Contacts of the strand formed by residues 89 - 94 (chain B) in PDB entry 6DDE


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 LYS 89 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ALA*     4.5     2.3    -      -       -      +
     15A  ARG*     5.1     3.8    -      -       -      +
     16A  SER*     2.4    39.4    +      -       -      +
     19A  ILE*     3.6    33.2    -      -       +      -
     20A  ASP*     3.5    24.6    +      -       +      +
     23A  LEU*     4.3     5.8    -      -       +      -
     52B  ARG      3.8     7.7    +      -       -      -
     53B  GLY*     3.7    14.1    -      -       -      -
     80B  ILE*     3.9    15.9    -      -       +      -
     81B  ILE      3.8     8.5    -      -       -      +
     82B  TRP*     3.5    37.8    -      -       +      +
     87B  THR      5.1     2.0    +      -       -      -
     88B  ASN*     1.3    78.7    -      -       -      +
     90B  VAL*     1.3    67.4    +      -       -      +
     91B  HIS      4.8     2.5    -      -       -      +
    102E  TYR*     5.3     1.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ARG*     3.3    24.9    +      -       -      +
     19A  ILE*     5.5     3.3    -      -       -      +
     69B  LEU*     4.2    11.2    -      -       +      -
     81B  ILE*     3.1    31.1    +      -       +      +
     82B  TRP      4.1     6.1    -      -       -      +
     83B  ASP*     4.9     7.9    -      -       +      +
     88B  ASN*     5.9     1.1    -      -       +      -
     89B  LYS*     1.3    79.9    -      -       -      +
     91B  HIS*     1.3    89.3    +      -       +      +
    102E  TYR*     3.8    31.9    -      -       +      -
    103E  TYR*     4.0    20.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ARG*     3.9    13.9    +      -       -      +
     19A  ILE*     4.6     6.8    -      -       -      +
     80B  ILE*     3.2     6.8    -      -       -      +
     81B  ILE*     2.9    53.3    +      -       +      +
     89B  LYS*     3.9     1.1    -      -       -      +
     90B  VAL*     1.3   105.9    +      -       +      +
     92B  ALA*     1.3    60.1    +      -       -      +
     93B  ILE*     3.8    11.2    -      -       +      -
    126B  LEU*     4.6    19.7    +      -       +      +
    127B  LYS*     5.5     3.0    +      -       -      -
    132B  ASN*     5.8     2.9    -      -       -      +
    133B  VAL*     3.5    28.1    +      -       +      +
    102E  TYR*     3.8    33.3    +      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ILE*     3.8    31.7    -      -       +      +
     22A  ASN*     6.3     1.1    -      -       +      -
     23A  LEU*     4.1    16.4    -      -       +      -
     78B  LYS*     5.2     4.7    +      -       +      +
     79B  LEU      3.8     0.2    -      -       -      -
     80B  ILE*     3.7    22.0    -      -       +      -
     91B  HIS*     1.3    73.3    -      -       -      +
     93B  ILE*     1.3    63.7    +      -       -      +
     94B  PRO*     3.3     9.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77B  GLY      4.0     0.2    -      -       -      +
     78B  LYS*     3.9     4.9    -      -       -      -
     79B  LEU*     2.9    54.7    +      -       +      +
     81B  ILE*     4.1     8.3    -      -       +      -
     91B  HIS*     4.2     9.0    -      -       +      -
     92B  ALA*     1.3    70.8    -      -       -      +
     94B  PRO*     1.3    76.8    -      -       +      +
     95B  LEU*     3.8     1.0    +      -       -      +
    112B  VAL*     4.3     2.2    -      -       +      -
    124B  TYR*     3.6    35.0    -      -       +      -
    126B  LEU*     3.8    29.4    -      -       +      -
    133B  VAL*     3.7    32.3    -      -       +      -
    135B  VAL*     6.1     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  LYS*     3.2    28.9    -      -       -      +
     92B  ALA      3.3     9.6    -      -       -      +
     93B  ILE*     1.3    98.4    -      -       +      +
     95B  LEU*     1.3    62.1    +      -       -      +
    124B  TYR*     4.4     2.6    +      -       -      -
    132B  ASN*     6.3     1.8    -      -       -      +
    133B  VAL*     4.9     7.2    -      -       +      -
    135B  VAL*     5.4     5.4    -      -       -      +
----------------------------------------------------------
 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