Contacts of the strand formed by residues 561 - 568 (chain A) in PDB entry 1KWA


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 GLY 561 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494A  GLN*     3.5    14.6    -      -       -      -
    495A  LYS*     2.9    36.1    +      -       -      -
    496A  ASN*     4.7     4.1    -      -       -      +
    560A  ARG*     1.3    75.3    -      -       -      +
    562A  SER*     1.3    64.9    +      -       -      -
    563A  ILE*     3.5     4.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 562 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    492A  GLN*     3.1    26.5    +      -       -      +
    493A  PHE      3.9     0.4    -      -       -      -
    494A  GLN*     3.2    20.8    -      -       -      +
    540A  ASN*     3.6    14.8    +      -       -      +
    560A  ARG      4.1     2.3    +      -       -      +
    561A  GLY*     1.3    71.7    -      -       -      -
    563A  ILE*     1.3    62.8    +      -       -      +
    564A  THR*     4.2     3.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 563 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    491A  VAL      3.9     0.5    -      -       -      +
    492A  GLN*     3.3     3.4    -      -       -      -
    493A  PHE*     3.0    50.1    +      -       +      +
    495A  LYS*     3.7    36.1    -      -       +      -
    501A  MET*     5.1     3.8    -      -       -      -
    539A  ILE*     4.1    17.5    -      -       +      -
    540A  ASN*     3.6     5.8    -      -       -      +
    556A  LEU*     5.1     3.1    -      -       +      +
    559A  MET*     3.9    26.2    -      -       +      +
    560A  ARG      5.1     1.8    -      -       -      +
    561A  GLY      3.8     8.3    -      -       -      +
    562A  SER*     1.3    80.2    +      -       -      +
    564A  THR*     1.3    64.3    +      -       -      +
    565A  PHE*     3.7    30.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 564 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    490A  LEU*     4.0    31.6    -      -       +      -
    491A  VAL      3.3    10.8    -      -       -      +
    492A  GLN*     3.6    18.7    -      -       +      +
    538A  GLU      3.7     0.5    -      -       -      +
    539A  ILE*     3.4     4.5    -      -       -      +
    540A  ASN*     2.7    47.1    +      -       -      +
    541A  GLY      4.8     1.2    +      -       -      +
    562A  SER*     4.5     3.1    +      -       -      -
    563A  ILE*     1.3    76.9    -      -       -      +
    565A  PHE*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 565 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489A  ARG      3.5     0.9    -      -       -      +
    490A  LEU*     3.4     3.5    -      -       -      -
    491A  VAL*     2.7    43.0    +      -       +      +
    493A  PHE*     3.1    33.4    -      +       -      -
    501A  MET*     3.6    22.9    -      -       +      -
    503A  ILE*     5.2     0.4    -      -       +      -
    529A  THR*     4.8     5.2    -      -       -      -
    530A  LEU*     4.7    15.7    -      -       +      -
    536A  ILE*     3.8    33.4    -      -       +      -
    538A  GLU      3.3     1.8    -      -       -      +
    539A  ILE*     3.9    22.7    -      -       +      -
    556A  LEU*     3.9    21.8    -      -       +      -
    563A  ILE*     3.7    13.0    -      -       +      -
    564A  THR*     1.3    77.4    -      -       -      +
    566A  LYS*     1.3    61.4    +      -       -      +
    567A  ILE*     3.6    18.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 566 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488A  SER*     2.9    36.1    +      -       -      +
    489A  ARG      3.3     6.7    -      -       -      +
    490A  LEU*     3.8    19.5    -      -       +      +
    536A  ILE*     3.8     0.3    -      -       -      -
    537A  ARG*     2.7    46.8    +      -       +      +
    538A  GLU*     2.9    52.4    +      -       +      +
    564A  THR      4.2     0.4    +      -       -      -
    565A  PHE*     1.3    71.0    -      -       -      +
    567A  ILE*     1.3    56.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 567 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    488A  SER*     3.4     6.3    -      -       -      -
    489A  ARG*     2.7    62.0    +      -       +      +
    491A  VAL*     3.8    24.0    -      -       +      -
    529A  THR      4.8     0.9    -      -       -      +
    530A  LEU*     4.0    15.5    -      -       +      -
    534A  ASP*     3.9    27.6    -      -       +      +
    535A  GLU      3.0    13.2    -      -       -      +
    536A  ILE*     4.1    10.1    -      -       +      -
    537A  ARG*     4.5     0.7    -      -       -      +
    565A  PHE*     3.8    22.7    -      -       +      +
    566A  LYS*     1.3    80.0    -      -       -      +
    568A  VAL*     1.3    63.9    +      -       -      +
    569A  PRO*     3.4     9.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 568 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    487A  ARG      5.1     5.4    -      -       -      +
    488A  SER*     4.8    10.3    -      -       -      +
    533A  GLY      4.7     0.3    -      -       -      +
    534A  ASP*     3.6     0.7    -      -       -      -
    535A  GLU*     2.8    48.8    +      -       +      +
    537A  ARG*     4.1    24.2    -      -       +      +
    567A  ILE*     1.3    76.0    -      -       -      +
    569A  PRO*     1.3    73.0    -      -       +      +
    570A  SER*     4.5     0.5    -      -       -      -
    572A  ARG*     6.1     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