Contacts of the strand formed by residues 269 - 272 (chain B) in PDB entry 2NVX


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 ILE 269 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256B  VAL*     4.3    17.3    -      -       +      -
    257B  LYS      3.1    18.4    -      -       -      +
    258B  LEU*     3.3    19.3    -      -       +      -
    267B  ARG      4.4     1.3    -      -       -      +
    268B  THR*     1.3    75.3    +      -       -      +
    270B  LYS*     1.3    66.8    +      -       -      +
    281B  PRO*     3.6     6.2    -      -       -      +
    282B  ILE*     3.5    36.0    +      -       +      +
    313B  MET      5.4     1.8    -      -       -      +
    314B  LEU*     4.4    11.2    -      -       +      -
    317B  CYS*     4.2    15.3    -      -       -      +
    382B  ILE*     3.8    18.6    -      -       +      -
    385B  LEU*     4.4     5.2    -      -       +      -
    386B  LEU*     3.4    35.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 270 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256B  VAL*     3.7     1.2    -      -       -      -
    257B  LYS*     2.9    33.4    +      -       -      +
    259B  TYR*     3.7    30.0    -      -       +      +
    268B  THR*     3.2    34.7    +      -       -      +
    269B  ILE*     1.3    81.4    -      -       -      +
    271B  ALA*     1.3    62.2    +      -       -      +
    279B  ASP*     4.0    26.2    -      -       +      +
    280B  ILE      3.3    11.2    -      -       -      +
    281B  PRO*     4.0    17.3    -      -       +      -
    282B  ILE*     4.6     1.3    -      -       -      +
    320B  ASP*     3.9    17.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 271 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254B  LEU*     5.0     3.4    -      -       +      -
    255B  GLN      3.3    12.6    -      -       -      +
    256B  VAL*     4.2    12.6    -      -       +      -
    257B  LYS*     4.6     0.4    -      -       -      +
    270B  LYS*     1.3    75.4    -      -       -      +
    272B  THR*     1.3    65.7    +      -       -      +
    273B  LEU*     4.0    12.7    +      -       +      +
    279B  ASP*     3.6     4.9    -      -       -      -
    280B  ILE*     2.7    41.0    +      -       -      +
    282B  ILE*     4.4    15.3    -      -       +      -
    285B  ILE*     5.1     5.4    -      -       +      -
    360B  PHE*     6.3     0.2    -      -       +      -
    378B  LEU*     5.4     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 272 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253B  THR      4.4     2.3    -      -       -      +
    254B  LEU*     3.1    23.5    -      -       -      +
    255B  GLN*     2.8    30.9    +      -       -      +
    257B  LYS*     2.9    32.2    +      -       -      +
    271B  ALA*     1.3    73.7    -      -       -      +
    273B  LEU*     1.3    70.5    +      -       -      +
    276B  ILE*     4.7     1.6    -      -       +      -
    277B  LYS      5.5     3.4    -      -       -      +
    278B  GLN      4.4     6.3    -      -       -      +
    279B  ASP*     3.3    18.6    +      -       -      +
----------------------------------------------------------
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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