Contacts of the strand formed by residues 189 - 194 (chain H) in PDB entry 2FD6


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 THR 189 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149H  TRP*     3.5     5.5    -      -       -      -
    150H  ASN*     2.7    41.8    +      -       -      -
    187H  THR*     3.3    18.4    -      -       -      +
    188H  VAL*     1.3    77.9    +      -       -      +
    190H  CYS*     1.3    65.3    +      -       -      +
    191H  ASN*     3.8    15.2    +      -       -      +
    202H  ASP*     3.8    10.1    -      -       +      -
    203H  LYS      3.5    28.9    -      -       -      +
    204H  LYS*     3.4    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 190 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121H  VAL*     4.1     0.9    -      -       -      -
    122H  TYR      5.3     0.4    -      -       -      -
    134H  GLY      4.3     0.4    -      -       -      -
    135H  CYS*     2.0    48.9    -      -       +      -
    147H  VAL*     4.5     4.3    -      -       +      -
    148H  THR      3.2     9.2    -      -       -      +
    149H  TRP*     3.6    27.7    -      -       +      -
    189H  THR*     1.3    72.3    -      -       -      +
    191H  ASN*     1.3    62.2    +      -       -      +
    192H  VAL*     3.9     0.7    +      -       -      +
    201H  VAL      3.6     1.7    -      -       -      +
    202H  ASP*     3.4     1.9    -      -       -      -
    203H  LYS*     2.9    54.0    +      -       -      +
    205H  ILE*     4.3     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 191 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146H  THR      3.1     6.1    -      -       -      +
    147H  VAL*     3.2     1.9    -      -       -      -
    148H  THR*     2.7    54.3    +      -       -      +
    150H  ASN*     3.6     1.6    +      -       -      +
    151H  SER*     2.7    40.3    +      -       -      +
    189H  THR*     3.8    16.1    +      -       -      +
    190H  CYS*     1.3    77.3    -      -       -      +
    192H  VAL*     1.3    63.1    +      -       -      +
    193H  ALA*     5.7     0.2    -      -       -      -
    201H  VAL      3.4     4.3    -      -       -      +
    202H  ASP*     3.1    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 192 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119H  PRO*     4.2    11.0    -      -       +      -
    121H  VAL*     3.7    45.1    -      -       +      -
    135H  CYS*     4.0    10.1    -      -       -      -
    137H  VAL*     3.9    33.7    -      -       +      -
    145H  VAL*     4.5    10.1    -      -       +      -
    146H  THR      3.3     4.9    -      -       -      +
    147H  VAL*     4.2     8.3    -      -       +      -
    190H  CYS*     4.7     0.2    -      -       -      -
    191H  ASN*     1.3    77.7    -      -       -      +
    193H  ALA*     1.3    65.7    +      -       -      +
    194H  HIS      4.3     0.2    +      -       -      -
    200H  LYS*     3.2     2.9    -      -       -      +
    201H  VAL*     2.8    42.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 193 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145H  VAL*     3.2     5.5    -      -       -      -
    146H  THR*     2.8    52.1    +      -       +      +
    191H  ASN      5.7     0.2    -      -       -      -
    192H  VAL*     1.3    79.3    -      -       -      +
    194H  HIS*     1.3    60.6    +      -       -      +
    195H  PRO*     3.5    10.9    -      -       +      +
    199H  THR      3.4     7.2    -      -       -      +
    200H  LYS*     4.4    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 194 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117H  THR      3.2    15.1    +      -       -      -
    118H  PRO*     4.0     0.8    -      -       -      +
    119H  PRO*     3.6    16.6    -      -       +      -
    140H  TYR*     4.1     2.7    -      +       -      -
    141H  PHE      3.1    27.7    +      -       -      -
    142H  PRO      2.8    26.8    +      -       -      -
    144H  PRO      3.6     7.4    -      -       -      -
    145H  VAL*     3.5    23.6    -      -       +      -
    192H  VAL*     4.3     0.6    -      -       -      +
    193H  ALA*     1.3    73.3    -      -       -      +
    195H  PRO*     1.3    67.1    -      -       -      +
    196H  ALA*     3.5    17.9    -      -       +      +
    197H  SER*     2.6    26.9    +      -       -      -
    198H  SER      3.1     2.8    +      -       -      -
    199H  THR*     2.8    40.8    +      -       -      +
----------------------------------------------------------
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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