Contacts of the strand formed by residues 989 - 994 (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 THR 989 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352A  VAL*     4.3    11.2    -      -       +      +
    353A  ILE      4.3     4.7    +      -       -      -
    354A  SER*     4.7     3.6    -      -       -      -
    482A  PHE*     2.9    29.1    +      -       -      +
    484A  GLY*     3.9    19.1    -      -       -      +
    837B  ASP      3.5     0.8    +      -       -      -
    838B  SER*     3.2     6.5    +      -       -      -
    839B  MET*     2.9    26.3    +      -       -      +
    977B  GLY*     3.6    18.4    -      -       -      +
    978B  ASP      3.4     8.5    -      -       -      -
    979B  LYS*     3.6    25.8    -      -       +      -
    988B  GLY*     1.3    76.6    -      -       -      -
    990B  ILE*     1.3    68.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 990 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  SER*     4.2     6.4    -      -       -      -
    838B  SER*     4.5     0.4    -      -       -      -
    839B  MET*     3.4    12.6    -      -       +      +
    841B  MET*     3.4    45.1    -      -       +      -
    846B  ILE*     4.8     0.9    -      -       +      -
    974B  PRO      4.3     6.1    -      -       -      +
    975B  GLN      3.3    18.4    -      -       -      +
    976B  ILE*     2.3    43.2    +      -       -      +
    978B  ASP      3.6     3.2    +      -       -      +
    980B  PHE*     3.8    25.4    -      -       +      -
    989B  THR*     1.3    82.1    +      -       -      +
    991B  GLY*     1.3    60.3    +      -       -      +
    992B  ILE      3.6    26.5    -      -       -      +
    993B  THR*     4.6     4.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 991 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  SER*     4.3     8.5    -      -       -      -
    355A  GLY      5.6     0.7    -      -       -      -
    469A  ARG*     2.4    41.3    +      -       -      -
    833B  TYR*     3.6    20.4    -      -       -      +
    838B  SER*     4.0     8.3    -      -       -      -
    839B  MET      2.6    15.0    +      -       -      +
    976B  ILE*     4.3     1.3    -      -       -      -
    989B  THR      3.6     2.6    +      -       -      -
    990B  ILE*     1.3    74.1    -      -       -      +
    992B  ILE*     1.3    56.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 992 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465A  TYR*     5.9     0.2    -      -       +      -
    469A  ARG*     3.9     2.5    -      -       -      +
    833B  TYR*     3.8    27.8    +      -       +      -
    839B  MET      3.8     1.2    +      -       -      -
    840B  ILE*     3.4    23.2    -      -       +      +
    841B  MET      3.0    24.6    +      -       -      -
    976B  ILE*     3.9     7.4    -      -       +      -
    990B  ILE*     3.6     6.5    -      -       -      +
    991B  GLY*     1.3    80.2    -      -       -      +
    993B  THR*     1.3    72.9    +      -       -      +
    994B  TYR*     3.6    34.5    -      -       +      -
     66K  PRO*     5.0     7.6    -      -       +      -
     67K  PHE*     3.1    43.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 993 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465A  TYR*     4.1    21.6    +      -       +      -
    841B  MET*     3.2    14.6    -      -       +      +
    843B  GLN*     3.3    31.2    +      -       -      +
    846B  ILE*     4.0    17.7    -      -       +      -
    974B  PRO      4.8     5.2    -      -       -      +
    975B  GLN*     5.5     1.1    -      -       -      -
    976B  ILE*     4.6     8.9    -      -       +      +
    990B  ILE*     4.7    11.2    -      -       +      -
    992B  ILE*     1.3    79.3    -      -       -      +
    994B  TYR*     1.3    67.8    +      -       -      +
    995B  ARG*     4.3     5.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 994 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    830B  TYR*     4.2    14.8    -      +       -      -
    831B  SER*     2.8    38.1    +      -       -      -
    833B  TYR*     2.8    21.3    -      -       -      -
    840B  ILE*     3.5    18.1    -      -       +      +
    841B  MET      3.4     6.3    +      -       -      -
    842B  ASN*     3.4     5.5    -      -       -      -
    843B  GLN*     2.7    27.3    +      -       -      -
    992B  ILE*     3.6    26.3    +      -       +      -
    993B  THR*     1.3    80.7    -      -       -      +
    995B  ARG*     1.3    63.1    +      -       -      +
    998B  ASP*     4.3    18.8    -      -       +      -
    999B  MET*     3.5    25.1    -      -       +      -
   1076B  HIS*     5.4     7.6    -      +       -      -
     66K  PRO*     4.1    19.4    -      -       +      +
----------------------------------------------------------
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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