Contacts of the strand formed by residues 567 - 578 (chain B) in PDB entry 3KCZ


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 567 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    412B  GLU*     3.8    21.5    -      -       -      +
    416B  PHE*     3.7     6.4    -      -       -      -
    443B  LEU*     4.4    13.5    -      -       +      +
    461B  ILE*     4.1    15.3    -      -       +      -
    463B  PHE*     3.8    25.6    -      -       +      -
    488B  SER*     3.9    25.4    -      -       -      +
    489B  GLU      3.5     2.7    -      -       -      -
    490B  VAL*     5.1     0.2    -      -       +      -
    561B  VAL*     3.8    17.5    -      -       +      -
    564B  PRO*     3.0    20.3    +      -       +      +
    565B  ASN*     3.2     2.2    -      -       -      -
    566B  GLN*     1.3    84.9    -      -       -      +
    568B  ARG*     1.3    67.9    +      -       -      +
    569B  MET*     4.3     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 568 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    408B  GLU*     4.8    10.9    +      -       -      +
    412B  GLU*     3.6    16.6    -      -       +      +
    413B  LYS*     4.0    49.2    -      -       -      +
    416B  PHE*     3.7    24.4    -      -       +      -
    488B  SER*     4.0     2.2    -      -       -      -
    489B  GLU*     2.8    63.4    +      -       +      +
    567B  VAL*     1.3    75.2    -      -       -      +
    569B  MET*     1.3    72.1    +      -       -      +
    570B  ARG*     3.0    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 569 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367B  CYS*     4.6     0.2    -      -       -      -
    407B  VAL*     3.3    32.8    -      -       +      +
    408B  GLU*     5.0     1.4    -      -       -      -
    409B  LYS*     3.7    32.7    +      -       +      -
    412B  GLU*     2.8    24.6    +      -       -      +
    438B  ILE*     3.7    30.5    -      -       -      +
    439B  LEU*     4.1    12.8    -      -       -      +
    442B  GLY*     4.0     7.2    -      -       -      -
    443B  LEU*     4.7     4.7    -      -       +      +
    486B  LEU*     3.8    28.7    -      -       +      -
    488B  SER*     3.6    18.8    -      -       -      +
    567B  VAL*     4.7     6.1    -      -       +      -
    568B  ARG*     1.3    78.0    +      -       -      +
    570B  ARG*     1.3    63.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 570 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406B  GLU*     3.3    39.0    +      -       -      +
    407B  VAL*     2.8    49.0    +      -       -      +
    408B  GLU*     4.6     9.7    +      -       -      +
    425B  LEU*     4.4     4.9    -      -       +      -
    487B  LEU      2.9     9.1    +      -       -      +
    489B  GLU*     3.5    34.4    +      -       +      +
    532B  ASN*     5.4     6.9    -      -       -      +
    568B  ARG*     3.0    47.3    +      -       -      +
    569B  MET*     1.3    80.8    +      -       -      +
    571B  TYR*     1.3    95.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 571 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372B  LEU*     4.0    24.7    -      -       +      -
    378B  GLU*     4.1    11.8    -      -       +      +
    382B  ILE*     3.5    34.5    -      -       +      -
    404B  LEU*     4.2     8.7    -      -       +      -
    405B  PHE      3.2    12.1    -      -       -      +
    406B  GLU*     4.3     9.2    -      -       +      -
    407B  VAL*     3.7     3.8    -      -       -      +
    425B  LEU*     4.1     9.2    -      -       +      -
    485B  LEU      3.9     0.2    -      -       -      +
    486B  LEU*     3.4     7.6    -      -       -      +
    487B  LEU*     2.8    51.4    +      -       +      -
    531B  LEU*     3.6    27.8    -      -       +      +
    532B  ASN*     4.1    12.8    +      -       -      -
    570B  ARG*     1.3   109.2    +      -       +      +
    572B  LEU*     1.3    61.9    +      -       -      +
    573B  LEU*     4.2     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 572 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  LEU*     4.1    26.5    -      -       +      -
    369B  LEU*     4.6     6.1    -      -       +      -
    404B  LEU*     3.6     2.8    -      -       -      +
    405B  PHE*     2.8    45.8    +      -       +      +
    407B  VAL*     3.6    13.0    -      -       +      +
    435B  TRP*     4.1    17.7    -      -       +      -
    439B  LEU*     4.4    21.8    -      -       +      -
    484B  LEU*     4.0    36.3    -      -       +      -
    485B  LEU      3.5    12.8    -      -       -      +
    486B  LEU*     4.1    15.9    -      -       +      -
    571B  TYR*     1.3    75.3    -      -       -      +
    573B  LEU*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 573 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382B  ILE*     3.7    23.3    -      -       +      -
    386B  LEU*     4.2    16.6    -      -       +      -
    401B  LEU*     3.5    25.4    -      -       +      -
    403B  ASP      3.7     4.7    -      -       -      -
    404B  LEU*     3.7    20.0    -      -       +      -
    427B  TRP*     3.7    30.5    -      -       +      -
    484B  LEU*     3.1    11.3    -      -       -      +
    485B  LEU*     2.8    41.1    +      -       +      +
    487B  LEU*     4.2    12.6    -      -       +      -
    571B  TYR*     4.3     4.7    -      -       +      +
    572B  LEU*     1.3    75.6    -      -       -      +
    574B  LYS*     1.3    60.3    +      -       -      +
    575B  VAL*     3.6     8.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 574 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237B  ARG      5.7     0.4    +      -       -      -
    240B  GLU*     4.4    23.6    +      -       -      +
    241B  LEU*     5.1     5.9    -      -       +      +
    244B  LEU*     4.4    13.8    -      -       +      +
    401B  LEU*     3.7     2.4    -      -       -      +
    402B  LEU*     2.8    48.9    +      -       +      +
    403B  ASP*     3.0    29.6    +      -       +      +
    405B  PHE*     4.6    12.9    -      -       +      -
    482B  THR*     4.0    25.1    -      -       +      -
    484B  LEU*     3.5    20.6    -      -       +      -
    572B  LEU      4.0     1.6    +      -       -      -
    573B  LEU*     1.3    71.7    -      -       -      +
    575B  VAL*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 575 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386B  LEU*     4.7     4.5    -      -       +      -
    399B  MET*     3.7    30.7    -      -       +      -
    400B  THR      3.5     6.5    -      -       -      +
    401B  LEU*     4.4     5.6    -      -       +      -
    402B  LEU*     4.4     3.4    -      -       -      -
    481B  ASN      3.6     0.2    -      -       -      +
    482B  THR*     3.4     6.8    -      -       -      +
    483B  GLY      2.8    38.8    +      -       -      +
    485B  LEU*     4.4    21.3    -      -       +      +
    573B  LEU*     3.8    28.0    -      -       +      +
    574B  LYS*     1.3    79.4    -      -       -      +
    576B  GLN*     1.3    75.1    +      -       -      +
    577B  PHE*     3.8    13.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 576 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399B  MET*     3.3     4.5    -      -       -      -
    400B  THR*     2.7    55.6    +      -       -      +
    402B  LEU*     3.6    34.0    -      -       +      +
    481B  ASN*     3.6    22.2    -      -       -      +
    482B  THR*     4.8     1.6    -      -       -      +
    575B  VAL*     1.3    72.8    -      -       -      +
    577B  PHE*     1.3    62.1    +      -       -      +
    578B  ASN*     2.7    26.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 577 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397B  TYR*     3.6    37.2    -      +       +      -
    398B  THR      3.6     3.1    -      -       -      +
    399B  MET*     4.2     6.7    -      -       +      +
    471B  ALA*     3.7    36.1    -      -       +      -
    474B  CYS*     3.9    12.6    -      -       +      -
    476B  ALA*     3.6    19.3    -      -       +      -
    481B  ASN*     2.7    46.6    +      -       -      +
    483B  GLY*     3.8    21.3    -      -       -      -
    485B  LEU*     5.6     1.1    -      -       +      -
    575B  VAL*     3.9    17.0    -      -       +      -
    576B  GLN*     1.3    74.6    -      -       -      +
    578B  ASN*     1.3    61.7    +      -       -      +
    579B  PHE*     3.4    22.8    +      +       +      -
    580B  GOL      3.7    10.1    -      -       -      -
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Residues in contact with ASN 578 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397B  TYR*     3.2     6.2    -      -       -      +
    398B  THR*     2.6    60.2    +      -       -      +
    399B  MET      3.9     0.6    -      -       -      -
    400B  THR*     2.8    27.7    +      -       -      +
    481B  ASN*     5.4     0.3    +      -       -      -
    576B  GLN*     2.7    34.0    +      -       -      +
    577B  PHE*     1.3    70.0    -      -       -      +
    579B  PHE*     1.3    64.2    +      -       -      +
----------------------------------------------------------
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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