Contacts of the strand formed by residues 46 - 53 (chain J) 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 46 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38J  ILE*     3.6    22.4    -      -       +      -
     39J  ARG      3.4    16.2    -      -       -      +
     40J  LEU*     3.5    24.7    -      -       +      -
     44J  ASN      4.2     1.0    +      -       -      -
     45J  LYS*     1.3    75.5    -      -       -      +
     47J  GLU*     1.3    61.5    +      -       -      +
     95J  TYR*     5.1     1.8    -      -       +      -
     36K  TYR*     5.9     0.7    -      -       +      -
     44K  ILE*     4.4    14.6    -      -       +      -
     87K  PHE*     3.6    41.9    -      -       +      -
     97K  THR*     5.5     2.1    -      -       -      +
     98K  PHE*     3.5    56.3    +      -       +      +
     99K  GLY      4.5     3.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 47 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38J  ILE*     3.4     7.2    -      -       -      +
     39J  ARG*     2.7    71.0    +      -       -      -
     41J  PHE*     4.1    14.5    -      -       +      -
     45J  LYS*     3.9     2.4    +      -       +      +
     46J  LEU*     1.3    75.5    -      -       -      +
     48J  TRP*     1.3    65.4    +      -       -      +
     49J  VAL*     3.4     1.7    +      -       -      +
     61J  ASN*     4.2    16.3    -      -       -      +
     63J  SER*     4.7     8.4    +      -       -      -
     64J  LEU*     3.4    23.9    -      -       -      +
     98K  PHE*     4.4     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 48 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36J  ASN*     3.3    20.9    +      -       +      +
     37J  TRP      4.2     1.3    -      -       -      -
     38J  ILE*     4.1    20.0    -      -       +      -
     47J  GLU*     1.3    73.3    -      -       -      +
     49J  VAL*     1.3    59.6    +      -       -      +
     50J  GLY*     3.3    24.6    -      -       -      +
     51J  TYR*     3.8    14.8    -      +       -      -
     59J  ASN*     3.0    39.7    -      -       -      -
     60J  TYR      3.8     1.8    -      -       -      -
     61J  ASN*     2.9    55.1    +      -       +      +
     62J  PRO*     5.1     0.2    -      -       +      -
    109J  MET*     5.1     1.8    -      -       +      -
     94K  PHE*     4.2     7.6    -      +       +      -
     95K  PRO*     3.6    31.9    -      -       +      -
     96K  TRP*     3.4    48.7    +      +       +      +
     98K  PHE*     4.2    10.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 49 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37J  TRP*     3.0    25.5    +      -       +      +
     38J  ILE*     3.8    14.4    -      -       -      +
     39J  ARG*     4.0    24.9    -      -       +      +
     47J  GLU*     4.0     4.9    -      -       -      +
     48J  TRP*     1.3    73.3    -      -       -      +
     50J  GLY*     1.3    58.9    +      -       -      +
     60J  TYR*     3.8     0.2    -      -       -      -
     61J  ASN*     3.1    21.8    +      -       -      +
     64J  LEU*     3.5    16.6    -      -       +      -
     68J  LEU*     3.2    36.3    -      -       +      +
     70J  ILE*     5.3     1.1    -      -       +      -
     81J  LEU*     4.2    18.8    -      -       +      -
     83J  LEU*     5.9     1.6    -      -       +      -
     94J  TYR*     4.8     7.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 50 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36J  ASN*     3.4     1.4    -      -       -      +
     37J  TRP*     3.0    26.9    +      -       -      +
     48J  TRP*     3.3    24.4    -      -       -      -
     49J  VAL*     1.3    81.3    -      -       -      +
     51J  TYR*     1.3    60.4    +      -       -      -
     59J  ASN      3.4     7.2    -      -       -      -
     60J  TYR*     4.0     3.4    -      -       -      -
     70J  ILE*     3.6    15.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 51 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34J  TYR*     4.1    41.0    +      +       +      -
     35J  TRP      3.1    18.4    -      -       -      +
     36J  ASN*     3.6    24.0    -      -       -      +
     48J  TRP*     3.9    12.1    -      +       -      -
     50J  GLY*     1.3    75.0    -      -       -      +
     52J  ILE*     1.3    72.1    +      -       -      +
     53J  SER*     4.0     1.8    -      -       -      -
     57J  ASP*     3.9    13.9    -      -       +      -
     58J  ASN*     3.5    21.3    +      -       -      +
     59J  ASN*     3.2    33.6    +      -       +      +
     70J  ILE*     3.7    10.3    -      -       -      +
    107J  TYR*     5.2     0.5    +      -       -      -
     94K  PHE*     3.6    40.1    -      +       -      -
     96K  TRP*     4.6     3.8    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 52 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29J  ILE*     5.5     1.6    -      -       +      -
     35J  TRP*     3.0    43.3    +      -       +      +
     51J  TYR*     1.3    80.8    -      -       -      +
     53J  SER*     1.3    70.2    +      -       -      +
     56J  GLY*     4.2    14.1    -      -       -      +
     57J  ASP      3.4     8.5    -      -       -      +
     58J  ASN*     3.8    13.5    -      -       -      +
     70J  ILE*     3.9    28.9    -      -       +      +
     71J  THR*     4.1     4.5    -      -       -      -
     72J  ARG*     3.8    38.8    -      -       +      +
     79J  PHE*     4.1    13.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 53 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29J  ILE*     4.8     0.2    -      -       -      +
     33J  TYR      3.9     1.8    -      -       -      -
     34J  TYR*     3.5    34.5    -      -       -      -
     35J  TRP*     4.2     4.0    -      -       -      -
     51J  TYR*     4.0     2.9    -      -       -      -
     52J  ILE*     1.3    81.9    -      -       -      +
     54J  ASN*     1.3    64.3    +      -       -      +
     55J  VAL*     3.1    13.4    +      -       -      +
     56J  GLY      3.3     8.0    +      -       -      -
     57J  ASP*     3.1    37.4    +      -       -      +
     72J  ARG*     3.2    15.2    +      -       -      -
----------------------------------------------------------
 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