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


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 LEU 33 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4K  LEU*     3.6    28.0    -      -       +      -
     23K  CYS*     4.4     3.4    -      -       +      -
     29K  ILE*     3.6    26.0    -      -       +      -
     31K  ASN      2.6    12.8    +      -       -      +
     32K  PHE*     1.3    72.7    -      -       -      +
     34K  ASN*     1.3    68.3    +      -       -      +
     35K  TRP*     3.2    41.4    -      -       +      +
     49K  TYR      3.9     1.0    +      -       -      -
     50K  TYR*     3.4     3.3    +      -       -      +
     51K  THR*     3.0    26.7    +      -       -      +
     71K  TYR*     3.5    40.8    -      -       +      -
     88K  CYS*     4.6     1.3    -      -       +      -
     89K  GLN      3.2     8.1    -      -       -      +
     91K  HIS*     3.9     1.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 34 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107J  TYR      3.4     9.5    +      -       -      +
    108J  ALA*     3.7     5.3    -      -       -      -
     33K  LEU*     1.3    75.7    -      -       -      +
     35K  TRP*     1.3    65.0    +      -       -      +
     36K  TYR*     3.9    20.0    -      -       +      -
     46K  LEU*     4.4     2.5    -      -       +      -
     48K  ILE      3.2     9.6    -      -       -      +
     49K  TYR*     3.1    30.2    -      -       -      +
     50K  TYR      3.1     9.3    -      -       -      +
     88K  CYS*     3.3     9.2    -      -       -      +
     89K  GLN*     2.9    46.5    +      -       +      -
     91K  HIS*     3.0    28.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 35 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6K  GLN*     4.3     4.5    -      -       -      -
     21K  ILE*     4.1    13.7    -      -       +      -
     22K  SER*     4.1    11.2    -      -       -      -
     23K  CYS*     3.4    39.3    -      -       -      -
     33K  LEU*     3.2    26.9    -      -       +      +
     34K  ASN*     1.3    77.8    -      -       -      +
     36K  TYR*     1.3    63.8    +      -       -      +
     46K  LEU*     4.1     1.1    -      -       -      +
     47K  LEU*     2.9    31.2    +      -       +      +
     48K  ILE*     2.9    34.1    +      -       +      +
     51K  THR      4.9     5.3    +      -       -      -
     64K  GLY*     5.9     0.2    -      -       -      -
     65K  SER      5.8     0.4    +      -       -      -
     71K  TYR*     4.7     0.4    -      -       -      +
     72K  SER*     3.6    33.7    +      -       -      +
     73K  LEU*     3.6    45.5    -      -       +      -
     86K  TYR*     4.6     7.4    -      -       +      -
     87K  PHE      3.2    25.4    -      -       -      -
     88K  CYS*     3.8     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 36 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46J  LEU*     5.9     0.2    -      -       +      -
    109J  MET*     3.2    37.3    +      -       +      +
    112J  TRP*     3.4    30.1    -      +       -      -
     34K  ASN*     3.8    15.0    +      -       +      -
     35K  TRP*     1.3    77.4    -      -       -      +
     37K  GLN*     1.3    60.7    +      -       -      +
     38K  GLN      4.2     0.2    -      -       -      -
     44K  ILE*     4.6    12.3    -      -       +      -
     45K  LYS      3.3    17.5    -      -       -      +
     46K  LEU*     3.7    11.2    -      -       +      -
     47K  LEU*     4.2     1.8    -      -       -      -
     86K  TYR*     3.3     9.0    -      -       -      +
     87K  PHE*     3.0    38.2    +      -       +      +
     88K  CYS*     4.8     2.9    -      -       -      -
     89K  GLN*     2.6    51.8    +      -       +      -
     98K  PHE*     3.9    18.2    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 37 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36K  TYR*     1.3    73.7    -      -       -      +
     38K  GLN*     1.3    61.2    +      -       -      +
     39K  LYS*     3.8    24.1    +      -       -      +
     43K  THR      3.7     1.4    -      -       -      +
     44K  ILE*     3.6     1.6    -      -       -      -
     45K  LYS*     2.9    50.0    +      -       +      +
     47K  LEU*     3.5    28.5    -      -       +      +
     62K  PHE*     4.2    11.9    -      -       -      -
     81K  GLU*     4.6     8.3    +      -       -      +
     82K  ASP*     4.4     4.6    +      -       -      +
     84K  ALA*     3.9    19.5    -      -       +      -
     85K  THR      3.4     2.9    -      -       -      -
     86K  TYR*     3.1    33.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 38 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40J  LEU*     3.0    33.6    -      -       +      +
     44J  ASN*     4.8     5.3    +      -       -      +
     95J  TYR*     4.8     7.2    -      -       +      +
     36K  TYR      4.2     0.4    -      -       -      -
     37K  GLN*     1.3    69.7    -      -       -      +
     39K  LYS*     1.3    75.8    +      -       -      +
     40K  PRO*     5.3     2.4    +      -       -      +
     42K  GLY*     4.9     4.4    -      -       -      -
     43K  THR      3.3    12.1    -      -       -      +
     44K  ILE*     4.3    12.6    -      -       +      +
     84K  ALA*     3.1     3.9    -      -       -      +
     85K  THR*     2.6    68.8    +      -       -      +
     87K  PHE*     3.9    19.1    -      -       +      -
----------------------------------------------------------
 Back to top of page


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