Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 2YYO


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 ARG 106 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  GLU*     2.9    37.2    +      -       -      +
     45A  VAL      3.2    12.3    -      -       -      +
     46A  SER*     3.8    17.9    -      -       -      +
     47A  ILE*     5.3     0.2    -      -       -      -
    104A  GLY      5.3     0.4    -      -       -      +
    105A  ASP*     1.3    76.2    -      -       -      +
    107A  ILE*     1.3    64.6    +      -       -      +
    127A  LYS*     3.4     5.9    -      -       -      +
    128A  ASN*     2.8    62.2    +      -       -      +
    129A  GLY*     3.4    22.6    -      -       -      +
    160A  HIS*     5.9     0.9    -      -       -      -
    165A  LEU*     6.1     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  GLU*     3.3     3.6    -      -       -      -
     45A  VAL*     2.7    39.4    +      -       -      +
     47A  ILE*     4.6     9.6    -      -       +      -
     56A  ILE*     5.6     0.9    -      -       +      -
     58A  VAL*     3.8    39.4    -      -       +      +
     80A  TYR*     3.5    43.1    -      -       +      +
     82A  ALA*     4.0    21.3    -      -       +      +
    101A  CYS*     3.9    23.1    -      -       +      -
    106A  ARG*     1.3    79.2    -      -       -      +
    108A  GLY*     1.3    67.0    +      -       -      +
    125A  PHE*     5.0     0.7    -      -       +      -
    126A  THR      3.4     8.3    -      -       -      +
    127A  LYS*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  TYR*     3.8     8.7    -      -       -      -
     43A  PHE      3.3     9.9    -      -       -      -
     44A  GLU*     3.9     3.3    +      -       -      +
     58A  VAL*     5.3     0.7    -      -       -      -
    106A  ARG*     4.3     0.4    -      -       -      +
    107A  ILE*     1.3    77.4    -      -       -      +
    109A  CYS*     1.3    62.9    +      -       -      +
    125A  PHE*     3.3    10.2    -      -       -      -
    126A  THR*     2.9    47.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     4.5     0.3    -      -       -      +
     42A  TYR*     3.5     6.6    -      -       -      -
     43A  PHE*     2.9    53.4    +      -       +      -
     58A  VAL*     4.8     2.9    -      -       +      -
     59A  GLY*     4.2     5.2    -      -       -      -
     60A  LEU*     3.7    34.5    -      -       -      -
    108A  GLY*     1.3    75.1    -      -       -      +
    110A  GLY*     1.3    63.0    +      -       -      +
    123A  ILE*     3.8     5.2    -      -       -      -
    124A  PHE      3.4     5.4    -      -       -      -
    125A  PHE*     3.4    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     4.3     3.8    -      -       -      -
     41A  ASN      3.0    13.9    -      -       -      -
     42A  TYR*     3.8     3.3    -      -       -      -
    109A  CYS*     1.3    77.5    -      -       -      +
    111A  ILE*     1.3    64.3    +      -       -      -
    123A  ILE*     3.4     9.2    -      -       -      +
    124A  PHE*     2.9    49.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  LEU*     3.9    20.6    -      -       +      -
     41A  ASN*     2.5    41.5    +      -       -      +
     60A  LEU*     3.9    13.9    -      -       +      -
    110A  GLY*     1.3    78.1    -      -       -      +
    112A  GLU*     1.3    61.1    +      -       -      +
    113A  PRO      3.2     0.2    -      -       -      -
    115A  SER*     3.0    26.7    -      -       -      +
    116A  PHE*     3.7    32.1    -      -       +      -
    121A  ALA*     4.7     1.1    -      -       +      -
    122A  GLN      3.4    10.3    -      -       -      +
    123A  ILE*     4.2     7.2    -      -       +      -
    124A  PHE*     3.8     3.1    -      -       -      -
    141A  PRO*     4.3    10.5    -      -       +      -
    142A  ASP      5.0     1.1    -      -       -      +
    144A  LEU*     4.0    29.8    -      -       +      -
----------------------------------------------------------
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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