Contacts of the strand formed by residues 1024 - 1030 (chain B) in PDB entry 1RQQ


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 GLU1024 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1014B  ASN*     3.8    21.9    +      -       +      +
   1015B  ALA      3.2    10.5    -      -       -      +
   1016B  ARG*     4.8     2.9    -      -       +      -
   1022B  GLU*     3.1    13.2    -      -       -      +
   1023B  ALA*     1.3    81.0    +      -       +      +
   1025B  THR*     1.3    64.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR1025 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1014B  ASN*     3.5     3.8    -      -       -      -
   1015B  ALA      2.8    29.8    +      -       -      -
   1018B  ILE*     3.1    34.4    -      -       +      +
   1019B  ILE*     4.1     8.1    -      -       +      -
   1022B  GLU*     2.7    39.1    +      -       -      +
   1024B  GLU*     1.3    73.8    -      -       -      +
   1026B  ARG*     1.3    77.2    +      -       +      +
   1027B  VAL*     3.4    11.3    +      -       +      +
   1063B  LEU*     4.9     2.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG1026 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1012B  GLU*     3.0    26.6    +      -       -      +
   1013B  GLY      3.4    10.3    -      -       -      +
   1014B  ASN*     4.0    11.8    -      -       -      +
   1024B  GLU      4.5     0.2    +      -       -      -
   1025B  THR*     1.3    79.8    -      -       +      +
   1027B  VAL*     1.3    63.3    +      -       -      +
   1063B  LEU*     5.2     0.7    -      -       -      +
   1078B  LEU*     3.5    33.1    +      -       +      +
   1080B  ALA*     5.8     6.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1027 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    996B  ILE*     5.7     1.1    -      -       +      -
   1012B  GLU*     3.4     9.5    -      -       -      +
   1013B  GLY      2.9    41.5    +      -       -      +
   1014B  ASN      4.6     2.2    -      -       -      +
   1015B  ALA*     4.2    13.9    -      -       +      -
   1018B  ILE*     4.9     0.2    -      -       +      -
   1025B  THR*     3.4    16.6    -      -       +      +
   1026B  ARG*     1.3    80.8    -      -       -      +
   1028B  ALA*     1.3    64.6    +      -       -      +
   1029B  VAL*     4.0    11.9    -      -       +      -
   1063B  LEU*     3.3    28.0    -      -       +      -
   1075B  VAL*     3.6    22.7    -      -       +      -
   1076B  MET      3.4    10.1    -      -       -      +
   1078B  LEU*     3.8     9.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA1028 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1002B  LEU*     4.4     2.7    -      -       +      -
   1010B  VAL*     4.6     2.9    -      -       +      -
   1011B  TYR      3.3     7.0    -      -       -      +
   1027B  VAL*     1.3    77.4    -      -       -      +
   1029B  VAL*     1.3    67.9    +      -       -      +
   1030B  LYS*     4.3     0.4    -      -       +      -
   1074B  VAL      3.8     0.4    -      -       -      +
   1075B  VAL*     3.5     0.9    -      -       -      -
   1076B  MET*     3.1    33.6    +      -       +      +
   1077B  GLU      3.9     5.4    -      -       -      +
   1078B  LEU*     4.1     7.9    -      -       +      +
    117F  112      3.5    44.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1029 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    996B  ILE*     4.3    16.6    -      -       +      -
    998B  LEU*     3.4    18.6    -      -       +      -
   1009B  MET      3.6     1.6    -      -       -      +
   1010B  VAL*     3.4     3.8    -      -       -      +
   1011B  TYR*     2.7    71.8    +      -       +      +
   1012B  GLU      4.3     3.1    -      -       -      +
   1013B  GLY*     5.5     1.6    -      -       -      +
   1027B  VAL*     4.0    12.3    -      -       +      -
   1028B  ALA*     1.3    80.6    -      -       -      +
   1030B  LYS*     1.3    63.7    +      -       -      +
   1031B  THR*     4.7     3.1    -      -       +      -
   1073B  LEU*     5.3     7.0    -      -       +      -
   1074B  VAL      3.4     4.3    -      -       -      +
   1075B  VAL*     3.9    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS1030 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1009B  MET      3.9     3.1    -      -       -      -
   1010B  VAL*     3.9    17.0    -      -       +      +
   1029B  VAL*     1.3    73.4    -      -       -      +
   1031B  THR*     1.3    64.6    +      -       -      +
   1044B  PHE*     3.5    22.9    -      -       +      -
   1047B  GLU*     3.3    36.3    +      -       -      +
   1073B  LEU*     3.7     3.1    -      -       -      +
   1074B  VAL*     2.9    39.0    +      -       +      +
   1076B  MET*     4.1    22.1    -      -       +      +
   1150B  ASP*     4.5    12.3    -      -       -      +
    117F  112      3.2    53.1    +      -       -      +
----------------------------------------------------------
 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