Contacts of the strand formed by residues 638 - 643 (chain A) in PDB entry 4YZC


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 GLN 638 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599A  LYS      3.5     1.4    -      -       -      +
    600A  ARG*     3.5     3.8    -      -       -      +
    601A  ILE*     3.1    56.5    +      -       +      +
    603A  PRO*     3.7    28.9    -      -       +      +
    610A  ASP*     4.9    10.9    -      -       -      +
    613A  VAL*     4.6    13.3    -      -       -      +
    631A  THR*     5.0    14.2    -      -       -      +
    632A  GLU      3.4    11.9    -      -       -      +
    633A  LYS*     4.0    29.4    +      -       +      -
    637A  PHE*     1.3    74.2    -      -       -      +
    639A  TYR*     1.3    60.0    +      -       -      +
    640A  ILE*     5.2     2.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 639 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564A  VAL*     4.9     4.9    -      -       -      +
    566A  VAL*     3.8    26.9    -      -       +      +
    569A  ILE*     3.6    20.8    -      -       +      +
    571A  PHE*     3.6    31.2    -      +       -      -
    598A  VAL*     4.1    12.8    -      -       +      -
    599A  LYS      3.5     2.5    -      -       -      -
    600A  ARG*     3.5    35.0    +      -       +      -
    631A  THR*     3.2     4.7    -      -       -      -
    632A  GLU*     2.5    48.3    +      -       +      +
    634A  ASP*     3.0    40.1    +      -       -      -
    637A  PHE*     3.6    23.0    -      -       +      -
    638A  GLN*     1.3    75.2    -      -       -      +
    640A  ILE*     1.3    60.6    +      -       -      +
    641A  ALA      4.0     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 640 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    569A  ILE*     4.6     0.9    -      -       -      -
    597A  ALA      3.5     1.0    -      -       -      +
    598A  VAL*     3.5     3.3    -      -       -      -
    599A  LYS*     2.9    65.1    +      -       +      +
    601A  ILE*     3.6    34.5    -      -       +      -
    613A  VAL*     3.7    20.0    -      -       +      -
    616A  LEU*     4.8     5.2    -      -       +      -
    628A  TYR*     3.9    22.7    -      -       +      -
    630A  CYS      3.5     2.9    -      -       -      -
    631A  THR*     3.9    13.7    -      -       +      -
    638A  GLN*     4.8     2.9    -      -       +      +
    639A  TYR*     1.3    77.0    -      -       -      +
    641A  ALA*     1.3    61.1    +      -       -      +
    642A  ILE*     3.6    22.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 641 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    569A  ILE*     3.9    18.6    -      -       +      +
    591A  PHE*     4.1    21.8    -      -       +      -
    596A  VAL*     4.5     6.1    -      -       +      -
    597A  ALA      3.5     6.7    -      -       -      +
    598A  VAL*     4.7     2.0    -      -       +      +
    628A  TYR*     4.0     1.7    -      -       -      -
    629A  PHE*     2.9    33.1    +      -       +      -
    630A  CYS*     2.7    27.2    +      -       +      +
    639A  TYR      4.0     1.6    +      -       -      -
    640A  ILE*     1.3    71.4    -      -       -      +
    642A  ILE*     1.3    62.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 642 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  VAL*     5.3     0.4    -      -       +      -
    596A  VAL*     3.4     6.1    -      -       -      +
    597A  ALA*     2.8    44.8    +      -       +      +
    599A  LYS*     4.2    18.2    -      -       +      -
    616A  LEU*     3.8    28.9    -      -       +      -
    626A  ILE*     4.7     9.6    -      -       +      -
    627A  ARG      3.4    12.1    -      -       -      +
    628A  TYR*     4.2     2.9    -      -       -      -
    629A  PHE*     3.6     7.2    -      -       -      -
    640A  ILE*     3.9    13.7    -      -       +      +
    641A  ALA*     1.3    80.4    -      -       -      +
    643A  GLU*     1.3    63.0    +      -       -      +
    644A  LEU      3.3     0.3    +      -       -      -
   1001A  STU      3.5    44.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 643 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    625A  VAL      4.9     0.2    -      -       -      +
    626A  ILE*     4.0     8.6    -      -       +      +
    627A  ARG*     2.9    48.7    +      -       +      +
    629A  PHE*     3.5    15.2    -      -       +      -
    642A  ILE*     1.3    71.8    -      -       -      +
    644A  LEU*     1.3    66.1    +      -       -      +
    645A  CYS*     3.7     0.9    +      -       -      -
    697A  SER*     4.6     6.6    -      -       -      -
    698A  MET      5.4     2.3    +      -       -      +
    706A  LYS*     5.0     5.8    +      -       -      -
    708A  MET*     3.5    32.2    -      -       +      +
   1001A  STU      2.7    31.0    +      -       -      -
----------------------------------------------------------
 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