Contacts of the strand formed by residues 409 - 415 (chain D) in PDB entry 5ON2


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 409 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230D  VAL*     4.9     1.1    -      -       -      -
    231D  GLU*     3.0    18.4    -      -       -      -
    232D  ILE*     4.2     1.1    -      -       -      -
    233D  THR*     4.3     5.6    +      -       -      -
    403D  LEU*     3.7    10.0    +      -       -      -
    404D  THR*     3.4    26.2    -      -       -      +
    407D  GLY*     3.7     1.9    -      -       -      -
    408D  VAL*     1.3    77.6    +      -       -      +
    410D  GLU*     1.3    66.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 410 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230D  VAL*     3.9     8.2    -      -       -      +
    231D  GLU*     2.8    36.3    +      -       +      +
    404D  THR*     4.2    14.6    -      -       +      +
    409D  GLY*     1.3    76.8    -      -       -      +
    411D  ARG*     1.3    70.6    +      -       -      +
    412D  LYS*     3.6    26.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 411 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229D  GLY      3.6     9.9    -      -       -      +
    230D  VAL*     4.2    14.8    -      -       +      +
    396D  PHE*     3.8    16.7    -      -       +      -
    397D  ASN*     3.3    36.6    +      -       -      +
    400D  ALA*     3.7    13.9    -      -       +      +
    401D  ASP*     2.8    29.5    +      -       -      -
    404D  THR*     4.9     7.5    +      -       -      +
    410D  GLU*     1.3    79.1    -      -       -      +
    412D  LYS*     1.3    67.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 412 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228D  GLU*     4.0     1.5    -      -       -      -
    229D  GLY      3.2    31.2    +      -       -      +
    231D  GLU*     3.2    43.7    +      -       +      +
    246D  TYR*     3.7    10.5    -      -       +      -
    410D  GLU*     3.6    27.2    +      -       +      +
    411D  ARG*     1.3    81.7    -      -       -      +
    413D  VAL*     1.3    69.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 413 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226D  ARG*     3.7    39.3    -      -       -      +
    227D  SER      3.5     8.3    -      -       -      +
    228D  GLU*     4.7     8.7    -      -       +      +
    412D  LYS*     1.3    82.0    -      -       -      +
    414D  ASN*     1.3    67.6    +      -       -      +
    415D  TYR*     3.6    28.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 414 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226D  ARG*     3.6     2.1    -      -       -      -
    227D  SER*     2.9    35.3    +      -       -      -
    231D  GLU*     5.7     2.0    +      -       -      -
    246D  TYR*     3.4    41.6    -      -       +      +
    330D  TYR*     3.1    30.5    +      -       -      -
    331D  GLY*     3.8    24.5    +      -       -      +
    413D  VAL*     1.3    78.5    +      -       -      +
    415D  TYR*     1.3    78.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 415 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196D  THR*     5.5     5.4    -      -       +      -
    199D  ALA*     3.6    39.3    -      -       +      -
    200D  ASP*     3.1    35.6    +      -       +      +
    203D  LEU*     4.7     1.6    -      -       +      -
    224D  ILE*     3.8    23.8    -      -       +      +
    225D  GLY      3.6     2.0    -      -       -      -
    226D  ARG*     3.3    33.3    +      -       +      -
    330D  TYR*     3.4    15.3    -      -       -      -
    413D  VAL*     3.6    17.5    -      -       +      -
    414D  ASN*     1.3    84.1    +      -       -      +
    416D  ARG*     1.3    62.2    +      -       -      +
    417D  LEU*     4.2    15.9    -      -       +      +
----------------------------------------------------------
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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