Contacts of the strand formed by residues 224 - 231 (chain A) in PDB entry 6BFN


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 GLY 224 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  GLU*     3.4     0.9    -      -       -      +
    221A  GLY      2.9    28.0    +      -       -      +
    222A  GLY      3.3     3.6    +      -       -      -
    223A  PHE*     1.3    91.0    -      -       -      +
    225A  CYS*     1.3    66.2    +      -       -      -
    240A  ARG      3.1    11.2    -      -       -      -
    242A  LYS*     3.7    20.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 225 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  LYS*     3.5    31.4    -      -       -      -
    219A  GLY      3.6     4.0    -      -       -      -
    220A  GLU*     4.1     8.5    -      -       -      +
    224A  GLY*     1.3    79.1    -      -       -      -
    226A  VAL*     1.3    64.1    +      -       -      +
    227A  TYR*     3.8    23.9    -      -       +      +
    238A  VAL      3.7     0.9    -      -       -      +
    239A  LYS*     3.5     3.3    -      -       -      +
    240A  ARG*     2.8    36.8    +      -       +      +
    242A  LYS*     4.4    13.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  LYS*     3.6     3.6    -      -       -      +
    218A  ILE*     2.8    47.9    +      -       +      -
    219A  GLY*     2.9    30.6    +      -       -      +
    223A  PHE*     3.6    25.6    -      -       +      -
    225A  CYS*     1.3    78.7    -      -       -      +
    227A  TYR*     1.3    61.7    +      -       -      +
    237A  ALA*     4.4     6.5    -      -       +      -
    238A  VAL      3.3     9.4    -      -       -      +
    239A  LYS*     4.2     8.1    -      -       +      +
    288A  TYR*     6.5     0.4    -      -       +      -
    601A  DL1      3.8    40.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  THR*     4.0    21.1    -      -       +      -
    212A  PHE*     3.6    53.7    +      +       +      +
    213A  SER      3.4    26.2    -      -       -      -
    214A  GLU*     5.4     1.2    +      -       -      -
    216A  LEU*     3.2     9.9    -      -       +      +
    217A  LYS*     3.7    26.2    -      -       +      +
    218A  ILE*     3.9     7.1    -      -       -      +
    225A  CYS*     3.8    34.7    -      -       +      +
    226A  VAL*     1.3    73.4    -      -       -      +
    228A  ARG*     1.3    61.6    +      -       -      +
    237A  ALA*     3.3     6.8    -      -       -      +
    238A  VAL*     2.9    41.8    +      -       +      +
    240A  ARG*     4.1    18.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  THR*     5.0     0.3    -      -       -      -
    216A  LEU*     2.9    39.0    +      -       +      +
    218A  ILE*     4.0    21.6    -      -       +      +
    227A  TYR*     1.3    72.6    -      -       -      +
    229A  ALA*     1.3    61.1    +      -       -      +
    230A  VAL*     4.0    19.4    -      -       -      +
    235A  VAL*     3.8    35.3    -      -       +      +
    236A  TYR      3.6     3.4    -      -       -      -
    290A  PHE*     3.8    31.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208A  GLY*     3.6    19.1    -      -       -      +
    209A  THR*     3.9    11.4    -      -       +      -
    227A  TYR      3.8     0.6    +      -       -      -
    228A  ARG*     1.3    73.5    -      -       -      +
    230A  VAL*     1.3    65.9    +      -       -      +
    231A  MET*     4.1    11.2    -      -       +      -
    235A  VAL*     3.4     7.3    -      -       -      +
    236A  TYR*     2.9    33.4    +      -       +      +
    238A  VAL*     3.8    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208A  GLY*     3.6    17.5    +      -       -      +
    228A  ARG*     4.0    20.4    -      -       -      +
    229A  ALA*     1.3    78.3    -      -       -      +
    231A  MET*     1.3    68.3    +      -       -      +
    233A  ASN*     4.4    10.1    -      -       -      +
    234A  THR      3.3    19.3    -      -       -      +
    235A  VAL*     4.2    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  TRP*     3.8    33.9    -      -       +      -
    204A  GLU*     3.6    33.4    -      -       +      +
    205A  ILE*     3.7    28.0    -      -       +      -
    208A  GLY*     4.1     6.1    -      -       -      -
    229A  ALA*     4.1     4.7    -      -       +      -
    230A  VAL*     1.3    81.3    -      -       -      +
    232A  ARG*     1.3    73.3    +      -       -      +
    233A  ASN      3.2     1.6    -      -       -      -
    234A  THR*     2.9    24.8    +      -       -      +
    236A  TYR*     3.4    27.3    -      -       +      -
    238A  VAL*     4.5     6.5    -      -       +      -
    287A  VAL*     3.9    18.8    -      -       +      -
----------------------------------------------------------
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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