Contacts of the strand formed by residues 328 - 334 (chain A) in PDB entry 6FQS


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 328 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  LEU*     3.8    18.1    -      -       -      +
    242A  GLN*     3.1    31.3    +      -       -      +
    243A  MET      3.4    12.6    -      -       -      +
    244A  ARG*     2.9    37.1    +      -       +      +
    322A  TYR*     3.6    31.9    +      -       +      +
    325A  THR      3.2    17.8    +      -       -      +
    326A  PRO*     4.1     0.5    -      -       -      +
    327A  LEU*     1.3    76.3    -      -       -      +
    329A  THR*     1.3    64.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  GLN*     3.7     5.4    -      -       -      +
    243A  MET*     2.7    46.2    +      -       +      +
    265A  PRO*     3.8    14.3    -      -       -      +
    268A  VAL*     3.9    11.6    -      -       +      +
    326A  PRO*     2.5    37.7    +      -       +      +
    327A  LEU      4.0     0.6    -      -       -      -
    328A  GLN*     1.3    73.0    +      -       -      +
    330A  SER*     1.3    66.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  SER*     2.7    22.9    +      -       -      -
    241A  ILE      3.3     4.7    +      -       -      -
    242A  GLN*     3.3    27.8    +      -       -      -
    243A  MET*     4.6     3.2    -      -       -      +
    329A  THR*     1.3    88.8    -      -       -      +
    331A  PHE*     1.3    63.8    +      -       -      +
    332A  GLY*     4.0     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  ASN*     3.3    37.7    -      -       -      -
    183A  ILE      4.1     3.1    -      -       -      -
    184A  PRO*     3.6    46.0    -      -       +      -
    218A  PHE*     4.7     5.2    -      +       +      -
    239A  GLY      3.7     0.2    -      -       -      +
    240A  SER*     3.7     0.2    -      -       -      -
    241A  ILE*     2.6    41.5    +      -       +      +
    243A  MET*     4.0    24.7    -      -       +      +
    266A  PHE*     4.0    21.8    -      +       -      -
    267A  GLN*     3.7    23.1    -      -       -      -
    329A  THR      4.2     0.2    +      -       -      -
    330A  SER*     1.3    74.5    +      -       -      +
    332A  GLY*     1.3    59.4    +      -       -      +
    333A  VAL*     3.3    21.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 332 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  ASN*     2.8    31.9    +      -       -      +
    239A  GLY      3.9     4.3    -      -       -      -
    240A  SER*     4.8     4.0    -      -       -      -
    330A  SER*     4.0     4.3    +      -       -      -
    331A  PHE*     1.3    72.5    -      -       -      +
    333A  VAL*     1.3    63.8    +      -       -      -
    334A  ASN*     3.5     2.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182A  ASN      3.5     8.5    -      -       -      +
    184A  PRO*     4.1    13.2    -      -       +      -
    233A  ALA*     3.9    22.2    -      -       +      -
    234A  TYR*     6.4     0.7    -      -       +      -
    237A  GLY      3.8     3.4    -      -       -      +
    238A  ARG*     3.3     8.0    -      -       -      +
    239A  GLY      2.9    35.0    +      -       -      +
    241A  ILE*     3.8    27.6    -      -       +      -
    331A  PHE*     3.3    19.7    +      -       +      +
    332A  GLY*     1.3    70.4    -      -       -      -
    334A  ASN*     1.3    63.3    +      -       -      +
    335A  MET*     3.5    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 334 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180A  ALA*     3.0    36.8    +      -       -      +
    181A  THR*     3.1     2.2    +      -       -      +
    182A  ASN*     2.8    40.3    +      -       +      +
    237A  GLY      3.4     3.6    -      -       -      -
    238A  ARG*     2.8    43.2    +      -       +      +
    332A  GLY      3.5     5.4    +      -       -      +
    333A  VAL*     1.3    75.4    -      -       -      +
    335A  MET*     1.3    60.1    +      -       -      +
    336A  ILE*     3.0     9.0    +      -       -      +
    345A  LEU*     3.9     4.5    -      -       -      +
----------------------------------------------------------
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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