Contacts of the strand formed by residues 33 - 38 (chain B) in PDB entry 1K4C


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 33 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     4.2     4.3    -      -       +      -
     23B  CYS*     3.8    26.2    -      -       -      -
     29B  ILE*     3.9    20.9    -      -       +      -
     31B  THR      2.9     6.5    +      -       -      -
     32B  ASP*     1.3    73.4    -      -       -      +
     34B  HIS*     1.3    64.5    +      -       -      +
     35B  TRP*     4.3    10.8    -      -       -      +
     50B  TYR      3.2     5.5    +      -       -      -
     51B  ALA*     2.7    47.0    +      -       +      -
     71B  PHE*     3.4    40.8    -      -       +      -
     88B  CYS*     4.1    11.4    -      -       +      -
     89B  GLN      3.4    23.6    -      -       -      +
     90B  GLN*     4.1     3.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  GLY      3.5    22.7    +      -       -      -
    104A  TYR*     3.6    18.2    -      +       +      +
     32B  ASP      4.3     1.4    -      -       -      -
     33B  ILE*     1.3    79.2    -      -       -      +
     35B  TRP*     1.3    64.9    +      -       -      +
     36B  TYR*     3.9    12.0    -      -       +      +
     46B  LEU*     4.3     2.5    -      -       +      -
     48B  ILE      3.4     9.2    -      -       -      +
     49B  LYS*     3.6     4.8    -      -       -      -
     50B  TYR*     3.0    55.8    +      +       -      -
     87B  TYR      3.8     0.5    -      -       -      +
     88B  CYS*     3.3     4.2    -      -       -      -
     89B  GLN*     2.8    55.4    +      -       -      +
     91B  SER*     3.0    23.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLN*     3.7    20.9    -      -       -      -
     21B  PHE*     4.0    24.2    -      -       +      -
     22B  SER      4.1     5.6    -      -       -      -
     23B  CYS*     3.5    33.4    -      -       +      -
     33B  ILE*     4.3    16.1    -      -       +      +
     34B  HIS*     1.3    78.6    -      -       -      +
     36B  TYR*     1.3    57.9    +      -       -      +
     46B  LEU*     3.7     5.2    -      -       -      +
     47B  LEU*     2.8    33.1    +      -       +      -
     48B  ILE*     2.9    37.8    +      -       +      +
     51B  ALA      4.8     3.7    +      -       -      -
     64B  GLY*     5.6     0.2    -      -       -      -
     65B  SER      5.8     0.2    +      -       -      -
     71B  PHE*     4.3     6.4    -      -       +      +
     72B  THR      4.0    11.9    +      -       -      -
     73B  LEU*     3.6    54.1    -      -       +      +
     86B  TYR*     4.8     3.6    -      -       +      -
     87B  TYR      3.4    20.9    -      -       -      -
     88B  CYS*     4.0     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  LEU*     5.7     0.9    -      -       +      -
    104A  TYR*     3.7     5.5    -      -       -      +
    105A  PHE*     2.8    46.5    +      +       +      -
    108A  TRP*     3.6    22.7    -      +       -      -
     34B  HIS*     3.9    10.1    -      -       +      -
     35B  TRP*     1.3    73.6    -      -       -      +
     37B  GLN*     1.3    60.7    +      -       -      +
     44B  PRO*     4.3     9.6    -      -       +      -
     45B  ARG      3.3    10.8    -      -       -      +
     46B  LEU*     3.7    28.9    -      -       +      -
     47B  LEU*     4.0     4.7    -      -       -      -
     85B  ASN      3.9     0.2    -      -       -      +
     86B  TYR*     3.4     8.0    -      -       -      +
     87B  TYR*     2.8    49.8    +      -       +      +
     89B  GLN*     2.6    46.3    +      -       +      -
     98B  PHE*     4.4     9.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  TYR*     1.3    73.0    -      -       -      +
     38B  GLN*     1.3    64.4    +      -       -      +
     39B  ARG*     3.2    42.0    +      -       +      +
     43B  SER      3.9     1.2    -      -       -      +
     44B  PRO*     3.4     2.1    -      -       -      +
     45B  ARG*     2.8    44.7    +      -       +      +
     47B  LEU*     3.6    27.6    -      -       +      +
     62B  PHE*     3.9    16.2    -      -       -      -
     81B  GLU      4.2     6.7    +      -       -      -
     82B  ASP*     4.3     2.2    +      -       -      +
     84B  ALA*     3.9    16.8    -      -       +      +
     85B  ASN      3.6     3.1    -      -       -      -
     86B  TYR*     3.0    27.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  GLN*     3.0    43.1    +      -       -      -
     45A  LEU*     4.3     0.5    -      -       -      +
     95A  TYR*     3.2     8.7    +      -       -      -
     37B  GLN*     1.3    76.4    -      -       -      +
     39B  ARG*     1.3    64.4    +      -       -      +
     42B  GLY      3.0    30.1    +      -       -      +
     43B  SER      4.3     3.8    -      -       -      -
     44B  PRO*     3.9    23.5    -      -       +      +
     84B  ALA*     3.7     3.0    -      -       -      -
     85B  ASN*     2.8    43.6    +      -       +      +
     87B  TYR*     3.7    21.6    +      -       +      -
----------------------------------------------------------
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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