Contacts of the strand formed by residues 83 - 87 (chain I) in PDB entry 2NVT


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 ASN 83 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70I  ARG*     3.6    16.2    -      -       -      +
     71I  SER*     2.6    53.4    +      -       -      +
     73I  ARG*     3.5    15.4    +      -       -      +
     75I  CYS*     6.0     1.3    -      -       +      -
     80I  SER      5.7     0.7    -      -       -      +
     81I  ARG      2.8    23.8    +      -       -      +
     82I  GLU*     1.3    74.6    -      -       -      +
     84I  VAL*     1.3    64.3    -      -       -      +
    101I  PHE*     3.7    20.5    -      -       +      +
    102I  VAL      3.5    13.9    -      -       -      +
    103I  CYS*     4.2     6.5    -      -       +      +
    104I  LEU*     4.0     4.1    -      -       -      +
    110I  PHE*     4.7     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 84 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62I  ILE*     4.7    10.8    -      -       +      -
     63I  GLY*     4.8     6.3    -      -       -      -
     65I  ASP      5.0     0.7    -      -       -      +
     68I  LEU*     3.7    33.7    -      -       +      -
     69I  PRO      3.4    19.7    -      -       -      +
     70I  ARG*     3.5    25.4    -      -       -      +
     83I  ASN*     1.3    74.9    -      -       -      +
     85I  PHE*     1.3    69.7    +      -       -      +
     86I  PHE*     4.7     7.2    -      -       +      -
    101I  PHE*     3.2     6.6    -      -       -      +
    102I  VAL*     3.0    36.0    +      -       +      +
    104I  LEU*     3.8    15.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 85 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    790A  ASP*     5.4     6.7    -      -       +      -
     68I  LEU*     4.3     1.7    -      -       -      +
     69I  PRO*     3.2    57.3    +      -       +      +
     70I  ARG      4.0     8.3    -      -       -      -
     71I  SER*     3.7    28.3    -      -       -      -
     84I  VAL*     1.3    81.9    -      -       -      +
     86I  PHE*     1.3    76.4    +      -       -      +
     99I  LEU*     4.3    26.2    -      -       +      -
    100I  PHE      3.1    15.7    -      -       -      +
    101I  PHE*     3.3    32.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with PHE 86 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    790A  ASP*     3.4    20.0    -      -       -      +
    620B  ARG*     4.3    20.2    -      -       -      +
     54I  GLU      4.9     4.7    -      -       -      -
     55I  THR*     5.3     2.5    -      -       -      -
     56I  ALA      5.2     1.1    -      -       -      -
     58I  VAL*     4.2    23.6    -      -       +      -
     62I  ILE*     5.4     5.8    -      -       +      -
     68I  LEU*     4.7     4.0    -      -       +      -
     69I  PRO*     5.4     0.2    -      -       +      -
     84I  VAL*     4.7     6.7    -      -       +      -
     85I  PHE*     1.3    92.0    -      -       -      +
     87I  GLN*     1.3    81.3    +      -       -      +
     89I  GLN*     3.5    33.0    -      -       +      -
     99I  LEU*     4.4     4.5    -      -       -      -
    100I  PHE*     2.9    57.0    +      +       +      +
    102I  VAL*     4.1    19.7    -      -       +      -
    109I  ILE*     5.9     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 87 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    698A  GLN*     5.1     6.1    -      -       -      +
    711A  ARG*     2.8    26.2    +      -       -      +
    790A  ASP*     3.6    24.5    +      -       +      +
    792A  TYR*     3.0    41.5    -      -       -      -
     86I  PHE*     1.3    92.2    -      -       -      +
     88I  SER*     1.3    69.1    +      -       -      +
     89I  GLN*     3.2     2.8    +      -       -      +
     91I  ARG*     3.4     9.6    +      -       -      +
     97I  MET*     3.6    27.0    +      -       -      +
     98I  VAL      3.6    17.3    -      -       -      +
     99I  LEU*     3.8    15.8    -      -       +      +
    100I  PHE*     4.4     1.8    -      -       -      -
----------------------------------------------------------
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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