Contacts of the strand formed by residues 446 - 451 (chain A) in PDB entry 6N8P


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 THR 446 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442A  HIS*     3.0    31.8    +      -       -      +
    444A  ASP*     2.6    37.2    +      -       -      +
    445A  GLY*     1.3    80.9    -      -       -      +
    447A  VAL*     1.3    64.2    +      -       -      +
    448A  ARG*     2.8    31.3    +      -       -      +
    462A  LYS*     4.6    13.2    -      -       +      -
    463A  LEU      3.1    11.0    -      -       -      +
    464A  SER*     4.3    17.5    -      -       -      +
    507A  ILE*     4.1     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 447 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    439A  LEU*     4.4     9.9    -      -       +      -
    440A  THR      3.3     6.3    -      -       -      +
    445A  GLY      4.8     1.1    -      -       -      +
    446A  THR*     1.3    78.2    -      -       -      +
    448A  ARG*     1.3    67.5    +      -       -      +
    449A  PHE*     4.0    19.2    -      -       +      -
    461A  TYR      4.1     0.5    -      -       -      +
    462A  LYS*     3.5     1.4    -      -       -      -
    463A  LEU*     2.7    50.6    +      -       +      +
    465A  THR*     4.9     5.2    -      -       +      -
    507A  ILE*     3.9    21.3    -      -       +      -
    510A  ILE*     3.7    30.3    -      -       +      -
    519A  LEU*     5.2     1.3    -      -       +      -
    521A  VAL*     4.2    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 448 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382A  LEU      5.8     0.2    -      -       -      -
    384A  CYS*     3.1    34.2    -      -       -      -
    385A  SER*     4.8     2.4    -      -       -      +
    439A  LEU*     3.2     7.8    -      -       -      +
    440A  THR*     3.1    31.5    +      -       -      +
    442A  HIS*     3.3    27.2    +      -       -      +
    444A  ASP*     4.7     1.6    +      -       -      -
    446A  THR*     2.8    30.9    +      -       -      +
    447A  VAL*     1.3    75.4    -      -       -      +
    449A  PHE*     1.3    62.6    +      -       -      +
    450A  TRP*     3.5    36.4    -      -       -      +
    459A  LEU*     3.6    15.6    -      -       +      +
    461A  TYR      3.5     2.9    -      -       -      -
    462A  LYS*     3.3    48.7    -      -       +      +
    495A  SER*     5.5     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 449 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404A  ILE*     4.2    12.3    -      -       +      -
    437A  LEU*     3.8    23.8    -      -       +      -
    438A  LEU      3.7     2.9    -      -       -      -
    439A  LEU*     3.5    31.6    -      -       +      -
    447A  VAL*     4.0    20.2    -      -       +      -
    448A  ARG*     1.3    75.3    -      -       -      +
    450A  TRP*     1.3    57.5    +      -       -      +
    459A  LEU*     3.6     2.0    -      -       -      +
    460A  LEU*     2.7    35.0    +      -       +      +
    461A  TYR*     2.8    52.7    +      +       +      +
    463A  LEU*     4.5     4.0    -      -       +      -
    512A  LEU*     3.9    13.7    -      -       +      -
    519A  LEU*     4.0    11.9    -      -       +      -
    577A  PHE*     3.5    29.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with TRP 450 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  ALA*     4.0    24.5    -      -       +      -
    381A  SER      5.3     2.0    -      -       -      -
    382A  LEU*     3.5    40.4    -      -       +      -
    437A  LEU*     3.2    12.2    -      -       -      +
    438A  LEU*     2.6    53.6    +      -       +      +
    440A  THR*     3.0    35.0    +      -       +      +
    442A  HIS*     5.5     0.2    -      -       -      -
    448A  ARG*     3.5    36.5    -      -       +      +
    449A  PHE*     1.3    73.7    -      -       -      +
    451A  ASP*     1.3    59.4    +      -       -      +
    452A  ALA      3.2     1.3    +      -       -      -
    457A  LEU*     3.6    35.7    -      -       +      -
    458A  ARG*     3.5     8.3    -      -       -      -
    459A  LEU*     3.5    44.0    -      -       +      -
    460A  LEU*     4.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 451 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401A  TRP*     3.1    24.9    -      -       +      -
    436A  ASP      4.1     2.9    -      -       -      -
    450A  TRP*     1.3    68.8    -      -       -      +
    452A  ALA*     1.3    53.1    +      -       -      +
    453A  SER*     2.3    34.2    +      -       -      -
    456A  CYS      2.6    29.7    -      -       -      +
    457A  LEU*     3.7     5.0    -      -       -      -
    458A  ARG*     2.8    28.1    +      -       +      +
    460A  LEU*     3.6    24.6    -      -       +      +
----------------------------------------------------------
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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