Contacts of the strand formed by residues 315 - 319 (chain A) in PDB entry 4NSW


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 CYS 315 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309A  VAL*     3.8    28.7    -      -       +      -
    311A  ASP      4.4     0.2    -      -       -      +
    312A  LEU*     3.7    11.7    +      -       -      +
    313A  ARG      3.5     4.6    +      -       -      +
    314A  LEU*     1.3    79.4    -      -       -      +
    316A  THR*     1.3    70.8    +      -       -      +
    331A  VAL*     4.2    11.0    -      -       +      -
    332A  VAL      3.0    20.0    -      -       -      +
    333A  SER*     4.2     0.7    -      -       -      -
    355A  VAL*     4.6     4.7    -      -       -      -
    359A  ILE*     3.6    40.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  CYS*     1.3    76.7    +      -       -      +
    317A  VAL*     1.3    85.3    +      -       -      +
    318A  LYS*     5.3    10.1    -      -       +      -
    330A  GLU      3.6     0.6    -      -       -      +
    331A  VAL*     3.4     9.0    -      -       -      +
    332A  VAL*     3.0    36.0    +      -       -      +
    359A  ILE*     4.4     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  CYS*     4.8     0.2    -      -       -      -
    316A  THR*     1.3    87.3    -      -       -      +
    318A  LYS*     1.3    67.6    +      -       -      +
    329A  PHE*     3.7    26.2    -      -       +      -
    330A  GLU      3.4    12.3    -      -       -      +
    331A  VAL*     4.1     7.4    -      -       +      -
    352A  VAL*     4.4    12.8    -      -       +      -
    355A  VAL*     3.0    39.0    -      -       +      -
    356A  GLN*     4.4    22.6    +      -       +      +
    359A  ILE*     3.7    12.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316A  THR*     5.3     9.2    -      -       +      -
    317A  VAL*     1.3    80.4    -      -       -      +
    319A  LEU*     1.3    69.2    +      -       -      +
    320A  CYS*     4.1     4.3    -      -       -      -
    329A  PHE*     3.4     5.1    -      -       -      -
    330A  GLU*     3.1    67.2    +      -       +      +
    332A  VAL*     4.6    12.7    -      -       +      +
    352A  VAL*     5.5     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318A  LYS*     1.3    81.6    -      -       -      +
    320A  CYS*     1.3    67.8    +      -       -      +
    321A  PRO*     3.8    18.8    -      -       +      +
    328A  CYS      4.3     2.5    -      -       -      -
    329A  PHE*     4.4     0.2    -      -       -      -
    348A  LEU*     3.7    31.4    -      -       +      -
    349A  GLN*     6.2     0.7    -      -       +      -
    352A  VAL*     3.9    30.7    -      -       +      -
    356A  GLN*     5.8     5.8    -      -       -      +
----------------------------------------------------------
 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