Contacts of the strand formed by residues 465 - 469 (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 465 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B    A      5.6     2.1    -      -       -      -
     17B    C      5.1     1.0    +      -       -      +
   1242I  LYS*     3.3    43.2    -      -       -      +
    352J  ARG*     2.6    47.3    +      -       -      +
    353J  SER      3.3     9.4    -      -       -      +
    354J  VAL*     3.8    18.1    -      -       +      +
    425J  ARG*     4.4     3.7    +      -       -      +
    426J  ALA*     4.4    18.9    +      -       -      +
    463J  GLY      3.9     9.1    +      -       -      +
    464J  ASP*     1.3    80.1    -      -       -      +
    466J  MET*     1.3    66.4    +      -       -      +
     19R    U      5.1    12.0    +      -       -      +
     20R    A      6.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 466 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352J  ARG*     3.5     3.7    -      -       -      -
    353J  SER      3.0    29.9    +      -       -      +
    355J  ILE*     3.7    29.5    -      -       +      +
    423J  LEU*     3.7    16.4    -      -       +      -
    424J  ASN      3.4    36.6    -      -       -      +
    425J  ARG*     3.7    16.8    -      -       +      +
    447J  ILE*     3.7    12.6    -      -       +      +
    449J  LEU*     3.6    25.4    -      -       -      -
    457J  TYR*     3.6    32.5    -      -       +      -
    459J  ALA*     5.4     0.9    -      -       -      -
    465J  GLN*     1.3    79.5    -      -       -      +
    467J  ALA*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 467 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1268I  GLN*     4.4    14.6    -      -       +      -
    351J  GLY      3.2    12.6    -      -       -      +
    352J  ARG*     3.7    17.3    -      -       +      -
    422J  LEU      3.5     1.0    -      -       -      +
    423J  LEU*     3.6     0.7    -      -       -      -
    424J  ASN*     2.9    47.3    +      -       +      +
    466J  MET*     1.3    74.7    -      -       -      +
    468J  VAL*     1.3    61.7    +      -       -      +
    469J  HIS*     4.5     7.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 468 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    350J  SER*     3.3     5.5    -      -       -      -
    351J  GLY      2.8    35.9    +      -       -      +
    368J  LEU*     4.2    15.3    -      -       +      -
    372J  MET*     3.7    26.9    -      -       +      -
    376J  LEU*     3.8    22.0    -      -       +      -
    421J  VAL*     5.0     2.9    -      -       +      -
    422J  LEU      3.2     5.2    -      -       -      +
    423J  LEU*     3.7    30.7    -      -       +      -
    447J  ILE*     3.8    19.5    -      -       +      -
    466J  MET      4.3     0.2    +      -       -      -
    467J  ALA*     1.3    77.8    -      -       -      +
    469J  HIS*     1.3    65.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 469 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1268I  GLN*     4.3    22.2    -      -       +      +
   1269I  ARG      5.4     0.8    +      -       -      -
   1270I  PHE*     3.8    34.2    -      +       +      +
   1290I  MET*     4.5    10.0    -      -       +      -
   1294I  LYS*     4.4     8.7    -      -       -      +
    347J  VAL*     4.4    10.2    -      -       +      +
    349J  TYR      3.9     4.3    -      -       -      -
    350J  SER*     3.4    25.1    -      -       -      -
    421J  VAL*     3.4     8.7    -      -       -      +
    422J  LEU*     2.8    50.0    +      -       +      +
    424J  ASN*     4.0    26.6    +      -       +      +
    434J  ILE*     6.4     0.2    -      -       +      -
    467J  ALA*     4.5     5.7    -      -       +      +
    468J  VAL*     1.3    75.3    -      -       -      +
    470J  VAL*     1.3    64.0    +      -       -      +
    471J  PRO*     4.3     0.9    -      -       -      -
----------------------------------------------------------
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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