Contacts of the strand formed by residues 993 - 999 (chain K) in PDB entry 6R90


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 GLN 993 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    950K  ASN*     5.6     0.4    -      -       -      +
    977K  CYS*     3.3    17.2    -      -       -      -
    978K  GLN*     3.2     8.0    +      -       +      +
    979K  LYS      5.7     0.2    -      -       -      -
    980K  ASP*     4.6    21.7    +      -       +      +
    991K  HIS*     3.5    31.6    +      -       -      +
    992K  LEU*     1.3    88.3    +      -       -      +
    994K  GLU*     1.3    61.1    +      -       -      +
    995K  VAL*     2.9    28.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 994 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    948K  ASP*     5.3     0.8    -      -       -      +
    950K  ASN*     3.1    42.4    +      -       -      +
    952K  ASN*     4.9     6.6    +      -       -      +
    975K  PHE*     4.9     7.2    -      -       +      +
    976K  VAL      3.7     6.7    -      -       -      +
    977K  CYS*     3.9    13.5    -      -       -      -
    992K  LEU      4.2     0.4    +      -       -      -
    993K  GLN*     1.3    69.1    -      -       -      +
    995K  VAL*     1.3    61.5    +      -       -      +
    996K  GLY      3.4     4.1    +      -       -      +
    997K  LEU*     3.8    34.7    -      -       +      +
   1076K  PHE*     5.4     2.6    -      -       -      -
   1081K  LYS*     3.4    22.8    +      -       -      -
   1083K  GLU*     5.1     0.9    -      -       -      +
   1086K  THR*     5.3     1.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 995 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1K  MET*     3.4    29.2    -      -       +      +
      2K  SER*     4.5    13.1    -      -       -      +
    976K  VAL*     2.9     8.8    +      -       -      +
    978K  GLN*     4.5    22.2    -      -       +      +
    993K  GLN*     3.2    28.5    -      -       +      +
    994K  GLU*     1.3    75.0    -      -       -      +
    996K  GLY*     1.3    57.0    +      -       -      +
   1086K  THR*     3.5    19.4    +      -       -      +
   1087K  GLY*     4.4     5.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 996 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2K  SER      5.5     1.3    -      -       -      -
    975K  PHE*     3.1     9.9    -      -       -      +
    976K  VAL*     2.9    40.8    +      -       -      +
    994K  GLU      3.4     0.7    -      -       -      -
    995K  VAL*     1.3    80.8    +      -       -      +
    997K  LEU*     1.3    66.3    +      -       -      +
   1086K  THR*     3.3    10.5    -      -       -      -
   1087K  GLY*     4.3     5.2    -      -       -      -
   1088K  PHE*     4.2     5.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 997 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    974K  LEU      3.4     3.8    -      -       -      +
    975K  PHE*     3.4    20.2    -      -       +      +
    994K  GLU*     3.8    30.1    -      -       +      +
    996K  GLY*     1.3    83.7    -      -       -      +
    998K  PHE*     1.3    63.9    +      -       -      +
   1076K  PHE*     3.5    41.7    -      -       +      -
   1081K  LYS*     5.4     0.4    -      -       -      +
   1083K  GLU*     3.0    40.8    -      -       -      +
   1084K  PRO      4.8     1.3    -      -       -      +
   1085K  ALA*     3.5     4.1    -      -       -      +
   1086K  THR*     2.7    46.1    +      -       +      +
   1088K  PHE*     3.9     2.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 998 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6K  VAL*     5.4     8.7    -      -       +      -
    973K  ASN*     3.2     5.7    -      -       -      -
    974K  LEU*     2.8    44.8    +      -       +      +
    997K  LEU*     1.3    76.3    -      -       -      +
    999K  HIS*     1.3    72.6    +      -       -      +
   1000K  LEU*     3.3    26.0    +      -       +      -
   1055K  GLN*     6.1     0.2    -      -       -      -
   1074K  ARG*     3.6    43.7    -      -       +      -
   1076K  PHE*     4.6     3.6    -      -       -      +
   1085K  ALA*     4.4    16.2    -      -       +      -
   1088K  PHE*     3.6    42.2    -      +       +      -
   1089K  ILE      4.9     1.3    -      -       -      -
   1090K  ASP*     4.1    28.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 999 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60K  LYS*     5.3     5.1    -      -       +      +
     83K  LYS*     3.5    24.0    +      -       +      -
    971K  ALA      3.8    11.9    +      -       -      -
    972K  PHE*     3.1    27.1    -      +       -      +
    973K  ASN*     3.2    19.8    +      -       -      +
    998K  PHE*     1.3    80.0    -      -       -      +
   1000K  LEU*     1.3    62.0    +      -       -      +
   1001K  GLY*     3.2    24.7    -      -       -      -
   1073K  TRP*     3.4    25.1    +      +       -      +
   1074K  ARG*     3.3    32.1    +      -       -      +
   1075K  SER      3.3    22.5    +      -       -      +
   1076K  PHE      4.6     1.4    -      -       -      +
   1077K  HIS*     4.6     6.2    -      +       +      +
----------------------------------------------------------
 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