Contacts of the strand formed by residues 49 - 53 (chain B) in PDB entry 1KOJ


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 HIS 49 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547A  PHE*     3.9    19.4    -      -       +      -
    550A  GLN*     4.9     5.7    +      -       -      -
    551A  GLN*     3.6    27.3    +      -       -      +
     42B  THR*     4.2    14.4    -      -       +      +
     43B  LEU      3.2     6.1    +      -       -      +
     44B  ASN*     3.4    43.1    +      -       +      +
     48B  GLY*     1.3    81.2    -      -       -      -
     50B  ILE*     1.3    62.8    +      -       -      +
     51B  LEU      4.1     0.4    -      -       -      -
    477B  VAL      3.9     0.2    -      -       -      +
    478B  PHE*     3.2     6.8    -      -       -      +
    479B  THR*     2.9    35.2    +      -       -      +
    485B  ILE*     5.1     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 50 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    547A  PHE*     4.6     1.3    -      -       -      -
     41B  LEU      3.7     1.4    -      -       -      +
     42B  THR*     3.5     1.7    -      -       -      -
     43B  LEU*     2.7    55.9    +      -       +      +
     45B  THR*     4.6    11.0    -      -       +      -
     49B  HIS*     1.3    80.7    -      -       -      +
     51B  LEU*     1.3    62.6    +      -       -      +
     52B  LEU*     3.9     3.8    +      -       +      +
    302B  MET*     4.6    12.6    -      -       +      -
    476B  ILE*     4.3    23.1    -      -       +      -
    477B  VAL      3.5     4.3    -      -       -      +
    478B  PHE*     4.1    11.0    -      -       +      -
    485B  ILE*     4.4    16.6    -      -       +      -
    488B  ALA*     4.4    22.7    -      -       +      -
    489B  LEU*     4.3    19.1    -      -       +      -
    492B  MET*     5.2     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543A  GLY      4.6     0.4    -      -       -      +
    544A  LEU*     3.9    22.2    -      -       +      -
    547A  PHE*     3.5    49.0    -      -       +      -
     36B  PHE*     4.2    27.4    -      -       +      -
     40B  SER*     4.3     5.4    -      -       -      -
     41B  LEU      3.5     7.6    -      -       -      +
     42B  THR*     3.5    21.3    -      -       -      +
     50B  ILE*     1.3    73.7    -      -       -      +
     52B  LEU*     1.3    68.1    +      -       -      +
     53B  ASP*     4.3     6.5    -      -       +      +
    475B  SER      3.5     1.0    -      -       -      +
    476B  ILE*     3.3     6.8    -      -       -      +
    477B  VAL*     2.7    41.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  SER*     3.4     2.3    -      -       -      -
     41B  LEU*     2.7    53.7    +      -       +      +
     43B  LEU*     6.3     2.2    -      -       +      -
     50B  ILE*     3.9     6.6    +      -       +      +
     51B  LEU*     1.3    72.3    -      -       -      +
     53B  ASP*     1.3    66.4    +      -       -      +
     54B  TYR*     3.7    16.7    +      -       +      -
    315B  ALA*     4.1    27.6    -      -       +      +
    318B  LEU*     4.9     5.8    -      -       +      -
    319B  LEU*     3.8    41.3    -      -       +      -
    322B  LEU*     6.4     0.2    -      -       +      -
    474B  ASN*     4.6     8.7    -      -       +      +
    475B  SER      3.8     1.8    -      -       -      +
    476B  ILE*     3.9    21.3    -      -       +      +
    492B  MET*     5.4     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540A  SER*     2.7    22.4    +      -       -      -
    544A  LEU*     3.5    25.1    -      -       +      +
     36B  PHE*     3.4    29.8    -      -       +      -
     39B  PHE      3.8     0.9    -      -       -      +
     40B  SER*     4.2     5.2    -      -       -      -
     51B  LEU*     3.8     3.5    -      -       +      -
     52B  LEU*     1.3    72.2    -      -       -      +
     54B  TYR*     1.3    58.8    +      -       -      +
     55B  SER*     2.6    29.1    +      -       -      -
     56B  LYS*     4.5     3.0    +      -       -      +
    473B  THR      4.4     1.4    -      -       -      +
    474B  ASN*     3.7     2.8    -      -       -      -
    475B  SER*     2.9    39.9    +      -       -      +
----------------------------------------------------------
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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