Contacts of the strand formed by residues 228 - 233 (chain C) 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 PHE 228 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  PHE      3.9     0.3    -      -       -      +
     21C  ILE*     3.4     4.3    -      -       -      +
     22C  LEU*     2.7    44.4    +      -       -      +
     25C  VAL*     3.8    20.0    -      -       +      -
     26C  ASP      4.2     3.1    -      -       -      -
     27C  LEU*     3.3    42.0    -      -       +      -
     30C  ALA*     4.0    10.3    -      -       +      -
    178C  PHE*     3.6    25.1    -      +       +      -
    179C  GLU      3.5     5.4    -      -       -      +
    180C  TYR*     3.6    32.3    -      +       +      -
    225C  ALA      3.6    12.1    -      -       -      -
    227C  THR*     1.3   107.6    -      -       -      +
    229C  TYR*     1.3    63.1    +      -       -      +
    230C  MET*     3.7    21.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 229 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  ARG*     4.5     5.6    -      -       -      +
     19C  ASP*     6.0     0.4    -      -       -      +
     20C  PHE      3.6     4.3    -      -       -      +
     21C  ILE*     3.6    32.9    -      -       +      +
    177C  GLU*     3.5     1.2    -      -       -      +
    178C  PHE*     3.2     6.6    +      -       -      -
    179C  GLU*     2.9    45.3    +      -       +      +
    181C  ASP*     4.2    17.0    -      -       -      -
    182C  PRO*     5.1     2.5    -      -       +      -
    206C  ASN*     3.0    44.0    -      -       +      +
    209C  TYR*     3.4    33.0    +      -       +      -
    210C  GLU*     3.7    16.1    +      -       -      +
    227C  THR*     3.9    27.5    -      -       +      +
    228C  PHE*     1.3    74.0    -      -       -      +
    230C  MET*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 230 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  VAL      4.0     0.9    -      -       -      -
     19C  ASP*     3.1    11.6    -      -       -      +
     20C  PHE*     2.9    59.5    +      -       +      -
     22C  LEU*     3.6    28.3    -      -       +      -
     30C  ALA*     3.7    28.7    -      -       +      +
     33C  LEU*     5.7     6.1    -      -       +      -
     34C  ARG*     5.6     3.4    -      -       -      -
     37C  MET*     6.1     2.2    -      -       -      +
    176C  ILE*     5.2     6.1    -      -       +      -
    177C  GLU*     3.1    13.9    -      -       -      +
    178C  PHE*     3.7    22.0    -      -       +      -
    228C  PHE*     3.7    15.7    -      -       +      -
    229C  TYR*     1.3    81.3    -      -       -      +
    231C  ASN*     1.3    64.2    +      -       -      +
    232C  VAL*     4.8     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 231 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  GLU*     4.8     4.0    -      -       -      +
     17C  ASN*     3.2    38.0    +      -       -      +
     18C  VAL      2.9    11.5    +      -       -      -
     19C  ASP*     3.7    24.4    -      -       -      +
    175C  ALA      4.0     1.7    -      -       -      +
    176C  ILE*     3.7     1.9    -      -       -      -
    177C  GLU*     3.0    58.8    +      -       +      +
    230C  MET*     1.3    81.5    -      -       -      +
    232C  VAL*     1.3    63.6    +      -       -      +
    233C  GLU*     5.1     0.9    -      -       -      +
     42J  LYS*     5.0     3.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 232 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  ASP      3.8     0.2    -      -       -      +
     17C  ASN*     3.4     5.0    -      -       -      -
     18C  VAL*     3.0    42.4    +      -       +      +
     20C  PHE*     4.0    24.0    -      -       +      -
     37C  MET*     3.8    25.8    -      -       +      -
    173C  ALA      5.1     1.3    -      -       -      +
    176C  ILE*     4.2    23.3    -      -       +      -
    230C  MET*     4.8     2.9    -      -       +      -
    231C  ASN*     1.3    77.8    +      -       -      +
    233C  GLU*     1.3    67.0    +      -       -      +
    234C  SER      4.3     0.9    -      -       -      +
    240C  VAL*     4.1     1.3    -      -       +      +
    243C  VAL*     4.3    26.7    -      -       +      -
    244C  VAL*     4.3     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 233 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  ASP*     3.2    22.1    -      -       +      +
     17C  ASN*     3.3    23.1    +      -       -      +
    173C  ALA*     2.6    28.2    +      -       -      +
    174C  ALA*     3.3    20.9    -      -       +      +
    175C  ALA      3.5    17.7    +      -       -      +
    231C  ASN*     5.1     1.1    -      -       -      +
    232C  VAL*     1.3    80.3    -      -       -      +
    234C  SER*     1.3    69.9    +      -       -      +
    243C  VAL*     6.1     0.2    -      -       -      +
     12J  LYS*     3.4    32.2    +      -       -      +
     42J  LYS*     5.7     0.3    -      -       -      -
     43J  ARG*     3.4    29.2    +      -       -      +
----------------------------------------------------------
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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