Contacts of the strand formed by residues 212 - 216 (chain A) in PDB entry 3NTY


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 212 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  VAL*     4.3    19.7    -      -       +      -
      9A  LYS      5.1     4.3    -      -       -      +
     10A  LEU*     4.2    19.5    -      -       +      -
     11A  ASN      6.1     0.4    -      -       -      +
     16A  MET*     4.8     2.0    -      -       -      -
    187A  VAL      3.1    16.7    +      -       -      +
    188A  CYS*     3.1     8.3    -      -       +      +
    189A  ASN*     2.9    27.5    +      -       -      -
    206A  CYS*     4.8     0.7    -      -       -      -
    210A  ASP      4.2     1.5    -      -       -      +
    211A  ILE*     1.3    73.7    -      -       -      +
    213A  LEU*     1.3    69.0    +      -       -      +
    214A  VAL*     4.1     6.5    -      -       +      -
    264A  GLY      5.1     4.5    -      -       -      +
    266A  VAL*     3.7    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  ASN*     3.6     4.9    -      -       +      +
    191A  VAL*     3.9    29.2    -      -       +      -
    193A  CYS*     4.3    14.8    -      -       +      -
    199A  GLN*     4.3     9.9    -      -       +      +
    202A  LEU*     4.1     8.3    -      -       +      +
    203A  LEU*     3.3    58.9    -      -       +      +
    206A  CYS*     4.8     8.7    -      -       +      -
    211A  ILE      3.7     2.2    +      -       -      -
    212A  VAL*     1.3    72.7    -      -       -      +
    214A  VAL*     1.3    69.3    +      -       -      +
    215A  ALA      4.0     3.1    -      -       -      +
    264A  GLY      5.1     2.8    +      -       -      -
    265A  VAL*     3.3    21.4    -      -       +      +
    266A  VAL      3.0    22.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  MET*     4.3    10.1    -      -       +      -
     48A  HIS*     5.1     3.1    -      -       +      -
    113A  LEU*     5.8     0.7    -      -       +      -
    188A  CYS*     3.9    29.6    -      -       +      -
    189A  ASN      3.1     6.9    +      -       -      -
    190A  GLN*     3.2    36.4    -      -       +      +
    191A  VAL      2.9    28.5    +      -       -      +
    212A  VAL*     4.1     4.5    -      -       +      -
    213A  LEU*     1.3    72.4    -      -       -      +
    215A  ALA*     1.3    61.2    +      -       -      +
    266A  VAL*     3.2    27.8    -      -       +      +
    268A  LEU*     4.0    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 215 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  VAL      3.3     5.4    -      -       -      -
    193A  CYS*     3.4    36.6    -      -       +      +
    213A  LEU*     3.7     2.5    +      -       -      -
    214A  VAL*     1.3    71.0    -      -       -      +
    216A  TYR*     1.3    60.9    +      -       -      +
    218A  ALA*     4.1     4.9    -      -       -      +
    260A  GLN*     4.2     8.7    -      -       +      -
    265A  VAL*     3.5    20.9    -      -       +      -
    266A  VAL      2.8    11.4    +      -       -      +
    267A  VAL*     4.6     3.6    -      -       +      -
    268A  LEU*     3.2    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167A  ASN*     2.8    27.1    +      -       -      -
    190A  GLN*     3.8    10.8    -      -       +      +
    191A  VAL*     2.7    26.5    +      -       -      -
    192A  GLU*     3.4    33.9    +      -       +      +
    193A  CYS      3.0    20.4    +      -       -      +
    214A  VAL      3.5     0.8    +      -       -      -
    215A  ALA*     1.3    72.4    -      -       -      +
    217A  SER*     1.3    78.8    +      -       -      +
    218A  ALA      3.0     3.6    +      -       -      -
    268A  LEU*     4.2     4.0    -      -       +      -
    306A  LEU*     3.9    18.9    +      -       +      +
    308A  LEU*     4.4     4.3    -      -       -      +
    319A  PHE*     4.7     2.3    -      -       -      -
    351A  NAP      3.2    82.1    +      +       +      +
----------------------------------------------------------
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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