Contacts of the strand formed by residues 153 - 158 (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 THR 153 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  VAL*     3.9     7.2    -      -       +      -
    145A  VAL      3.3     9.6    -      -       -      +
    146A  VAL*     3.5    13.0    -      -       +      +
    151A  GLY      2.9    16.5    +      -       -      -
    152A  PHE*     1.3    75.6    -      -       -      +
    154A  TRP*     1.3    69.1    +      -       -      +
    155A  LEU*     3.6    27.1    -      -       +      -
    223A  LYS*     3.4    27.4    +      -       +      +
    227A  ILE*     4.4     0.9    -      -       +      -
    250A  GLN*     3.3    12.4    -      -       -      +
    253A  LEU*     5.8     4.3    -      -       +      -
    254A  ASN*     2.6    35.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  PHE*     4.0    28.9    -      +       -      -
    125A  PHE*     4.1    15.0    -      +       -      -
    143A  LEU      3.5     3.1    -      -       -      +
    145A  VAL*     2.8    46.6    +      -       +      +
    147A  ASP*     4.2    11.2    -      -       +      -
    152A  PHE*     3.6    42.5    -      +       +      -
    153A  THR*     1.3    80.8    -      -       -      +
    155A  LEU*     1.3    66.8    +      -       -      +
    156A  TYR*     3.6    33.0    -      +       +      -
    173A  LEU*     3.3    34.2    -      -       +      +
    176A  ILE*     5.1    11.1    -      -       +      +
    250A  GLN*     3.5     9.0    -      -       -      +
    269A  LEU*     4.7     6.7    -      -       +      -
    176B  ILE*     4.0    29.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  VAL*     4.3     8.1    -      -       +      -
    143A  LEU      3.5     1.6    -      -       -      -
    144A  VAL*     4.0    12.3    -      -       +      -
    153A  THR*     3.6    11.9    -      -       +      -
    154A  TRP*     1.3    84.8    -      -       -      +
    156A  TYR*     1.3    74.3    +      -       -      +
    157A  PRO*     4.3     3.7    -      -       -      +
    227A  ILE*     3.5    33.7    -      -       +      -
    246A  LEU*     3.7    45.5    -      -       +      +
    249A  VAL*     4.3    12.8    -      -       +      -
    250A  GLN*     2.9    36.8    +      -       +      +
    253A  LEU*     6.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  VAL*     3.3     2.5    -      -       -      +
    143A  LEU*     2.6    54.8    +      -       +      +
    145A  VAL*     4.5     3.1    -      -       +      -
    154A  TRP*     3.6    36.3    -      +       +      -
    155A  LEU*     1.3    81.0    -      -       -      +
    157A  PRO*     1.3    71.4    -      -       +      +
    158A  THR*     3.8     0.8    -      -       +      +
    169A  SER*     3.4    48.0    -      -       -      +
    170A  LEU*     5.5     0.2    -      -       +      -
    172A  VAL*     4.2    18.2    -      -       +      +
    173A  LEU*     3.2    36.8    +      -       +      +
    246A  LEU*     4.2     3.6    -      -       -      -
    250A  GLN*     5.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  TYR*     3.6    24.4    -      -       +      -
    141A  TYR      3.4     7.6    -      -       -      +
    142A  VAL*     4.5     0.2    -      -       -      -
    155A  LEU      4.3     2.7    -      -       -      +
    156A  TYR*     1.3    88.3    -      -       +      +
    158A  THR*     1.3    63.9    +      -       -      +
    169A  SER*     5.3     0.3    +      -       -      -
    242A  TRP*     4.1     6.3    -      -       +      -
    243A  TYR*     3.5    33.4    -      -       +      +
    246A  LEU*     3.7    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  TYR*     3.6    19.6    -      -       +      +
    139A  TYR*     3.5     9.6    -      -       -      -
    140A  LEU      2.9     6.8    +      -       -      -
    141A  TYR*     2.8    48.6    +      -       -      +
    143A  LEU*     4.5     4.7    -      -       +      +
    156A  TYR      3.8    11.2    -      -       -      +
    157A  PRO*     1.3    79.5    -      -       -      +
    159A  LYS*     1.3    58.4    +      -       -      +
    160A  ALA      2.8    23.3    +      -       -      -
    165A  ALA*     4.0    22.0    -      -       +      -
    169A  SER*     4.5     9.2    -      -       -      +
----------------------------------------------------------
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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