Contacts of the strand formed by residues 442 - 448 (chain A) in PDB entry 6Q6Q


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 ASN 442 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  HIS*     4.5     4.0    -      -       +      -
    365A  ASP*     3.8     6.8    +      -       -      -
    366A  SER      2.6    30.5    +      -       -      +
    367A  ASP*     2.8    23.5    +      -       -      +
    370A  PRO*     4.3     4.3    -      -       +      +
    428A  PHE      3.2    15.0    -      -       -      +
    429A  ARG*     3.8    13.9    -      -       +      -
    439A  ALA*     4.0     6.7    -      -       +      +
    441A  VAL*     1.3    75.6    -      -       -      +
    443A  SER*     1.3    66.3    +      -       -      +
    463A  TYR*     3.6     6.2    -      -       -      -
    464A  GLY*     3.0    41.1    +      -       -      +
    522A  PHE*     4.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 443 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  HIS*     4.0     2.3    -      -       -      -
    370A  PRO*     4.2     8.9    -      -       -      +
    371A  ILE*     4.7     0.5    -      -       -      +
    426A  SER      4.9     0.2    -      -       -      -
    427A  ALA*     3.3     6.5    -      -       -      +
    428A  PHE*     2.8    33.8    +      -       -      +
    442A  ASN*     1.3    78.9    -      -       -      +
    444A  GLY*     1.3    61.5    +      -       -      +
    445A  MET*     3.2    29.4    -      -       -      +
    462A  SER      2.4    23.5    +      -       -      -
    463A  TYR*     3.4    17.6    -      -       -      -
    522A  PHE*     4.2    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 444 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    370A  PRO*     3.9    19.3    -      -       -      +
    371A  ILE*     4.5     7.4    -      -       -      -
    374A  VAL*     3.2    15.8    -      -       -      +
    425A  VAL*     5.8     0.2    -      -       -      -
    426A  SER      3.6     7.0    -      -       -      -
    427A  ALA*     4.3     3.1    -      -       -      -
    443A  SER*     1.3    75.8    +      -       -      +
    445A  MET*     1.3    62.5    +      -       -      +
    462A  SER*     2.9    28.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 445 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  VAL*     4.1     1.6    -      -       -      +
    425A  VAL*     3.1     4.5    -      -       -      +
    426A  SER      2.9    36.1    +      -       -      +
    428A  PHE*     4.5     5.4    -      -       +      -
    443A  SER*     3.2    22.4    -      -       -      +
    444A  GLY*     1.3    79.5    -      -       -      +
    446A  ARG*     1.3    59.4    -      -       -      +
    460A  CYS      3.6     4.0    -      -       -      -
    461A  ILE*     3.6    20.4    -      -       +      -
    463A  TYR*     3.3    26.9    -      -       +      +
    522A  PHE*     3.9    25.8    -      -       +      +
    523A  LEU*     3.9    13.0    -      -       +      +
    526A  PHE*     3.6    47.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 446 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  MET*     6.1     1.1    -      -       -      -
    374A  VAL*     2.5    34.6    +      -       +      +
    375A  GLY*     3.8    10.9    -      -       -      -
    376A  ASN*     3.4    24.1    +      -       -      +
    420A  ARG*     3.8     1.4    -      -       -      +
    423A  GLU*     2.7    41.0    +      -       +      +
    424A  PHE      3.5     9.6    -      -       -      +
    425A  VAL*     3.7    18.6    -      -       +      -
    445A  MET*     1.3    74.7    -      -       -      +
    447A  VAL*     1.3    67.8    +      -       -      +
    448A  PHE*     4.3     4.4    -      -       -      +
    458A  GLU*     3.0    37.8    +      -       -      +
    459A  LEU*     3.5     6.9    -      -       -      +
    460A  CYS*     2.9    48.4    +      -       -      +
    526A  PHE*     4.4     0.9    -      -       -      -
----------------------------------------------------------
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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
----------------------------------------------------------
    422A  TRP      4.2     0.2    -      -       -      +
    423A  GLU*     3.6     4.0    -      -       -      +
    424A  PHE*     2.9    40.4    +      -       +      +
    446A  ARG*     1.3    77.4    -      -       -      +
    448A  PHE*     1.3    65.7    +      -       -      +
    449A  PHE*     3.8    20.6    -      -       +      -
    456A  ILE*     4.3     7.4    -      -       +      -
    458A  GLU      3.7     7.6    -      -       -      +
    459A  LEU*     3.7    21.5    -      -       +      -
    485A  TRP*     3.9    20.4    -      -       +      -
    526A  PHE*     4.0    13.9    -      -       +      -
    530A  VAL*     3.8    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 448 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  ARG*     3.7    39.0    -      -       +      -
    421A  LYS      3.5    22.0    -      -       -      -
    422A  TRP      3.4    13.9    -      -       -      -
    423A  GLU*     3.5    19.3    -      -       +      -
    446A  ARG*     4.3     1.8    -      -       -      +
    447A  VAL*     1.3    76.5    -      -       -      +
    449A  PHE*     1.3    62.8    +      -       -      +
    450A  GLY*     3.7    21.5    -      -       -      -
    456A  ILE*     3.6     2.9    -      -       -      -
    457A  ARG*     2.8    33.1    +      -       +      -
    458A  GLU*     3.0    51.2    +      -       +      +
----------------------------------------------------------
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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