Contacts of the strand formed by residues 926 - 931 (chain C) in PDB entry 5NSS


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 GLY 926 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    875C  ALA      3.7     1.4    -      -       -      +
    876C  GLU*     4.2     1.0    -      -       -      -
    877C  VAL*     3.3    29.8    +      -       -      +
    925C  SER*     1.3    80.2    +      -       -      +
    927C  THR*     1.3    65.3    +      -       -      -
    928C  VAL      4.3     0.2    +      -       -      -
   1054C  LEU*     3.7    14.9    -      -       -      +
   1055C  ALA      3.5    10.5    -      -       -      -
   1056C  VAL*     3.7     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 927 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  HIS*     5.9     3.1    -      -       +      -
     68A  TYR*     3.6    22.9    -      -       -      -
    874C  GLY*     4.9     9.2    -      -       -      +
    875C  ALA      3.4    18.6    -      -       -      +
    876C  GLU*     5.1     3.6    -      -       +      -
    926C  GLY*     1.3    75.7    -      -       -      +
    928C  VAL*     1.3    59.7    +      -       -      +
   1054C  LEU*     3.7     2.9    -      -       -      -
   1055C  ALA*     2.4    48.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 928 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  HIS*     4.4     7.1    -      -       -      -
    871C  VAL*     5.2     6.1    -      -       +      -
    872C  TYR      4.1     8.5    -      -       -      +
    873C  ILE*     4.3     3.6    -      -       +      -
    874C  GLY*     3.3    34.4    +      -       -      +
    875C  ALA*     3.9    10.4    +      -       +      +
    877C  VAL*     4.5     8.7    -      -       +      -
    883C  LEU*     3.7    33.9    -      -       +      -
    927C  THR*     1.3    75.8    -      -       -      +
    929C  ILE*     1.3    67.2    +      -       -      +
    930C  ASP*     5.1     0.4    -      -       -      +
    931C  VAL*     5.7     5.2    -      -       +      -
   1052C  VAL*     4.2     9.6    -      -       +      -
   1053C  TYR      3.2    12.3    -      -       -      +
   1054C  LEU*     3.7    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 929 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  HIS*     4.0    12.6    +      -       -      +
     68A  TYR*     3.4    40.2    -      -       +      -
    756C  TYR*     3.9    25.1    -      -       +      +
    757C  THR*     5.9     0.4    -      -       -      -
    833C  ILE*     4.5    15.7    -      -       +      -
    873C  ILE*     3.3    23.9    -      -       -      +
    928C  VAL*     1.3    73.1    -      -       -      +
    930C  ASP*     1.3    67.2    +      -       +      +
   1053C  TYR*     2.5    34.5    +      -       +      +
   1054C  LEU      4.3     1.6    -      -       -      -
   1055C  ALA*     3.6    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 930 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    873C  ILE*     4.4    15.5    -      -       -      +
    928C  VAL*     5.1     0.4    -      -       -      +
    929C  ILE*     1.3    90.5    -      -       +      +
    931C  VAL*     1.3    81.7    +      -       -      +
    932C  GLN*     3.8     9.9    +      -       -      +
    948C  ILE*     4.0    22.6    -      -       -      +
   1052C  VAL*     3.7     1.4    -      -       -      -
   1053C  TYR*     2.9    36.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 931 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870C  ILE*     3.6    35.9    -      -       +      -
    871C  VAL*     5.7     2.2    -      -       +      -
    873C  ILE*     5.4    10.6    -      -       +      +
    883C  LEU*     5.1     2.2    -      -       +      -
    884C  VAL*     5.2     1.1    -      -       +      -
    928C  VAL*     5.7     5.2    -      -       +      -
    930C  ASP*     1.3    83.2    +      -       -      +
    932C  GLN*     1.3    62.0    +      -       -      +
    933C  VAL*     3.9    24.6    -      -       +      +
    944C  ARG*     6.2     1.3    -      -       +      -
    945C  ALA*     5.7     1.4    -      -       -      -
    948C  ILE*     4.7    11.6    -      -       -      +
   1050C  VAL*     4.8     4.7    -      -       +      -
   1051C  LYS      3.7     3.1    -      -       -      -
   1052C  VAL*     3.6    41.1    -      -       +      +
----------------------------------------------------------
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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