Contacts of the strand formed by residues 209 - 214 (chain A) in PDB entry 5DK3


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 209 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  PRO      5.6     0.9    -      -       -      +
    119A  VAL*     4.1    21.0    -      -       +      +
    198A  CYS      3.7     1.2    -      -       -      +
    199A  GLU*     3.5     0.9    -      -       -      -
    200A  VAL*     2.8    38.3    +      -       -      +
    205A  LEU*     3.6    35.6    -      -       +      +
    207A  SER      4.4     2.5    -      -       -      +
    208A  PRO*     1.3    76.3    -      -       -      +
    210A  THR*     1.3    63.6    +      -       -      +
    211A  LYS*     4.0    27.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  LYS*     5.6     3.1    -      -       -      -
    197A  ALA*     3.9    23.6    -      -       +      -
    198A  CYS      3.3    11.0    -      -       -      +
    199A  GLU*     3.6    24.2    +      -       +      +
    208A  PRO      4.1     2.7    +      -       -      -
    209A  VAL*     1.3    77.1    -      -       -      +
    211A  LYS*     1.3    72.2    +      -       -      +
    212A  SER*     4.1     6.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  VAL*     3.5    48.7    +      -       +      +
    120A  PHE*     4.6     1.3    -      -       -      -
    121A  ILE*     3.5    27.6    -      -       +      +
    197A  ALA*     3.4     2.1    -      -       -      +
    198A  CYS*     2.8    35.0    +      -       +      +
    209A  VAL*     4.0    19.9    +      -       +      -
    210A  THR*     1.3    79.4    -      -       -      +
    212A  SER*     1.3    59.4    +      -       -      +
    140B  GLU*     4.3    20.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 212 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ILE*     4.0    10.9    -      -       -      +
    195A  VAL*     4.2    11.6    -      -       -      +
    196A  TYR      3.1     9.0    +      -       -      -
    197A  ALA*     3.1    26.3    -      -       -      +
    210A  THR*     4.1     7.2    -      -       -      +
    211A  LYS*     1.3    71.1    -      -       -      +
    213A  PHE*     1.3    64.6    +      -       -      +
    214A  ASN*     5.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 213 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ILE*     3.9    22.9    -      -       +      -
    123A  PRO*     3.5    38.1    -      -       +      -
    124A  PRO*     4.1     2.2    -      -       +      -
    136A  VAL*     3.7    17.0    -      -       +      -
    190A  TYR*     3.5    22.7    -      +       -      -
    194A  LYS      3.8     0.2    -      -       -      +
    195A  VAL*     3.5     2.9    -      -       -      +
    196A  TYR*     3.0    66.5    +      +       +      -
    212A  SER*     1.3    74.9    -      -       -      +
    214A  ASN*     1.3    72.1    +      -       -      +
    215A  ARG*     4.1     4.0    -      -       -      -
    218A  CYS*     3.8    11.4    -      -       -      -
    134B  CYS*     3.9    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 214 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  LYS*     3.3    21.1    -      -       +      +
    195A  VAL*     3.2    32.1    -      -       -      +
    212A  SER*     5.9     0.5    -      -       -      -
    213A  PHE*     1.3    75.2    -      -       -      +
    215A  ARG*     1.3    63.7    +      -       -      +
    216A  GLY      3.4     0.2    +      -       -      -
    217A  GLU*     3.2    52.9    +      -       -      +
    218A  CYS*     3.8     8.8    -      -       -      -
    134B  CYS*     5.1     0.6    -      -       -      -
----------------------------------------------------------
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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