Contacts of the strand formed by residues 195 - 201 (chain E) 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 VAL 195 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155E  ARG*     4.0     4.2    -      -       -      +
    156E  LEU*     3.4    37.6    +      -       +      +
    161E  LYS*     3.7    24.7    -      -       +      -
    164E  LEU*     5.1     3.8    -      -       +      -
    165E  LEU*     5.8     0.2    -      -       +      -
    175E  LEU*     4.2    15.5    -      -       +      -
    193E  GLY      3.5    15.9    -      -       -      +
    194E  GLU*     1.3    74.6    +      -       -      +
    196E  VAL*     1.3    77.2    +      -       -      +
    211E  TYR*     4.4    10.5    -      -       +      -
    212E  ARG      3.2    24.2    -      -       -      +
    213E  ILE*     3.8    16.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 196 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153E  HIS*     4.3    11.2    -      -       +      -
    154E  ILE      3.9     7.4    -      -       -      +
    155E  ARG*     4.8     7.0    -      -       -      +
    156E  LEU*     4.1     2.9    -      -       -      -
    178E  ILE*     5.0     9.0    -      -       +      -
    188E  LEU*     4.9     9.2    -      -       +      -
    190E  LEU*     3.8    35.4    -      -       +      -
    194E  GLU      5.4     0.2    -      -       -      +
    195E  VAL*     1.3    83.0    -      -       -      +
    197E  LYS*     1.3    62.9    +      -       -      +
    198E  ILE*     3.9    26.2    -      -       +      -
    211E  TYR*     3.4     7.8    -      -       -      -
    212E  ARG*     3.0    40.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 197 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1009A  ASN*     5.9     4.4    -      -       -      +
    152E  LYS      3.8     1.0    -      -       -      +
    153E  HIS*     3.5     1.7    -      -       -      -
    154E  ILE*     2.9    43.4    +      -       +      +
    156E  LEU*     3.5    21.3    -      -       +      -
    196E  VAL*     1.3    70.8    -      -       -      +
    198E  ILE*     1.3    70.0    +      -       -      +
    199E  ILE*     4.0    31.1    -      -       +      +
    209E  ALA*     4.5    11.4    -      -       +      -
    210E  SER      3.4     4.9    -      -       -      +
    211E  TYR*     3.7    31.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 198 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1342A  GLU*     3.4    37.0    -      -       +      +
    151E  PRO*     3.9    28.3    -      -       +      -
    152E  LYS      3.9     5.4    -      -       -      +
    153E  HIS*     3.8    26.0    -      -       +      +
    196E  VAL*     3.9     6.1    -      -       +      -
    197E  LYS*     1.3    81.6    -      -       -      +
    199E  ILE*     1.3    63.9    +      -       -      +
    200E  ARG*     3.4     5.6    +      -       +      +
    208E  TYR      3.2     6.1    -      -       -      +
    209E  ALA*     3.7     0.3    -      -       -      -
    210E  SER*     2.8    47.7    +      -       -      +
    212E  ARG*     3.7    31.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 199 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1013A  ASP*     5.8     1.1    -      -       -      +
    151E  PRO*     4.1    10.1    -      -       -      +
    152E  LYS*     3.6    33.5    +      -       +      +
    154E  ILE*     4.3    23.3    -      -       +      -
    197E  LYS*     4.0    34.8    -      -       +      +
    198E  ILE*     1.3    76.0    -      -       -      +
    200E  ARG*     1.3    60.2    +      -       -      +
    201E  LYS*     4.0    14.9    +      -       -      +
    207E  ARG*     4.4    34.8    -      -       +      +
    208E  TYR      3.8     5.2    -      -       -      +
    209E  ALA*     5.5     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 200 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870A  GLU*     3.4    12.4    +      -       -      +
   1342A  GLU*     2.7    36.1    +      -       -      +
   1345A  ARG*     3.2    47.8    -      -       -      +
   1365A  TYR*     5.3     0.2    -      -       -      -
   1373A  ASP*     3.6     9.5    +      -       -      -
    151E  PRO*     4.1    23.6    -      -       +      -
    198E  ILE*     3.4     4.4    +      -       +      +
    199E  ILE*     1.3    76.1    -      -       -      +
    201E  LYS*     1.3    67.2    +      -       -      +
    202E  SER      4.0     0.3    +      -       -      -
    207E  ARG*     3.7     2.9    -      -       -      -
    208E  TYR*     3.1    69.9    +      -       +      +
    210E  SER*     3.7    13.3    +      -       -      -
    212E  ARG*     4.6     3.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 201 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    942A  PHE*     4.5    19.7    -      -       +      -
    945A  GLU*     3.4    36.3    +      -       +      +
    946A  VAL*     3.8    30.4    -      -       +      +
    152E  LYS*     5.9     7.1    -      -       -      +
    199E  ILE*     4.7    15.9    -      -       -      +
    200E  ARG*     1.3    80.0    -      -       -      +
    202E  SER*     1.3    59.9    +      -       -      +
    206E  GLY      3.3    17.5    -      -       -      +
    207E  ARG*     4.5    11.7    -      -       +      +
----------------------------------------------------------
 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