Contacts of the strand formed by residues 471 - 477 (chain A) in PDB entry 3QFS


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 SER 471 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290A  THR*     5.0     1.7    +      -       -      -
    307A  GLU*     3.8    11.0    +      -       -      +
    308A  LEU      3.2    13.2    +      -       -      -
    309A  ASP*     5.0     1.1    -      -       -      -
    310A  ILE*     3.8     1.9    -      -       -      +
    317A  TYR*     2.9    24.1    +      -       -      -
    463A  SER*     3.4     3.5    +      -       -      -
    468A  HIS*     3.0    18.6    +      -       -      +
    469A  PRO      3.5     1.0    -      -       -      -
    470A  ASN*     1.3    80.5    -      -       -      +
    472A  VAL*     1.3    65.3    +      -       -      +
    473A  HIS*     3.0    28.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 472 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  GLU*     3.7     0.2    -      -       -      -
    308A  LEU*     2.8    48.6    +      -       +      +
    310A  ILE*     3.8    30.7    -      -       +      -
    317A  TYR*     3.9    17.7    -      -       +      -
    323A  VAL*     3.9    23.8    -      -       +      -
    461A  ILE*     3.7    30.7    -      -       +      -
    463A  SER*     3.8     2.7    -      -       -      -
    471A  SER*     1.3    76.1    +      -       -      +
    473A  HIS*     1.3    65.6    +      -       -      +
    514A  MET*     4.4     9.0    -      -       +      -
    516A  VAL*     4.9     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  HIS*     3.6    19.2    +      -       -      +
    306A  LEU      3.1     6.1    -      -       -      +
    307A  GLU*     3.4    37.2    +      -       +      +
    461A  ILE*     3.5     8.1    -      -       -      -
    462A  ALA*     2.8    36.2    +      -       +      -
    463A  SER*     3.2    25.2    +      -       -      -
    468A  HIS*     3.8    34.8    -      +       -      -
    471A  SER*     3.0    33.8    +      -       -      -
    472A  VAL*     1.3    76.7    -      -       -      +
    474A  ILE*     1.3    65.4    +      -       -      +
    548A  GLN*     4.5     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  MET      3.6     0.7    -      -       -      +
    305A  HIS*     3.3     7.6    -      -       -      -
    306A  LEU*     2.9    45.5    +      -       +      +
    308A  LEU*     3.8    30.1    -      -       +      -
    323A  VAL*     3.8    26.5    -      -       +      -
    325A  VAL*     4.4    13.5    -      -       +      -
    459A  TYR*     3.9    34.1    -      -       +      -
    460A  SER      4.9     2.5    -      -       -      -
    462A  ALA*     4.6     0.9    -      -       -      -
    472A  VAL      4.9     0.9    -      -       -      +
    473A  HIS*     1.3    79.8    -      -       -      +
    475A  CYS*     1.3    68.6    +      -       -      +
    476A  ALA*     4.1     7.2    -      -       +      +
    497A  LEU*     4.8    16.6    -      -       +      -
    578A  TYR*     4.6     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 475 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  LEU*     3.9     7.6    -      -       -      -
    303A  LEU*     5.9     0.7    -      -       -      -
    304A  MET      3.4     4.0    -      -       -      -
    460A  SER      4.9     3.0    +      -       -      -
    462A  ALA*     4.4     6.2    -      -       +      +
    474A  ILE*     1.3    74.4    -      -       -      +
    476A  ALA*     1.3    62.1    -      -       -      +
    538A  THR*     4.3    15.7    -      -       -      +
    540A  VAL*     4.7     4.3    -      -       -      -
    541A  ALA*     4.2    14.6    -      -       +      -
    577A  LEU*     3.9    24.5    -      -       -      -
    578A  TYR*     3.3    38.4    -      -       +      +
    752A  FAD      3.0    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 476 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  LEU*     3.4     2.1    -      -       -      -
    304A  MET*     2.8    57.8    +      -       +      +
    459A  TYR*     3.8    23.1    -      -       +      -
    474A  ILE*     4.1     7.8    -      -       +      -
    475A  CYS*     1.3    76.6    -      -       -      +
    477A  VAL*     1.3    59.8    +      -       -      +
    494A  THR*     4.4     5.2    -      -       +      -
    497A  LEU*     5.3     1.1    -      -       +      -
    538A  THR*     4.2     5.2    -      -       -      -
    752A  FAD      3.1    13.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  ARG*     4.0    30.1    -      -       +      +
    302A  HIS      3.6     4.9    -      -       -      +
    303A  LEU*     4.0    17.5    -      -       +      -
    476A  ALA*     1.3    74.9    -      -       -      +
    478A  VAL*     1.3    73.8    +      -       -      +
    479A  VAL*     3.6     8.7    +      -       +      +
    494A  THR*     3.4    16.5    -      -       -      +
    538A  THR*     3.8    19.4    -      -       +      +
    752A  FAD      3.2    13.5    +      -       -      +
    753A  NAP      4.2    13.9    -      -       -      +
----------------------------------------------------------
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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