Contacts of the strand formed by residues 534 - 540 (chain A) in PDB entry 2CKH


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 TRP 534 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    466A  LEU*     2.8    30.6    +      -       +      -
    467A  ASN      4.1     0.4    -      -       -      -
    468A  ASP*     3.9    21.3    -      -       -      -
    471A  ILE*     4.3    16.2    -      -       +      -
    495A  THR*     3.9    15.5    -      -       +      -
    527A  PRO*     5.4     1.3    -      -       +      -
    528A  ILE      3.4    23.6    -      -       -      -
    529A  HIS*     4.0    15.7    -      +       +      -
    533A  HIS*     1.3    86.8    +      -       -      +
    535A  CYS*     1.3    73.7    +      -       -      +
    550A  ASP*     4.5     0.9    -      -       -      +
    551A  SER*     5.1     1.7    +      -       -      -
    602A  CYS*     3.8    10.4    -      -       -      +
    603A  GLY*     3.4    37.6    -      -       -      +
    606A  ALA*     4.7     5.1    -      -       +      +
     89B  GLN*     3.3    43.5    -      -       +      -
     90B  THR      4.5     0.4    -      -       -      -
     91B  GLY*     3.2    38.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 535 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    527A  PRO*     3.8     2.8    -      -       -      +
    528A  ILE*     2.8    40.1    +      -       +      +
    530A  LEU*     4.8     3.1    -      -       +      -
    533A  HIS*     3.4    24.0    -      -       -      -
    534A  TRP*     1.3    85.5    -      -       -      +
    536A  LEU*     1.3    61.2    +      -       -      +
    548A  TYR*     3.0    38.6    -      -       +      +
    549A  TYR      3.7     3.6    -      -       -      +
    550A  ASP*     3.6    19.3    -      -       -      -
    606A  ALA*     4.5    11.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 536 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    475A  MET*     4.7     9.6    -      -       +      -
    525A  LEU*     4.5     8.5    -      -       +      -
    526A  VAL      2.9    38.4    -      -       -      +
    527A  PRO*     3.7     9.2    -      -       +      -
    528A  ILE*     3.7     3.6    -      -       -      -
    535A  CYS*     1.3    77.4    -      -       -      +
    537A  ALA*     1.3    65.2    +      -       -      +
    538A  VAL*     4.0    16.8    -      -       +      -
    548A  TYR*     3.4     2.6    -      -       -      -
    549A  TYR*     2.6    49.4    +      -       +      +
    606A  ALA*     3.8    21.7    -      -       +      +
    609A  TYR*     4.5     2.9    -      -       +      -
    610A  ALA*     3.6    34.1    -      -       +      +
    613A  ILE*     4.5     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 537 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    526A  VAL*     2.7    45.1    +      -       +      +
    528A  ILE*     3.4    18.1    -      -       +      +
    536A  LEU*     1.3    74.5    -      -       -      +
    538A  VAL*     1.3    64.0    +      -       -      +
    546A  ILE*     5.2     2.0    -      -       +      -
    547A  THR      3.6     7.0    -      -       -      +
    548A  TYR*     4.2    11.9    -      -       +      +
    559A  ALA*     5.4     2.7    -      -       +      -
    560A  CYS*     5.8     0.4    -      -       -      -
    563A  LEU*     3.7    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 538 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523A  ILE*     3.5    26.7    -      -       +      -
    524A  LEU      3.5     2.7    -      -       -      -
    525A  LEU*     4.1     8.3    -      -       +      -
    536A  LEU*     4.0    11.7    -      -       +      -
    537A  ALA*     1.3    78.2    -      -       -      +
    539A  VAL*     1.3    67.7    +      -       -      +
    540A  ASP*     4.3     7.4    -      -       +      +
    545A  ASN      3.5     4.0    -      -       -      +
    546A  ILE*     3.4     4.0    -      -       -      +
    547A  THR*     2.9    40.9    +      -       +      +
    549A  TYR*     3.5    26.9    -      -       +      +
    613A  ILE*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 539 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523A  ILE*     3.2     5.7    -      -       -      +
    524A  LEU*     2.7    70.0    +      -       +      +
    526A  VAL*     5.0     5.1    -      -       +      +
    537A  ALA      4.3     0.2    +      -       -      -
    538A  VAL*     1.3    72.3    -      -       -      +
    540A  ASP*     1.3    58.5    +      -       -      +
    541A  PHE*     3.6    17.6    +      -       +      -
    546A  ILE*     3.7    29.4    -      -       +      -
    563A  LEU*     4.8    13.7    -      -       +      -
    567A  LEU*     4.3    15.0    -      -       +      -
    584A  TRP*     4.2    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 540 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    522A  ASP      3.9     4.7    -      -       -      +
    523A  ILE*     4.1    11.8    -      -       -      +
    538A  VAL*     3.5    14.3    +      -       +      +
    539A  VAL*     1.3    72.4    -      -       -      +
    541A  PHE*     1.3    52.8    +      -       -      +
    542A  ARG*     3.0    27.3    +      -       -      +
    543A  LYS*     2.8    58.7    +      -       +      +
    544A  LYS*     2.7    36.2    +      -       -      -
    545A  ASN*     3.5    16.2    +      -       -      +
    547A  THR*     5.7     1.8    -      -       +      -
    584A  TRP*     4.0     2.9    -      -       -      -
    613A  ILE*     5.6     2.4    -      -       -      +
    616A  ASP*     5.4     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