Contacts of the strand formed by residues 668 - 675 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  LEU*     6.2     0.2    -      -       -      +
    165A  PHE*     4.5    21.7    -      +       -      -
    169A  ASP*     4.7     5.5    +      -       -      -
    171A  GLU*     4.2    16.3    +      -       -      +
    172A  ASN      2.7    15.2    +      -       -      +
    173A  GLN*     2.6    27.5    +      -       -      +
    174A  SER      3.2    16.1    +      -       -      -
    494A  HIS*     3.6    21.0    +      +       -      -
    498A  LEU*     5.3     3.4    -      -       -      +
    667A  THR*     1.3    71.2    -      -       -      +
    669A  PRO*     1.3    85.7    +      -       +      +
    670A  HIS*     3.3    24.7    +      +       -      -
----------------------------------------------------------
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Residues in contact with PRO 669 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  LEU*     5.5     2.8    -      -       -      +
    174A  SER*     3.1    11.7    -      -       -      +
    176A  LEU*     4.5     1.1    -      -       +      -
    490A  PHE*     3.5    37.7    -      -       +      -
    494A  HIS*     3.6    36.8    +      -       +      +
    667A  THR      3.1    13.0    -      -       -      +
    668A  HIS*     1.3   106.4    +      -       +      +
    670A  HIS*     1.3    61.8    +      -       -      +
    671A  PHE*     3.7    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 670 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  LEU*     6.2     2.2    -      -       -      +
    158A  ILE*     4.5    17.6    +      -       +      +
    161A  ASN*     5.2     3.6    -      -       +      -
    162A  ALA*     4.1    14.6    -      -       +      -
    165A  PHE*     3.9    22.6    -      +       -      -
    173A  GLN*     3.2    33.7    +      -       +      +
    174A  SER*     2.7    17.3    +      -       -      +
    175A  ILE*     2.9    19.5    -      -       +      -
    176A  LEU*     2.7    32.9    +      -       -      +
    668A  HIS*     3.3    41.6    +      +       -      -
    669A  PRO*     1.3    72.8    +      -       -      +
    671A  PHE*     1.3    56.4    +      -       -      +
    672A  VAL*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 671 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  LEU*     3.7    20.2    +      -       +      +
    122A  PHE*     3.7    22.7    -      +       +      -
    123A  CYS*     3.5    17.7    +      -       -      +
    158A  ILE*     4.4     4.1    -      -       -      +
    176A  LEU*     3.9    25.4    -      -       +      -
    487A  LEU*     4.8     2.7    -      -       +      -
    490A  PHE*     4.1     8.5    -      +       -      -
    491A  PHE*     3.2    57.0    -      +       +      -
    494A  HIS*     4.2    15.5    -      +       -      -
    669A  PRO*     3.7    29.8    -      -       +      -
    670A  HIS*     1.3    71.8    -      -       -      +
    672A  VAL*     1.3    68.1    +      -       -      +
    673A  ARG*     3.9    24.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 672 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  CYS*     3.8    17.0    -      -       +      +
    125A  THR*     4.9     2.0    -      -       -      +
    155A  ILE*     4.5    23.6    -      -       +      -
    158A  ILE*     4.2    20.9    -      -       +      -
    175A  ILE*     3.8    22.2    -      -       +      -
    176A  LEU      2.8    21.4    +      -       -      +
    177A  ILE*     3.3    21.0    -      -       +      -
    178A  THR      3.3    12.8    +      -       -      -
    192A  VAL*     6.4     1.3    -      -       +      -
    671A  PHE*     1.3    77.7    -      -       -      +
    673A  ARG*     1.3    67.8    +      -       -      +
    674A  CYS*     4.5    12.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 673 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  PHE*     3.9    29.0    -      -       +      -
    123A  CYS      3.3    11.2    +      -       -      +
    124A  VAL*     3.4     5.6    -      -       -      -
    125A  THR      3.0    23.9    +      -       -      -
    176A  LEU*     3.0    35.8    +      -       -      +
    178A  THR*     3.6    30.9    +      -       -      +
    484A  ASN*     5.4     2.8    +      -       -      -
    487A  LEU*     5.2    16.0    -      -       -      +
    488A  GLN*     4.6     8.5    +      -       -      -
    491A  PHE*     5.9     1.2    -      -       -      +
    671A  PHE*     3.9    22.2    -      -       -      -
    672A  VAL*     1.3    76.2    +      -       -      +
    674A  CYS*     1.3    62.7    +      -       -      +
    675A  ILE*     3.9     5.8    +      -       +      +
    698A  ASN*     3.2    51.2    +      -       +      +
    700A  VAL*     4.7     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 674 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  THR*     3.6     7.6    -      -       +      +
    177A  ILE*     3.5    27.8    -      -       -      -
    178A  THR      2.9    13.5    +      -       -      +
    179A  GLY*     3.7    11.3    -      -       -      -
    183A  ALA*     3.4    31.8    -      -       +      +
    185A  LYS*     4.2     7.4    -      -       +      -
    188A  ASN*     2.9    32.8    -      -       -      +
    672A  VAL*     4.5     7.4    -      -       -      -
    673A  ARG*     1.3    72.8    -      -       -      +
    675A  ILE*     1.3    64.3    +      -       -      +
    694A  GLN*     4.6     2.6    -      -       -      +
    698A  ASN*     4.8     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 675 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     5.4     2.0    -      -       +      -
    124A  VAL*     3.0    34.1    -      -       +      -
    125A  THR      2.5    18.2    +      -       -      +
    126A  VAL*     3.6    22.9    -      -       +      -
    127A  ASN*     3.1    28.9    +      -       -      +
    183A  ALA*     3.9     6.8    -      -       -      +
    673A  ARG*     3.9    10.3    -      -       +      +
    674A  CYS*     1.3    77.2    -      -       -      +
    676A  ILE*     1.3    71.0    +      -       -      +
    677A  PRO*     4.8     0.7    -      -       +      -
    691A  VAL*     4.3    17.3    -      -       +      -
    694A  GLN*     4.1    17.3    -      -       +      +
    695A  LEU*     4.7    11.2    -      -       +      -
    698A  ASN*     3.8    23.1    -      -       -      +
    700A  VAL*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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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