4.6     4.5    -      -       +      -
    664D  ALA*     4.0    18.8    -      -       +      +
    665D  GLU*     1.3    77.2    -      -       -      +
    667D  THR*     1.3    79.3    +      -       -      +
    670D  ARG*     3.3    12.8    -      -       -      +
    671D  VAL*     3.8    18.4    -      -       +      -
    683D  PHE*     3.7    12.5    -      -       +      -
    685D  ASN*     2.7    27.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 667 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588D  LEU      4.4     2.8    +      -       -      -
    590D  THR      4.3     1.9    +      -       -      +
    591D  GLU*     3.9    29.2    -      -       +      -
    629D  VAL      3.4    13.4    +      -       -      -
    630D  ARG*     3.8    19.5    -      -       -      +
    631D  ALA      3.4    13.0    -      -       -      +
    632D  LYS      4.4     0.4    -      -       -      +
    633D  ILE*     4.5     0.7    -      -       -      -
    666D  THR*     1.3    86.3    +      -       -      +
    668D  LEU*     1.3    63.8    +      -       -      +
    669D  GLY*     3.2     4.0    +      -       -      -
    670D  ARG*     2.9    36.2    +      -       -      +
    671D  VAL*     3.2    21.6    +      -       -      +
----------------------------------------------------------
 Back to top of page


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