Contacts of the strand formed by residues 492 - 498 (chain A) in PDB entry 6KC4


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 TYR 492 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455A  LEU*     3.6    21.3    -      -       +      +
    461A  TYR*     4.1    24.0    +      +       -      -
    482A  VAL*     4.4     4.5    -      -       +      -
    483A  ARG      3.5    12.3    -      -       -      -
    484A  GLU*     4.7     6.7    -      -       +      -
    490A  GLY      4.5     2.9    -      -       -      -
    491A  GLU*     1.3    79.2    +      -       -      +
    493A  VAL*     1.3    62.1    -      -       -      +
    506A  ILE*     3.5     7.4    -      -       -      +
    507A  ILE*     2.9    40.4    +      -       +      +
    514A  TYR*     4.4    18.8    -      +       -      -
    524A  ILE*     3.4    30.7    -      -       +      -
    464E  ALA      3.7     2.9    +      -       -      -
    466E  PRO*     3.5    20.9    -      -       +      +
    486E  HIS*     3.0    44.4    +      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 493 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481A  LEU      3.9     0.2    -      -       -      +
    482A  VAL*     3.2     7.1    -      -       -      +
    483A  ARG*     2.8    56.0    +      -       +      +
    485A  SER*     3.6    34.1    -      -       -      +
    492A  TYR*     1.3    80.4    -      -       -      +
    494A  LEU*     1.3    67.0    -      -       -      +
    495A  SER*     3.6    20.3    +      -       -      +
    504A  HIS*     3.9     5.2    -      -       +      -
    505A  PHE      3.3    10.1    -      -       -      +
    506A  ILE*     4.1     2.7    -      -       +      -
    507A  ILE*     4.2     4.3    -      -       -      -
      3B  PTR      3.7    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 494 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    480A  PHE*     4.0    27.6    -      -       +      -
    481A  LEU      3.6    14.8    -      -       -      +
    482A  VAL*     4.0    13.2    -      -       +      -
    493A  VAL*     1.3    70.9    -      -       -      +
    495A  SER*     1.3    60.0    +      -       -      +
    496A  VAL*     3.7    12.3    -      -       +      -
    504A  HIS*     3.6     1.0    -      -       -      -
    505A  PHE*     2.8    45.3    +      -       +      +
    507A  ILE*     4.0     7.3    -      -       +      +
    516A  PHE*     3.5    36.1    -      -       +      -
    528A  ILE*     4.1     8.7    -      -       +      -
    538A  ILE*     3.6    33.2    -      -       +      -
    546A  LEU*     4.1     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 495 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    470A  ALA*     4.6     0.9    -      -       -      -
    474A  LEU*     3.5    22.0    -      -       -      +
    480A  PHE*     3.2     4.0    -      -       -      -
    481A  LEU*     2.9    44.6    +      -       -      -
    483A  ARG*     3.0    21.9    +      -       -      +
    493A  VAL*     3.6     4.2    -      -       -      +
    494A  LEU*     1.3    70.0    -      -       -      +
    496A  VAL*     1.3    62.1    +      -       -      +
    503A  ARG      3.4     5.2    -      -       -      -
    504A  HIS*     2.8    27.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 496 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    474A  LEU*     4.3     5.8    -      -       -      -
    478A  GLY*     4.3     8.7    -      -       -      -
    479A  ASP      3.1    14.8    -      -       -      +
    480A  PHE*     3.9     3.8    -      -       +      -
    494A  LEU*     3.7    25.1    -      -       +      -
    495A  SER*     1.3    79.5    -      -       -      +
    497A  TYR*     1.3    74.4    +      -       -      +
    498A  SER*     4.0     1.5    +      -       -      -
    501A  GLN      3.7     0.3    -      -       -      +
    502A  ARG*     3.3     5.5    -      -       -      +
    503A  ARG*     2.8    37.2    +      -       +      +
    505A  PHE*     4.5     9.4    -      -       +      -
    544A  VAL*     3.6    28.9    -      -       +      -
    545A  VAL      4.9     0.2    -      -       -      +
    546A  LEU*     3.8    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 497 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    474A  LEU*     3.3    24.8    -      -       +      +
    475A  LYS      3.4    20.4    -      -       -      +
    476A  LYS*     3.4    35.9    -      -       -      +
    477A  GLN*     3.7     4.7    -      -       -      -
    478A  GLY      2.8    28.6    +      -       -      -
    479A  ASP*     3.0     8.9    +      -       +      -
    496A  VAL*     1.3    73.8    -      -       -      +
    498A  SER*     1.3    66.7    +      -       -      +
    500A  GLY*     3.4    37.1    +      -       -      -
    501A  GLN      3.4    13.7    -      -       -      -
    502A  ARG*     3.8    29.7    +      -       +      -
    521I  PHE*     3.8    11.6    -      -       -      -
    526I  GLN*     3.3    17.1    +      -       -      +
    530I  HIS*     5.2     6.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 498 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    477A  GLN*     3.5    17.6    +      -       -      -
    478A  GLY      5.2     0.7    -      -       -      -
    496A  VAL*     4.0     1.3    -      -       -      -
    497A  TYR*     1.3    77.3    -      -       -      +
    499A  ASP*     1.3    80.0    +      -       -      +
    500A  GLY      3.2     2.0    -      -       -      -
    501A  GLN*     2.8    25.8    +      -       -      +
    503A  ARG*     4.1    14.5    +      -       -      -
    542A  SER      5.2     0.9    +      -       -      -
    543A  GLY      5.7     0.2    -      -       -      -
    544A  VAL*     3.7    38.9    -      -       -      +
    545A  VAL      5.5     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