Contacts of the strand formed by residues 90 - 98 (chain C) in PDB entry 5NXR


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 GLY 90 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85C  LYS*     3.3    13.7    -      -       -      +
     86C  PHE*     2.9    30.3    +      -       -      +
     88C  ASP*     3.6     2.2    -      -       -      +
     89C  PHE*     1.3    80.2    -      -       -      +
     91C  SER*     1.3    60.1    +      -       -      -
    136C  TYR*     3.9     4.3    -      -       -      -
    137C  ARG      3.1    14.8    -      -       -      -
    138C  ASN*     3.8     8.1    -      -       -      +
    139C  ASN      5.4     1.1    -      -       -      -
    439C  LDA      4.4     3.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 91 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  PHE*     4.3    14.6    -      -       -      -
     84C  LEU      3.2    11.7    -      -       -      -
     85C  LYS*     3.8    22.5    +      -       -      -
     90C  GLY*     1.3    74.8    -      -       -      -
     92C  ILE*     1.3    60.6    +      -       -      +
     93C  ASP*     5.1     4.0    +      -       -      -
    135C  THR      3.7     0.7    +      -       -      +
    136C  TYR*     3.1    10.6    -      -       -      -
    137C  ARG*     2.9    49.6    +      -       -      +
    439C  LDA      5.3     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 92 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  PHE*     3.8     1.4    -      -       -      -
     83C  GLY*     3.1     2.3    -      -       -      -
     84C  LEU*     2.8    41.3    +      -       +      +
     91C  SER*     1.3    74.5    -      -       -      +
     93C  ASP*     1.3    63.2    +      -       -      +
    134C  LEU*     3.9    22.4    -      -       +      -
    135C  THR      3.3    18.2    -      -       -      +
    136C  TYR*     3.7    24.5    -      -       +      -
    406C  LDA      3.8    45.0    -      -       +      +
    408C  LDA      3.9    13.9    -      -       +      -
    439C  LDA      4.5    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  PHE*     3.7    21.1    -      -       +      -
     81C  TYR*     4.2     7.6    -      -       +      +
     82C  ALA      3.3    13.2    -      -       -      +
     83C  GLY*     3.9     0.7    -      -       -      -
     91C  SER*     5.1     4.3    +      -       -      -
     92C  ILE*     1.3    76.4    -      -       -      +
     94C  TYR*     1.3    64.4    +      -       -      +
     97C  ASN*     3.3    34.1    +      -       -      +
    133C  LEU      4.6     1.0    -      -       -      +
    134C  LEU*     3.4     7.4    -      -       -      +
    135C  THR*     2.9    55.5    +      -       -      +
    137C  ARG*     5.1     7.1    +      -       -      +
    406C  LDA      5.1     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     3.6    25.8    -      -       +      +
     20B  ARG      3.4    31.1    +      -       -      -
     21B  HIS*     3.2    18.4    -      +       +      -
     36B  ASP*     3.3    17.0    +      -       -      -
     38B  SER*     4.0     7.0    -      -       -      -
    348B  LEU*     5.7     0.2    -      -       +      -
     81C  TYR*     3.3     7.0    -      -       -      +
     82C  ALA      2.9    30.7    +      -       -      +
     93C  ASP*     1.3    77.4    -      -       -      +
     95C  GLY*     1.3    64.9    +      -       -      +
    132C  ASN*     2.9    37.0    +      -       -      -
    133C  LEU      3.2    26.9    -      -       -      -
    134C  LEU*     4.0    15.0    -      -       +      -
    406C  LDA      4.6     5.1    -      -       +      +
    407C  LDA      3.6    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  VAL*     4.1     6.1    -      -       -      -
     36B  ASP*     4.3     5.6    -      -       -      -
     38B  SER*     4.6     2.2    -      -       -      -
     66B  THR      5.8     0.2    -      -       -      -
     80C  ALA      3.5     7.2    -      -       -      -
     81C  TYR*     4.2     0.2    -      -       -      -
     93C  ASP*     4.7     0.4    +      -       -      -
     94C  TYR*     1.3    91.9    -      -       -      +
     96C  ARG*     1.3    61.0    +      -       -      -
     97C  ASN*     3.9     1.8    +      -       -      +
    130C  ASN      3.9     0.5    -      -       -      +
    131C  ARG      3.6     0.7    -      -       -      -
    132C  ASN      3.0    26.6    +      -       -      -
    133C  LEU*     3.0    16.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  SER*     6.0     0.4    -      -       -      -
     66B  THR*     4.3    16.2    -      -       -      +
     68B  LYS      3.9    14.7    +      -       -      -
     70B  GLU*     3.1    33.9    +      -       -      +
     77C  ASN*     3.1    23.1    +      -       -      -
     78C  ARG      2.9    22.5    +      -       -      +
     79C  LEU*     3.6     2.9    -      -       -      +
     80C  ALA*     2.7    42.2    +      -       +      +
     81C  TYR*     3.4     8.9    -      -       -      +
     95C  GLY*     1.3    71.2    -      -       -      -
     97C  ASN*     1.3    64.0    +      -       -      +
    122C  THR*     3.4     2.8    -      -       -      +
    123C  ASP*     2.7    32.1    +      -       -      -
    129C  ARG*     3.4    17.2    +      -       -      +
    130C  ASN*     3.1    16.4    -      -       -      +
    131C  ARG*     3.5    19.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79C  LEU*     3.9     8.7    -      -       -      +
     81C  TYR*     3.1    40.8    -      -       +      -
     93C  ASP*     3.3    30.9    +      -       -      +
     95C  GLY      3.9     2.7    +      -       -      -
     96C  ARG*     1.3    72.6    -      -       -      +
     98C  TYR*     1.3    88.9    +      -       -      +
    129C  ARG*     3.2     4.2    -      -       -      -
    130C  ASN      2.8    34.2    +      -       -      +
    133C  LEU*     3.3    14.8    -      -       +      +
    135C  THR*     5.3     3.5    +      -       -      +
    137C  ARG*     6.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  ARG*     6.1     0.2    -      -       -      -
     61C  GLU*     5.1     0.8    +      -       -      -
     78C  ARG*     3.3    14.6    +      -       -      -
     79C  LEU*     3.9    22.2    -      -       +      -
     97C  ASN*     1.3    93.2    +      -       -      +
     99C  GLY*     1.3    68.3    +      -       -      +
    102C  TYR*     3.5    45.2    +      +       +      -
    103C  ASP*     4.8     5.8    -      -       -      +
    128C  SER*     3.8     4.3    -      -       -      -
    129C  ARG*     3.1    52.5    +      -       +      -
    133C  LEU*     4.0     1.4    -      -       -      +
    135C  THR*     4.7     1.0    +      -       -      +
    137C  ARG*     4.2    12.2    +      -       -      +
    153C  GLN*     3.2    12.8    -      -       -      +
----------------------------------------------------------
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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