Contacts of the strand formed by residues 427 - 432 (chain H) in PDB entry 1OAK


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 427 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341H  PRO*     3.8    16.4    -      -       +      -
    342H  PRO*     3.9     8.9    -      -       -      +
    420H  VAL      4.6     0.9    -      -       -      -
    421H  ALA*     3.6     2.4    -      -       -      +
    422H  HIS*     3.0    40.8    +      -       -      +
    425H  SER*     3.3    33.3    -      -       -      +
    426H  SER*     1.3    80.7    -      -       -      +
    428H  LYS*     1.3    62.5    +      -       -      +
    429H  VAL*     4.3     9.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 428 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374H  THR*     5.3     0.9    -      -       -      -
    376H  THR*     5.4     1.3    +      -       -      -
    419H  ASN*     3.5    34.9    -      -       -      +
    420H  VAL      3.5    12.6    -      -       -      +
    421H  ALA*     3.7    18.2    -      -       +      +
    426H  SER      4.3     0.8    +      -       -      +
    427H  THR*     1.3    76.8    -      -       -      +
    429H  VAL*     1.3    63.4    +      -       -      +
    430H  ASP*     4.0    10.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 429 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342H  PRO*     4.8    11.0    -      -       +      +
    344H  VAL*     4.0    28.7    -      -       +      +
    418H  CYS*     3.7     0.9    -      -       -      +
    419H  ASN*     3.3     0.9    -      -       -      +
    420H  VAL*     2.8    38.4    +      -       -      +
    427H  THR*     5.1     8.1    -      -       -      -
    428H  LYS*     1.3    80.7    -      -       -      +
    430H  ASP*     1.3    82.3    +      -       -      +
    431H  LYS*     4.0    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 430 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417H  THR*     4.3     9.6    -      -       +      -
    418H  CYS      3.5     3.4    -      -       -      -
    419H  ASN*     3.0    29.5    +      -       -      +
    428H  LYS*     4.0    10.8    +      -       -      -
    429H  VAL*     1.3    86.0    -      -       -      +
    431H  LYS*     1.3    70.1    +      -       -      +
    432H  LYS      4.0     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 431 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    344H  VAL*     3.5    38.6    -      -       +      +
    345H  TYR*     5.9     0.2    -      -       -      -
    346H  PRO*     3.5    23.4    -      -       +      +
    363H  CYS*     4.1     7.9    -      -       -      -
    417H  THR*     3.3     3.1    -      -       -      +
    418H  CYS*     2.9    28.7    +      -       -      -
    429H  VAL*     4.0    15.5    -      -       +      -
    430H  ASP*     1.3    81.3    -      -       -      +
    432H  LYS*     1.3    65.3    +      -       -      +
    433H  ILE*     3.6     9.4    +      -       -      +
    123L  GLU*     2.5    34.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 432 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346H  PRO*     3.7    13.2    -      -       -      +
    415H  THR*     3.8    30.1    -      -       +      +
    416H  VAL      3.7     5.8    -      -       -      +
    417H  THR*     3.3    23.9    -      -       +      +
    430H  ASP      4.0     1.0    +      -       -      -
    431H  LYS*     1.3    73.9    +      -       -      +
    433H  ILE*     1.3    66.5    +      -       -      +
    434H  VAL*     3.5    30.8    +      -       +      +
----------------------------------------------------------
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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