Contacts of the strand formed by residues 459 - 464 (chain A) in PDB entry 7ACN


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 459 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  PHE*     3.3    18.7    -      -       -      -
    430A  ARG*     3.9     5.8    -      -       -      +
    439A  ASN*     2.8    22.8    +      -       -      +
    441A  ILE*     3.8    31.6    -      -       +      -
    448A  ASN      5.8     0.2    -      -       -      +
    451A  GLY*     5.5     2.5    +      -       -      -
    453A  ASN*     5.6     2.0    -      -       +      +
    454A  ASP*     2.9    30.5    +      -       -      +
    456A  ASN*     3.1    22.6    +      -       -      +
    457A  PRO      3.3     0.4    -      -       -      +
    458A  GLU*     1.3    77.8    -      -       -      +
    460A  HIS*     1.3    63.5    +      -       -      +
    461A  ALA*     3.6     5.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 460 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  PRO*     4.0    13.2    -      -       +      -
    326A  PHE*     3.8    23.0    -      +       -      -
    346A  TRP*     3.6    32.7    -      +       -      -
    347A  PRO*     3.7    14.9    -      -       +      +
    438A  LYS*     3.8    20.6    +      -       +      +
    439A  ASN      2.7    14.9    +      -       -      +
    440A  THR*     3.4    14.1    -      -       -      +
    441A  ILE      3.0    24.3    +      -       -      +
    458A  GLU*     2.9    50.5    +      -       -      -
    459A  THR*     1.3    73.0    -      -       -      +
    461A  ALA*     1.3    58.4    +      -       -      +
    462A  PHE*     3.9     8.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 461 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  PRO*     3.4    14.0    +      -       -      +
    441A  ILE*     3.4    22.9    -      -       +      -
    443A  THR*     5.0     6.1    -      -       +      +
    448A  ASN*     3.0    41.4    +      -       +      +
    453A  ASN*     3.8    18.8    -      -       -      +
    459A  THR*     3.6     7.8    +      -       +      +
    460A  HIS*     1.3    72.8    -      -       -      +
    462A  PHE*     1.3    60.4    +      -       -      +
    463A  VAL*     5.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 462 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  ILE*     3.6    32.3    -      -       +      -
    323A  ASN      3.2     8.3    -      -       -      -
    324A  GLY      3.5    29.6    -      -       -      -
    325A  PRO*     3.8    14.6    -      -       +      -
    332A  HIS*     4.9     0.7    -      +       -      -
    337A  VAL*     4.3    13.9    -      -       +      -
    346A  TRP*     3.9    30.1    -      +       +      -
    440A  THR*     3.8    31.9    -      -       +      -
    441A  ILE      3.1     9.9    +      -       -      -
    442A  VAL*     3.3     8.9    -      -       +      +
    443A  THR*     2.8    27.3    +      -       -      +
    460A  HIS*     3.9    16.2    -      -       +      -
    461A  ALA*     1.3    73.1    -      -       -      +
    463A  VAL*     1.3    60.6    +      -       -      +
    478A  LEU*     4.1    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 463 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  LYS*     5.0     0.2    -      -       -      -
    222A  LEU*     3.9    15.6    -      -       +      +
    259A  MET*     4.4     6.1    -      -       +      -
    322A  ILE*     3.4     1.0    -      -       -      -
    323A  ASN*     2.9    52.7    +      -       +      +
    328A  PRO*     5.0     1.6    -      -       +      -
    443A  THR*     3.3    20.9    -      -       -      +
    445A  TYR      3.8    20.2    -      -       -      +
    446A  ASN      3.8    24.9    -      -       -      +
    447A  ARG      4.0    10.5    -      -       -      +
    448A  ASN*     4.2    14.1    -      -       +      +
    461A  ALA*     5.9     0.4    -      -       +      -
    462A  PHE*     1.3    72.1    -      -       -      +
    464A  THR*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 464 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  LYS*     2.7    33.6    +      -       -      -
    222A  LEU*     4.0     9.2    -      -       -      -
    321A  HIS      2.8    20.4    +      -       -      -
    322A  ILE*     4.0    18.7    -      -       +      +
    442A  VAL*     4.7     7.2    -      -       +      -
    443A  THR      2.9     9.1    +      -       -      +
    444A  SER*     3.2     8.7    -      -       -      -
    463A  VAL*     1.3    75.9    -      -       -      +
    465A  SER*     1.3    64.4    +      -       -      +
    468A  ILE*     3.5    27.1    -      -       +      +
    469A  VAL*     3.6    27.1    -      -       +      +
    472A  LEU*     5.0     0.2    -      -       +      -
----------------------------------------------------------
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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