Contacts of the strand formed by residues 328 - 332 (chain D) in PDB entry 4CKG


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 CYS 328 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146C  ARG*     3.6     9.7    +      -       -      +
    283D  TRP*     5.5     0.2    -      -       +      -
    319D  LEU      4.2     5.2    -      -       -      +
    320D  CYS*     3.8    18.6    -      -       -      +
    323D  SER*     3.6    21.3    -      -       -      -
    325D  ARG*     3.1    45.5    -      -       +      +
    326D  ARG      4.5     0.7    -      -       -      +
    327D  PHE*     1.3    80.2    -      -       -      +
    329D  PHE*     1.3    62.4    +      -       -      +
    339D  LEU*     5.0     9.9    -      -       +      -
    340D  LEU      3.4    13.9    -      -       -      +
    341D  GLN*     4.1     3.8    -      -       -      +
    348D  LEU*     3.6    11.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 329 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272D  LEU*     4.1    16.6    -      -       +      -
    317D  VAL*     4.5     2.7    -      -       +      -
    318D  LYS      3.3    17.0    -      -       -      +
    320D  CYS*     4.2     3.8    -      -       -      -
    327D  PHE      4.6     2.2    -      -       -      -
    328D  CYS*     1.3    74.6    -      -       -      +
    330D  GLU*     1.3    62.1    +      -       -      +
    331D  VAL*     4.2    22.4    -      -       +      -
    339D  LEU*     3.6     4.8    -      -       -      +
    340D  LEU*     2.9    67.9    +      -       +      +
    342D  ALA*     4.7     8.1    -      -       +      -
    348D  LEU*     3.6    17.5    -      -       +      -
    351D  TRP*     3.4    46.0    -      +       +      -
    352D  VAL*     3.6    22.9    -      -       +      -
    355D  VAL*     4.5     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 330 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316D  THR      3.8     0.5    -      -       -      +
    317D  VAL*     3.6     3.6    -      -       -      +
    318D  LYS*     2.7    77.9    +      -       +      +
    320D  CYS*     4.0     4.0    -      -       -      -
    329D  PHE*     1.3    76.4    -      -       -      +
    331D  VAL*     1.3    65.4    +      -       -      +
    332D  VAL*     3.3    15.2    -      -       +      +
    337D  SER*     4.0    10.0    +      -       -      +
    338D  CYS      3.7    12.8    -      -       -      +
    339D  LEU*     3.7    22.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 331 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295D  LEU*     4.9     8.1    -      -       +      -
    309D  VAL*     4.7    11.5    -      -       +      +
    312D  LEU*     5.8     1.3    -      -       +      -
    315D  CYS*     3.6    14.4    -      -       -      -
    316D  THR      3.6     2.7    -      -       -      +
    317D  VAL*     4.2     6.1    -      -       +      -
    329D  PHE*     4.2    12.8    -      -       +      -
    330D  GLU*     1.3    74.1    -      -       -      +
    332D  VAL*     1.3    61.7    +      -       -      +
    333D  SER      4.1     0.4    +      -       -      -
    337D  SER*     3.0     4.9    +      -       -      -
    338D  CYS*     2.9    50.8    +      -       +      +
    340D  LEU*     3.8    20.6    -      -       +      -
    355D  VAL*     3.7    39.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 332 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314D  LEU      4.1     0.9    -      -       -      +
    315D  CYS*     3.4     2.6    -      -       -      -
    316D  THR*     3.1    43.5    +      -       +      +
    318D  LYS*     3.7    22.9    -      -       +      +
    330D  GLU*     3.3    31.4    -      -       +      +
    331D  VAL*     1.3    73.5    -      -       -      +
    333D  SER*     1.3    64.7    +      -       -      +
    337D  SER*     3.5    17.9    -      -       -      +
----------------------------------------------------------
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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