Contacts of the strand formed by residues 117 - 122 (chain A) in PDB entry 2O8C


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 TRP 117 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  PHE*     3.6    20.9    -      +       -      -
     22A  PHE*     3.4    46.8    -      +       +      -
     37A  PHE*     3.5    25.1    -      +       +      -
     38A  ASP      3.8    11.2    -      -       -      -
     39A  ARG*     3.5    40.4    -      -       -      -
    103A  TYR*     3.6    26.4    -      -       +      -
    104A  LYS      3.4    20.6    -      -       -      -
    105A  ASN*     3.6    33.2    -      -       +      -
    115A  ASN*     3.5    35.3    +      -       +      +
    116A  ASP*     1.3    79.2    -      -       -      +
    118A  TYR*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  TYR*     3.2     9.7    -      -       -      -
    104A  LYS*     3.1    68.6    +      -       +      +
    105A  ASN      4.4     0.8    +      -       -      -
    106A  ARG*     3.4    51.9    -      -       -      +
    116A  ASP      4.1     3.8    -      -       -      -
    117A  TRP*     1.3    75.7    -      -       -      +
    119A  LEU*     1.3    60.2    +      -       -      +
    120A  ALA*     3.0    35.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  GLU*     3.6    41.7    -      -       +      +
    102A  VAL      3.4     8.5    -      -       -      +
    103A  TYR*     3.5    25.4    -      -       +      +
    118A  TYR*     1.3    72.1    -      -       -      +
    120A  ALA*     1.3    64.0    +      -       -      +
    121A  TYR      3.4    26.2    -      -       -      +
    122A  LYS*     4.6    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  VAL      3.0     6.3    +      -       -      +
    104A  LYS*     3.9    27.1    -      -       +      -
    118A  TYR*     3.0    31.9    +      -       +      -
    119A  LEU*     1.3    74.0    -      -       -      +
    121A  TYR*     1.3    82.5    +      -       +      +
    130A  GLN*     5.1     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ASP*     5.7     0.2    -      -       -      -
    100A  VAL      4.7     0.2    -      -       -      -
    101A  GLU*     3.7     0.2    -      -       -      -
    102A  VAL*     2.9    53.8    +      -       +      -
    104A  LYS*     4.1    29.7    +      -       -      -
    119A  LEU*     3.4    10.8    -      -       -      +
    120A  ALA*     1.3    95.4    -      -       +      +
    122A  LYS*     1.3    60.9    +      -       -      +
    123A  ALA      4.4     0.2    -      -       -      -
    130A  GLN*     3.6    29.2    -      -       +      +
    131A  PHE*     4.0    24.5    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  ARG*     5.6     9.0    -      -       -      +
    100A  VAL      3.6     4.7    -      -       -      +
    101A  GLU*     4.8    12.3    -      -       +      +
    119A  LEU*     4.6    20.4    -      -       +      -
    121A  TYR*     1.3    75.5    -      -       -      +
    123A  ALA*     1.3    66.8    +      -       -      +
    124A  SER*     4.7    11.0    -      -       -      +
    127A  ASN*     4.8     8.2    +      -       -      +
    130A  GLN*     3.3    31.2    -      -       +      +
    131A  PHE*     4.8     0.7    -      -       -      -
    227A  ARG*     3.4    28.9    -      -       -      +
    276A  PHE*     5.4     4.6    -      -       -      -
----------------------------------------------------------
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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