Contacts of the strand formed by residues 141 - 147 (chain A) in PDB entry 3OYG


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 TYR 141 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  TYR*     4.1    11.2    -      -       +      -
    130A  ILE      3.3    17.7    -      -       -      +
    131A  GLY*     3.4     9.2    -      -       -      -
    132A  PRO*     3.4    36.9    -      -       +      +
    133A  LEU*     5.2     0.7    -      -       -      -
    140A  LEU*     1.3   101.2    -      -       +      +
    142A  VAL*     1.3    65.6    +      -       -      +
    157A  PRO*     3.4     5.2    -      -       -      +
    158A  THR*     2.8    40.2    +      -       -      +
    159A  LYS      3.8    13.0    -      -       -      -
    160A  ALA*     3.8     1.3    -      -       +      -
    161A  PRO*     3.5    44.5    -      -       +      +
    242A  TRP*     3.7     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  ASP      3.7     0.5    -      -       -      +
    129A  TYR*     3.2     8.3    -      -       -      -
    130A  ILE*     2.9    44.4    +      -       +      +
    133A  LEU*     4.1    13.0    -      -       +      -
    141A  TYR*     1.3    79.5    -      -       -      +
    143A  LEU*     1.3    72.2    +      -       -      +
    144A  VAL*     3.7    15.1    +      -       +      +
    155A  LEU*     4.3    13.7    -      -       +      -
    156A  TYR      3.3    13.0    -      -       -      +
    227A  ILE*     5.6     3.4    -      -       +      -
    231A  LEU*     5.8     1.6    -      -       +      -
    242A  TRP*     3.6    24.7    -      -       +      -
    246A  LEU*     4.0    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ILE*     4.6     5.6    -      -       +      -
    128A  ASP      3.7    19.7    -      -       -      +
    129A  TYR*     3.6    35.8    -      -       +      +
    142A  VAL*     1.3    71.7    -      -       -      +
    144A  VAL*     1.3    61.4    +      -       -      +
    145A  VAL*     4.2    19.1    -      -       +      -
    154A  TRP      3.5     1.7    -      -       -      +
    155A  LEU*     3.5     5.7    -      -       -      -
    156A  TYR*     2.6    43.9    +      -       +      +
    158A  THR*     4.5     3.1    -      -       +      -
    166A  THR*     4.2    22.2    -      -       +      +
    169A  SER*     3.7    27.1    -      -       -      -
    170A  LEU*     4.5     4.9    -      -       +      -
    190A  PHE*     4.3    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ILE*     3.2     5.9    -      -       -      +
    128A  ASP      2.9    33.5    +      -       -      +
    130A  ILE*     3.7    20.2    -      -       +      -
    142A  VAL*     3.7    17.9    -      -       +      +
    143A  LEU*     1.3    76.5    -      -       -      +
    145A  VAL*     1.3    63.8    +      -       -      +
    146A  VAL*     4.0     5.4    -      -       +      -
    153A  THR*     3.9    14.6    -      -       +      -
    154A  TRP      3.6     2.7    -      -       -      -
    155A  LEU*     4.0     1.3    -      -       +      -
    220A  VAL*     3.6    14.0    -      -       +      +
    223A  LYS*     4.6     1.1    -      -       +      -
    224A  ASN*     3.5    24.5    -      -       -      +
    227A  ILE*     3.6    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  PHE*     3.6    26.9    -      -       +      -
    126A  PHE      3.5     2.9    -      -       -      -
    127A  ILE*     3.7    19.7    -      -       +      -
    143A  LEU*     4.2    15.5    -      -       +      -
    144A  VAL*     1.3    76.5    -      -       -      +
    146A  VAL*     1.3    65.1    +      -       -      +
    147A  ASP      4.2     0.2    -      -       -      -
    153A  THR*     3.3     4.9    -      -       -      +
    154A  TRP*     2.8    45.5    +      -       +      +
    156A  TYR*     4.5     4.5    -      -       +      -
    170A  LEU*     4.0    13.5    -      -       +      -
    173A  LEU*     3.6    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  PHE*     3.5     4.3    -      -       -      -
    126A  PHE*     2.8    42.9    +      -       +      +
    144A  VAL*     4.0     8.5    -      -       +      -
    145A  VAL*     1.3    76.7    -      -       -      +
    147A  ASP*     1.3    76.2    +      -       -      +
    148A  GLY      3.4     1.2    +      -       -      -
    151A  GLY*     4.1    17.5    -      -       -      +
    152A  PHE      3.6     2.2    -      -       -      -
    153A  THR*     3.5    22.2    -      -       +      +
    219A  LYS*     4.3    25.1    -      -       +      +
    220A  VAL*     4.1    11.7    -      -       +      -
    223A  LYS*     3.8    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  LYS      4.5     0.9    -      -       -      +
    121A  PRO*     3.5     7.1    -      -       -      +
    122A  PHE*     2.8    30.6    +      -       -      -
    124A  LYS      3.6     5.8    +      -       -      +
    125A  PHE*     3.6    20.4    -      -       +      -
    145A  VAL      4.2     0.6    -      -       -      -
    146A  VAL*     1.3    74.1    -      -       -      +
    148A  GLY*     1.3    61.7    +      -       -      +
    149A  MET      3.4     3.8    +      -       -      -
    150A  THR*     2.6    46.7    +      -       -      +
    151A  GLY*     2.8    31.9    +      -       -      -
    152A  PHE*     2.9    15.0    +      -       +      +
    154A  TRP*     4.2    10.9    -      -       +      -
    219A  LYS*     4.8     0.2    -      -       -      +
    269A  LEU*     5.5     1.3    -      -       +      -
----------------------------------------------------------
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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