Contacts of the strand formed by residues 668 - 675 (chain J) in PDB entry 1O18


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 HIS 668 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121J  LEU*     6.2     0.2    -      -       -      +
    165J  PHE*     4.5    21.9    -      +       -      -
    169J  ASP*     4.7     5.3    +      -       -      -
    171J  GLU*     4.2    16.5    +      -       -      +
    172J  ASN      2.7    13.9    +      -       -      +
    173J  GLN*     2.6    28.3    +      -       -      +
    174J  SER      3.2    16.5    +      -       -      -
    494J  HIS*     3.6    20.6    +      +       -      -
    498J  LEU*     5.3     3.8    -      -       -      +
    667J  THR*     1.3    70.2    -      -       -      +
    669J  PRO*     1.3    85.3    +      -       +      +
    670J  HIS*     3.3    24.9    +      +       -      -
----------------------------------------------------------
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Residues in contact with PRO 669 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121J  LEU*     5.5     2.8    -      -       -      +
    174J  SER*     3.1    10.8    -      -       -      +
    176J  LEU*     4.5     1.3    -      -       +      -
    490J  PHE*     3.5    38.4    -      -       +      -
    494J  HIS*     3.6    36.7    +      -       +      +
    667J  THR      3.1    13.7    -      -       -      +
    668J  HIS*     1.3   106.8    +      -       +      +
    670J  HIS*     1.3    63.1    +      -       -      +
    671J  PHE*     3.7    19.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 670 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121J  LEU*     6.2     2.0    -      -       -      +
    158J  ILE*     4.5    17.8    +      -       +      +
    161J  ASN*     5.2     4.0    -      -       +      -
    162J  ALA*     4.1    12.9    -      -       +      -
    165J  PHE*     3.9    23.5    -      +       -      -
    173J  GLN*     3.2    34.2    +      -       +      +
    174J  SER*     2.7    17.9    +      -       -      +
    175J  ILE*     2.9    18.2    -      -       +      -
    176J  LEU*     2.7    33.0    +      -       -      +
    668J  HIS*     3.3    41.2    +      +       -      -
    669J  PRO*     1.3    72.2    +      -       -      +
    671J  PHE*     1.3    56.8    +      -       -      +
    672J  VAL*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 671 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121J  LEU*     3.7    20.5    +      -       +      +
    122J  PHE*     3.7    23.8    -      +       +      +
    123J  CYS*     3.5    18.2    +      -       -      +
    158J  ILE*     4.4     4.4    -      -       -      +
    176J  LEU*     3.9    25.6    -      -       +      -
    487J  LEU*     4.8     2.7    -      -       +      -
    490J  PHE*     4.1     8.3    -      +       -      -
    491J  PHE*     3.2    56.3    -      +       +      -
    494J  HIS*     4.2    15.7    -      +       -      -
    669J  PRO*     3.7    29.4    -      -       +      -
    670J  HIS*     1.3    71.8    -      -       -      +
    672J  VAL*     1.3    68.8    +      -       -      +
    673J  ARG*     3.9    25.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 672 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123J  CYS*     3.8    16.4    -      -       +      +
    125J  THR*     4.9     2.0    -      -       -      +
    155J  ILE*     4.5    24.0    -      -       +      -
    158J  ILE*     4.2    21.5    -      -       +      -
    175J  ILE*     3.8    22.2    -      -       +      -
    176J  LEU      2.8    21.5    +      -       -      +
    177J  ILE*     3.4    20.8    -      -       +      -
    178J  THR      3.3    12.6    +      -       -      -
    192J  VAL*     6.4     1.1    -      -       +      -
    671J  PHE*     1.3    78.5    -      -       -      +
    673J  ARG*     1.3    68.4    +      -       -      +
    674J  CYS*     4.5    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 673 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122J  PHE*     3.9    29.2    -      -       +      -
    123J  CYS      3.3    11.1    +      -       -      +
    124J  VAL*     3.4     5.4    -      -       -      -
    125J  THR      3.0    23.7    +      -       -      -
    176J  LEU*     3.0    38.0    +      -       -      +
    178J  THR*     3.6    28.2    +      -       -      +
    484J  ASN*     5.4     3.2    +      -       -      -
    487J  LEU*     5.2    15.4    -      -       -      +
    488J  GLN*     4.6     8.5    +      -       -      +
    491J  PHE*     5.9     1.6    -      -       -      +
    671J  PHE*     3.9    21.9    -      -       -      -
    672J  VAL*     1.3    76.9    +      -       -      +
    674J  CYS*     1.3    62.4    +      -       -      +
    675J  ILE*     3.9     5.3    +      -       +      +
    698J  ASN*     3.2    52.2    +      -       +      +
    700J  VAL*     4.7     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 674 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125J  THR*     3.6     8.5    -      -       +      +
    177J  ILE*     3.5    28.0    -      -       -      -
    178J  THR      2.9    13.6    +      -       -      +
    179J  GLY*     3.7    10.9    -      -       -      -
    183J  ALA*     3.4    31.4    -      -       +      +
    185J  LYS*     4.2     7.0    -      -       +      -
    188J  ASN*     2.9    32.1    -      -       -      +
    672J  VAL*     4.5     7.2    -      -       -      -
    673J  ARG*     1.3    74.0    -      -       -      +
    675J  ILE*     1.3    64.1    +      -       -      +
    694J  GLN*     4.6     2.6    -      -       -      +
    698J  ASN*     4.8     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 675 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106J  LEU*     5.4     1.8    -      -       +      -
    124J  VAL*     3.0    33.2    -      -       +      -
    125J  THR      2.5    19.2    +      -       -      +
    126J  VAL*     3.6    22.9    -      -       +      -
    127J  ASN*     3.1    29.5    +      -       -      +
    183J  ALA*     3.9     7.7    +      -       -      +
    673J  ARG*     3.9    10.3    -      -       +      +
    674J  CYS*     1.3    75.7    -      -       -      +
    676J  ILE*     1.3    71.5    +      -       -      +
    677J  PRO*     4.2     0.7    -      -       +      -
    691J  VAL*     4.3    17.3    -      -       +      -
    694J  GLN*     4.1    17.0    -      -       +      +
    695J  LEU*     4.7    11.4    -      -       +      -
    698J  ASN*     3.7    23.8    -      -       -      +
    700J  VAL*     5.7     0.9    -      -       +      -
----------------------------------------------------------
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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