Contacts of the strand formed by residues 930 - 935 (chain I) in PDB entry 6PSS


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 ASP 930 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    873I  ILE*     3.7    14.3    -      -       -      +
    928I  VAL*     3.7     2.2    -      -       -      +
    929I  ILE*     1.3    84.3    -      -       +      +
    931I  VAL*     1.3    74.2    +      -       -      +
    932I  GLN*     4.7    11.5    +      -       +      +
   1051I  LYS      4.4     0.9    -      -       -      -
   1053I  TYR*     2.7    53.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 931 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870I  ILE*     3.7    24.0    -      -       +      -
    871I  VAL*     4.2    17.3    -      -       +      +
    873I  ILE*     3.7    10.9    -      -       +      +
    928I  VAL*     4.0    19.3    -      -       +      -
    930I  ASP*     1.3    83.6    +      -       -      +
    932I  GLN*     1.3    63.0    +      -       -      +
    933I  VAL*     4.4     1.6    -      -       +      -
    944I  ARG*     3.8    18.1    +      -       -      +
    948I  ILE*     3.4    25.7    -      -       +      +
   1050I  VAL*     3.8    15.3    -      -       +      -
   1051I  LYS      3.7     4.3    -      -       -      -
   1052I  VAL*     4.0    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 932 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87I  ILE*     3.7    33.8    +      -       -      +
    930I  ASP*     4.7    14.0    -      -       -      +
    931I  VAL*     1.3    79.4    -      -       -      +
    933I  VAL*     1.3    62.2    +      -       -      +
    934I  PHE*     3.9    23.3    -      -       +      -
    948I  ILE*     4.6     4.5    -      -       +      -
    952I  GLN*     6.1     1.8    -      -       -      +
   1049I  ILE      3.3     3.8    -      -       -      +
   1050I  VAL*     3.3     2.1    -      -       -      -
   1051I  LYS*     2.8    47.3    +      -       +      +
   1053I  TYR*     3.2    38.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 933 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870I  ILE*     3.8    20.9    -      -       +      -
    931I  VAL*     4.4     1.1    -      -       +      -
    932I  GLN*     1.3    75.7    -      -       -      +
    934I  PHE*     1.3    65.4    +      -       -      +
    935I  THR*     4.1     5.8    +      -       -      +
    944I  ARG*     4.6     0.7    -      -       +      -
    945I  ALA*     3.7    35.1    -      -       +      +
    948I  ILE*     3.9    23.7    -      -       +      +
   1048I  LYS*     3.8    28.7    -      -       +      -
   1049I  ILE      3.8     2.2    -      -       -      -
   1050I  VAL*     3.8    22.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 934 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87I  ILE*     4.0    29.6    -      -       +      -
     88I  ARG*     4.7    13.2    -      -       +      -
    932I  GLN*     3.9    37.9    -      -       +      -
    933I  VAL*     1.3    73.7    -      -       -      +
    935I  THR*     1.3    61.0    +      -       -      +
   1040I  ASP*     3.2    35.9    -      -       +      +
   1042I  LEU*     4.3    10.0    -      -       +      +
   1047I  LEU      3.5     0.9    -      -       -      +
   1048I  LYS*     3.2     8.3    -      -       -      +
   1049I  ILE*     3.0    54.2    +      -       +      +
   1051I  LYS*     3.8    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 935 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    933I  VAL*     4.1    14.1    +      -       -      +
    934I  PHE*     1.3    74.5    -      -       -      +
    936I  ARG*     1.3    74.5    +      -       -      +
    939I  VAL*     3.7    28.9    -      -       +      +
    940I  GLU      4.4     9.0    -      -       -      +
    941I  LYS*     4.3    22.5    -      -       -      +
    945I  ALA*     4.4     2.1    -      -       +      +
   1039I  GLY*     4.3     2.6    -      -       -      -
   1040I  ASP*     3.1    30.0    +      -       -      +
   1042I  LEU*     4.0     4.0    -      -       -      -
   1047I  LEU      3.4     6.3    -      -       -      +
   1048I  LYS*     4.0    15.3    -      -       +      +
----------------------------------------------------------
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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