Contacts of the strand formed by residues 548 - 553 (chain q) in PDB entry 6FF7


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 LYS 548 (chain q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413q  ILE*     5.4     5.6    -      -       +      +
    416q  HIS      4.9     6.3    -      -       -      +
    417q  GLN*     3.4    11.2    -      -       -      +
    516q  SER      3.0    11.5    +      -       -      +
    517q  VAL*     3.2    10.2    -      -       +      +
    518q  VAL*     2.9    26.2    +      -       -      +
    546q  GLU      3.8     1.5    +      -       -      +
    547q  LEU*     1.3    77.8    -      -       -      +
    549q  VAL*     1.3    62.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 549 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417q  GLN      2.8    13.5    +      -       -      +
    418q  VAL*     3.2    13.0    -      -       +      -
    419q  LEU*     3.0    24.8    +      -       -      +
    518q  VAL*     3.3    12.3    -      -       +      +
    537q  ILE*     5.4    13.2    -      -       +      -
    548q  LYS*     1.3    76.4    -      -       -      +
    550q  LEU*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 550 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419q  LEU*     3.4    10.8    -      -       +      +
    421q  ILE*     5.9     5.6    -      -       +      -
    518q  VAL      3.0     6.9    +      -       -      +
    519q  MET*     3.3    16.1    -      -       +      +
    520q  VAL*     2.9    26.2    +      -       -      +
    549q  VAL*     1.3    77.1    -      -       -      +
    551q  VAL*     1.3    64.0    +      -       -      +
    552q  ALA*     4.0     1.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 551 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    419q  LEU      2.8    15.0    +      -       -      +
    420q  ILE*     3.2    10.9    -      -       +      +
    421q  ILE*     2.7    33.2    +      -       -      +
    520q  VAL*     3.4    11.7    -      -       +      +
    523q  ALA*     4.9    10.8    -      -       +      -
    550q  LEU*     1.3    74.9    -      -       -      +
    552q  ALA*     1.3    55.8    +      -       -      +
    561q  PHE*     5.9     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 552 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421q  ILE*     3.2    15.5    -      -       +      +
    429q  LYS*     4.8    18.2    -      -       +      -
    519q  MET*     6.2     2.7    -      -       +      -
    520q  VAL      2.8     7.4    +      -       -      +
    521q  ASP*     3.5    19.0    -      -       +      -
    522q  GLU      3.1     8.7    +      -       -      +
    523q  ALA*     2.9    26.1    +      -       -      +
    550q  LEU*     4.0     2.0    +      -       +      +
    551q  VAL*     1.3    74.3    -      -       -      +
    553q  SER*     1.3    61.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 553 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421q  ILE      2.9     7.7    +      -       -      +
    422q  GLU*     3.1    27.6    -      -       -      +
    423q  GLY      3.1     5.2    +      -       -      +
    522q  GLU*     4.7     2.7    -      -       -      +
    523q  ALA*     4.1     9.6    -      -       -      +
    524q  HIS*     4.0    19.5    -      -       -      +
    551q  VAL      5.6     0.4    -      -       -      -
    552q  ALA*     1.3    77.4    -      -       -      +
    554q  ALA*     1.3    61.7    +      -       -      +
    555q  THR*     4.1    14.4    -      -       -      -
    557q  ASP      5.4     3.1    -      -       -      -
----------------------------------------------------------
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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