Contacts of the strand formed by residues 671 - 677 (chain A) in PDB entry 4WGK


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 VAL 671 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    663A  LYS*     5.9     0.7    -      -       -      -
    666A  TYR*     3.5    13.0    +      -       -      -
    669A  GLY      4.8     3.8    -      -       -      +
    670A  GLU*     1.3    81.2    -      -       -      +
    672A  ALA*     1.3    70.0    +      -       -      +
    673A  GLU*     3.7     7.0    +      -       +      +
    734A  GLU*     4.1    16.4    -      -       +      +
    735A  TRP      3.4     7.6    -      -       -      +
    736A  HIS*     3.3    48.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 672 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    662A  ALA*     4.6     1.1    -      -       +      -
    666A  TYR*     3.6    32.2    -      -       +      +
    670A  GLU      4.1     1.0    -      -       -      -
    671A  VAL*     1.3    72.4    -      -       -      +
    673A  GLU*     1.3    59.1    +      -       -      +
    733A  VAL      3.7     1.2    -      -       -      +
    734A  GLU*     3.3     3.1    -      -       -      -
    735A  TRP*     2.7    49.5    +      -       +      +
    737A  ILE*     4.3     6.4    -      -       +      +
    748A  ILE*     4.4     5.3    -      -       +      +
    775A  PHE*     4.0    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 673 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    660A  GLN*     3.8    22.2    -      -       -      +
    661A  PRO      3.8     5.7    -      -       -      +
    662A  ALA*     3.7    13.9    -      -       -      +
    666A  TYR*     3.8     6.1    +      -       -      -
    671A  VAL*     3.7     8.9    +      -       +      +
    672A  ALA*     1.3    74.9    -      -       -      +
    674A  VAL*     1.3    68.4    +      -       -      +
    675A  ILE*     3.9    15.6    -      -       +      +
    732A  THR*     3.7    24.9    -      -       +      +
    733A  VAL      3.5     2.9    -      -       -      -
    734A  GLU*     3.4    24.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 674 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    658A  VAL*     4.2     9.0    -      -       +      -
    660A  GLN      3.3    10.1    -      -       -      +
    661A  PRO*     4.5     0.7    -      -       +      -
    662A  ALA*     3.8    22.0    -      -       +      +
    673A  GLU*     1.3    80.9    -      -       -      +
    675A  ILE*     1.3    66.0    +      -       -      +
    676A  PHE*     3.5    35.0    -      -       +      -
    731A  ALA      3.8     1.4    -      -       -      +
    732A  THR*     3.5     2.1    -      -       -      +
    733A  VAL      3.0    34.6    +      -       -      +
    748A  ILE*     3.7    25.8    -      -       +      -
    772A  SER*     3.7    22.2    -      -       -      +
    775A  PHE*     4.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 675 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    658A  VAL*     3.6     5.7    -      -       -      +
    659A  LEU*     2.8    38.3    +      -       +      -
    660A  GLN*     2.9    51.9    +      -       +      +
    673A  GLU*     3.9    14.6    -      -       +      +
    674A  VAL*     1.3    77.2    -      -       -      +
    676A  PHE*     1.3    65.3    +      -       -      +
    730A  ASN*     3.7    33.4    -      -       +      +
    731A  ALA      3.7     2.0    -      -       -      +
    732A  THR*     3.8    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 676 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    656A  GLY      3.3    20.6    -      -       -      +
    657A  ASP      3.4     5.4    -      -       -      +
    658A  VAL*     3.8    24.0    -      -       +      -
    659A  LEU*     4.0     4.4    -      -       -      +
    674A  VAL*     3.5    30.3    -      -       +      -
    675A  ILE*     1.3    75.9    -      -       -      +
    677A  VAL*     1.3    62.5    +      -       -      +
    730A  ASN*     3.4     8.7    -      -       -      +
    731A  ALA      2.9    42.3    +      -       -      +
    733A  VAL*     4.0    14.1    -      -       +      -
    748A  ILE*     3.6    21.1    -      -       +      -
    750A  TYR*     3.6    44.9    -      +       +      -
    770A  GLY*     3.9    19.1    -      -       -      -
    771A  THR      4.0     1.1    -      -       -      -
    772A  SER      4.1     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 677 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    648A  ARG      4.5     1.6    -      -       -      +
    649A  ALA*     4.0     6.1    -      -       +      -
    650A  PRO*     3.6    29.6    -      -       +      -
    653A  ARG*     5.0     1.3    -      -       +      -
    654A  THR      3.1    22.7    -      -       -      +
    655A  PHE*     3.9    25.0    -      -       +      -
    656A  GLY*     3.1    22.5    +      -       -      -
    657A  ASP*     3.0    23.9    +      -       +      +
    659A  LEU*     3.6    24.8    -      -       +      +
    676A  PHE*     1.3    72.8    -      -       -      +
    678A  GLY*     1.3    61.5    +      -       -      +
    728A  LEU*     5.6     0.2    -      -       +      -
    729A  SER      3.7     6.7    -      -       -      +
    730A  ASN*     4.8     0.2    -      -       -      -
    750A  TYR*     3.9     2.8    -      -       -      -
    768A  PHE*     4.4     0.2    -      -       -      -
----------------------------------------------------------
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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