Contacts of the strand formed by residues 423 - 428 (chain G) 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 PHE 423 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365G  LEU*     3.4    27.1    -      -       +      -
    381G  TRP*     4.4     9.6    -      -       +      -
    382G  GLU      3.5     3.1    -      -       -      +
    383G  SER*     3.7    24.9    -      -       -      -
    384G  ASN      5.8     0.2    -      -       -      -
    388G  GLU*     3.9     9.0    -      -       -      -
    410G  LEU*     3.7    17.5    -      -       +      -
    412G  VAL*     3.9    25.6    -      -       +      -
    416G  ARG*     4.4    15.3    -      -       +      -
    417G  TRP*     4.1    18.8    -      +       +      -
    421G  ASN*     3.2    46.2    -      -       +      -
    422G  VAL*     1.3    73.3    -      -       -      +
    424G  SER*     1.3    61.6    +      -       -      +
    440G  SER*     3.2     5.2    -      -       -      -
    441G  LEU*     2.7    43.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 424 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381G  TRP*     3.2    11.7    -      -       -      -
    382G  GLU*     2.8    51.5    +      -       -      +
    422G  VAL*     4.8     2.6    -      -       -      +
    423G  PHE*     1.3    72.6    +      -       -      +
    425G  CYS*     1.3    60.0    +      -       -      +
    426G  SER      4.0     0.2    -      -       -      -
    438G  GLN*     3.7    33.6    +      -       -      +
    439G  LYS      3.5     3.4    -      -       -      -
    440G  SER*     3.1    22.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 425 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348G  VAL*     4.3     7.6    -      -       +      +
    350G  THR*     4.1     8.5    -      -       +      -
    367G  CYS*     2.0    55.0    -      -       +      -
    379G  VAL*     3.9    21.1    -      -       -      -
    380G  GLU      3.6     4.9    -      -       -      -
    381G  TRP*     4.1    12.3    -      -       +      -
    424G  SER*     1.3    69.9    -      -       -      +
    426G  SER*     1.3    59.3    +      -       -      +
    427G  VAL*     4.2     2.9    +      -       -      -
    437G  THR      4.2     0.2    -      -       -      +
    438G  GLN*     3.4     2.1    -      -       -      -
    439G  LYS*     2.9    36.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 426 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378G  ALA      3.9     0.5    -      -       -      +
    379G  VAL*     3.4     5.4    -      -       -      +
    380G  GLU*     2.8    54.0    +      -       -      +
    382G  GLU*     3.2    24.1    +      -       -      -
    424G  SER      4.0     0.8    +      -       -      -
    425G  CYS*     1.3    73.3    -      -       -      +
    427G  VAL*     1.3    62.0    +      -       -      +
    428G  MET*     5.2     3.0    -      -       -      +
    436G  TYR*     3.4    31.6    -      -       -      -
    437G  THR      3.4     5.8    -      -       -      -
    438G  GLN*     4.1     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 427 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346G  PRO*     4.5     4.3    -      -       +      -
    348G  VAL*     3.7    32.8    -      -       +      -
    369G  VAL*     3.9    23.3    -      -       +      -
    377G  ILE*     3.6    32.5    -      -       +      -
    378G  ALA      3.5     3.1    -      -       -      +
    379G  VAL*     4.1    10.3    -      -       +      -
    425G  CYS*     4.3     1.8    -      -       -      -
    426G  SER*     1.3    78.1    -      -       -      +
    428G  MET*     1.3    65.7    +      -       -      +
    432G  LEU*     3.5    15.6    -      -       +      +
    436G  TYR*     3.3     4.8    -      -       -      -
    437G  THR*     2.8    39.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 428 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248G  LYS*     3.6    33.2    -      -       +      -
    251G  LEU*     3.5    18.8    -      -       +      +
    252G  MET*     3.8    24.2    -      -       -      +
    377G  ILE*     3.5     6.1    -      -       -      +
    378G  ALA*     2.9    42.4    +      -       +      +
    380G  GLU*     3.6    27.4    -      -       +      +
    426G  SER*     5.2     4.7    -      -       -      +
    427G  VAL*     1.3    71.0    -      -       -      +
    429G  HIS*     1.3    63.0    +      -       -      +
    435G  HIS      3.1    17.7    -      -       -      +
    436G  TYR*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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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