Contacts of the strand formed by residues 365 - 369 (chain J) in PDB entry 6C6U


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 GLN 365 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360J  TYR      4.9     2.4    +      -       -      -
    361J  LEU*     3.6    22.1    -      -       +      +
    362J  ARG*     3.3    57.5    -      -       +      +
    363J  LEU      3.4     1.6    +      -       -      -
    364J  HIS*     1.3    91.2    -      -       +      +
    366J  CYS*     1.3    60.6    +      -       -      +
    437J  PHE*     3.8     7.8    -      -       -      -
    438J  GLU*     3.2    20.6    -      -       +      +
    440J  VAL*     3.4    24.2    -      -       +      +
    450J  HIS*     4.5     5.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 366 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361J  LEU*     3.9     4.9    -      -       -      -
    365J  GLN*     1.3    77.7    -      -       -      +
    367J  GLY*     1.3    67.6    +      -       -      +
    368J  LEU*     4.8     5.8    -      -       -      -
    421J  VAL*     4.7     4.0    -      -       -      -
    423J  LEU*     3.6    31.6    -      -       +      -
    437J  PHE*     3.7    19.9    -      -       +      +
    438J  GLU      3.5     2.2    +      -       -      -
    439J  PRO*     3.5     8.9    -      -       -      +
    440J  VAL*     2.9    26.8    +      -       -      -
    447J  ILE*     4.9     0.4    -      -       -      -
    448J  GLN      3.4    11.7    -      -       -      +
    449J  LEU*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 367 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361J  LEU*     3.9     7.2    -      -       -      +
    366J  CYS*     1.3    74.3    -      -       -      +
    368J  LEU*     1.3    60.7    +      -       -      +
    440J  VAL*     3.5     9.2    -      -       -      -
    442J  ILE*     3.6    17.3    -      -       -      -
    446J  ALA      4.7     0.2    -      -       -      -
    447J  ILE*     3.3    15.8    -      -       -      +
    448J  GLN*     2.5    42.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 368 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366J  CYS*     4.6     6.7    -      -       -      +
    367J  GLY*     1.3    76.2    -      -       -      +
    369J  PRO*     1.3    89.0    -      -       +      +
    372J  MET*     4.3     8.1    -      -       +      -
    373J  ALA*     3.6    26.2    -      -       +      +
    376J  LEU*     4.9     6.7    -      -       +      -
    377J  PHE*     5.3     2.7    -      -       +      -
    421J  VAL*     4.3    22.9    -      -       +      -
    439J  PRO*     4.3    20.6    -      -       +      -
    440J  VAL      2.9    11.7    +      -       -      +
    441J  LEU*     3.4     3.3    -      -       +      -
    442J  ILE*     2.9    24.2    +      -       -      +
    446J  ALA      4.5     0.2    -      -       -      -
    447J  ILE*     4.8     4.9    -      -       +      +
    468J  VAL*     4.2    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 369 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1243I  MET*     4.5     3.6    -      -       -      -
    368J  LEU*     1.3    94.4    -      -       +      +
    370J  LYS*     1.3    61.8    +      -       -      +
    371J  LYS*     3.3     2.9    -      -       +      +
    372J  MET*     3.7    42.0    -      -       +      +
    373J  ALA*     3.0    27.4    +      -       -      +
    441J  LEU*     5.1     0.2    -      -       -      -
    442J  ILE*     3.5    10.1    -      -       +      +
    444J  GLY      3.6    15.7    -      -       -      +
    445J  LYS*     4.0     4.3    -      -       -      -
    446J  ALA      3.4    33.9    -      -       -      +
    447J  ILE*     4.4     2.5    -      -       +      -
----------------------------------------------------------
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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