Contacts of the strand formed by residues 463 - 471 (chain B) in PDB entry 1KEK


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 ILE 463 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1199A  ASP      5.3     0.3    -      -       -      +
    423B  TRP*     3.4    37.7    -      -       +      -
    424B  GLY      3.9     0.2    -      -       -      +
    454B  SER      4.1     0.2    -      -       -      +
    455B  TYR      3.7     2.0    -      -       -      -
    456B  ASP*     2.8    52.7    +      -       -      +
    462B  GLY*     1.3    72.6    -      -       -      -
    464B  THR*     1.3    71.9    +      -       -      +
    465B  ILE*     3.9    11.3    -      -       +      +
    494B  TYR*     3.4    28.3    -      -       +      +
    498B  TYR*     4.0    27.1    -      -       +      +
    649B  GLN*     4.8    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 464 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1199A  ASP*     4.9     2.8    +      -       -      +
    422B  PHE      3.7     0.3    -      -       -      +
    423B  TRP*     3.6     0.5    -      -       -      -
    424B  GLY*     2.9    40.2    +      -       -      +
    425B  LEU      5.6     0.7    -      -       -      -
    426B  GLY*     4.7    12.5    -      -       -      -
    430B  THR*     6.1     2.2    -      -       -      -
    431B  VAL*     3.4    32.4    -      -       +      +
    453B  PHE*     4.7     2.5    -      -       +      -
    454B  SER      3.3    13.9    -      -       -      +
    455B  TYR*     3.7    25.2    -      -       +      -
    462B  GLY      4.0     0.7    +      -       -      -
    463B  ILE*     1.3    77.9    -      -       -      +
    465B  ILE*     1.3    75.8    +      -       -      +
    466B  SER*     4.0     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 465 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421B  GLN*     3.9    20.6    -      -       +      -
    422B  PHE      3.3     8.5    -      -       -      +
    423B  TRP*     3.9    31.0    -      -       +      +
    453B  PHE*     3.7     0.2    -      -       -      -
    454B  SER*     2.8    44.0    +      -       -      +
    463B  ILE*     3.9    25.8    -      -       +      +
    464B  THR*     1.3    79.2    -      -       -      +
    466B  SER*     1.3    75.8    +      -       -      +
    467B  HIS*     3.2    29.9    +      -       +      +
    649B  GLN*     5.6     5.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 466 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421B  GLN*     3.2     8.3    -      -       -      -
    422B  PHE*     2.7    41.8    +      -       -      -
    430B  THR*     4.3     3.6    -      -       -      +
    431B  VAL*     4.0     9.4    -      -       -      +
    434B  ASN*     2.6    35.2    +      -       -      -
    452B  TYR      3.7     4.0    -      -       -      -
    453B  PHE*     3.3    21.9    -      -       -      -
    464B  THR*     4.4     1.4    -      -       -      +
    465B  ILE*     1.3    77.3    -      -       -      +
    467B  HIS*     1.3    63.2    -      -       -      +
    468B  LEU*     4.1     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 467 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420B  CYS      3.5     4.3    -      -       -      -
    421B  GLN*     4.0     8.2    +      -       +      -
    450B  GLN*     3.8     3.2    -      -       -      +
    451B  GLY*     3.4     3.5    -      -       -      -
    452B  TYR*     2.8    48.8    +      -       +      +
    454B  SER*     4.5     6.3    -      -       -      -
    465B  ILE*     3.2    39.9    +      -       +      +
    466B  SER*     1.3    73.3    -      -       -      +
    468B  LEU*     1.3    62.2    +      -       -      +
    469B  ARG*     5.6     3.8    -      -       -      +
    480B  LEU*     3.6    38.2    -      -       +      +
    481B  VAL*     3.0    50.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 468 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418B  ILE      3.9     0.4    -      -       -      +
    419B  GLN*     3.4     2.9    -      -       -      -
    420B  CYS*     2.7    46.0    +      -       +      +
    422B  PHE*     3.9    22.2    -      -       +      -
    434B  ASN*     3.9    30.5    -      -       +      +
    437B  ALA*     4.9     4.7    -      -       +      -
    438B  ILE*     3.8    18.8    -      -       +      -
    450B  GLN      3.3     4.5    -      -       -      +
    451B  GLY*     3.9    15.0    -      -       -      -
    453B  PHE*     4.2     9.9    -      -       +      -
    466B  SER*     4.1     0.9    -      -       -      -
    467B  HIS*     1.3    86.1    -      -       -      +
    469B  ARG*     1.3    64.8    +      -       -      +
    470B  PHE*     3.8    33.0    -      -       +      -
    481B  VAL*     3.9     1.2    -      -       -      +
    567B  PHE*     5.0     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 469 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175B  ARG*     5.5     0.2    -      -       -      +
    413B  THR*     4.1     1.4    -      -       -      +
    417B  THR*     4.2     9.6    -      -       +      -
    418B  ILE      3.2     7.2    -      -       -      +
    419B  GLN*     2.8    32.0    +      -       +      -
    449B  ALA*     3.4     3.1    -      -       -      -
    450B  GLN*     2.7    70.4    +      -       +      +
    467B  HIS*     5.6     2.8    -      -       -      +
    468B  LEU*     1.3    79.8    -      -       -      +
    470B  PHE*     1.3    67.3    +      -       -      +
    475B  ILE*     4.0    16.4    -      -       +      -
    477B  SER*     3.2    28.5    +      -       -      -
    479B  TYR*     3.1    37.6    +      -       -      -
    480B  LEU*     3.1    28.5    +      -       -      +
    481B  VAL*     3.5    16.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 470 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416B  GLY      3.8     0.7    -      -       -      +
    417B  THR*     3.3     5.3    -      -       -      -
    418B  ILE*     2.8    39.0    +      -       +      +
    420B  CYS*     4.8     2.5    -      -       -      -
    438B  ILE*     4.2    15.3    -      -       +      -
    441B  ILE*     3.8    33.4    -      -       +      -
    447B  LEU*     4.5     7.9    -      -       +      -
    448B  PHE      3.2     7.4    -      -       -      +
    449B  ALA*     3.6    28.9    -      -       +      -
    468B  LEU*     3.8    37.5    -      -       +      -
    469B  ARG*     1.3    75.2    -      -       -      +
    471B  GLY*     1.3    60.6    +      -       -      +
    475B  ILE*     4.4     0.9    -      -       -      -
    567B  PHE*     3.6    28.9    -      +       -      -
    573B  VAL*     3.8    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 471 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416B  GLY      3.8    10.8    -      -       -      -
    417B  THR*     4.3     9.0    -      -       -      -
    447B  LEU*     3.5    12.6    -      -       -      +
    448B  PHE*     2.7    41.1    +      -       -      +
    470B  PHE*     1.3    76.7    -      -       -      +
    472B  GLU*     1.3    64.0    +      -       -      -
    473B  LYS      3.2     8.7    -      -       -      -
    475B  ILE*     4.2     2.7    -      -       -      +
----------------------------------------------------------
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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