Contacts of the strand formed by residues 155 - 159 (chain S) in PDB entry 6O81


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 ALA 155 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45S  GLY*     3.5     8.1    -      -       -      +
     47S  ILE*     6.2     1.1    -      -       +      +
    152S  MET*     4.5     9.7    +      -       +      +
    153S  ASP      3.9     2.0    -      -       -      -
    154S  ALA*     1.3    71.8    -      -       -      +
    156S  LEU*     1.3    55.5    +      -       -      +
    157S  LEU      4.0     0.7    -      -       -      +
    175S  ALA*     5.2    16.2    -      -       +      +
    178S  GLU*     6.2     3.6    -      -       +      -
    179S  ILE*     6.3     3.1    -      -       +      -
    184S  HIS      3.3    12.5    +      -       -      +
    185S  ILE*     3.4     9.0    -      -       +      -
    186S  LEU*     2.8    33.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 156 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44S  ILE*     5.9     2.7    -      -       +      -
     45S  GLY      2.7    17.8    +      -       -      +
     46S  THR*     3.6    11.3    -      -       -      -
     47S  ILE      3.1    25.1    +      -       -      +
    154S  ALA      4.7     1.6    -      -       -      +
    155S  ALA*     1.3    72.4    -      -       -      +
    157S  LEU*     1.3    59.5    +      -       -      +
    158S  LEU*     3.3     7.6    +      -       +      +
    186S  LEU*     3.4    15.3    -      -       +      +
    188S  LEU*     6.4     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 157 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47S  ILE      3.7    10.8    -      -       -      +
     48S  GLY*     4.8     0.9    -      -       -      -
    155S  ALA*     4.0     1.8    +      -       +      -
    156S  LEU*     1.3    69.3    -      -       -      +
    158S  LEU*     1.3    60.2    +      -       -      +
    159S  ILE*     3.0    10.0    +      -       +      +
    171S  SER*     6.2     2.5    -      -       -      -
    175S  ALA*     5.9     6.7    -      -       +      -
    185S  ILE*     5.5     5.8    -      -       +      -
    186S  LEU      2.6    17.0    +      -       -      +
    187S  ILE*     3.4    11.5    -      -       +      -
    188S  LEU*     2.9    25.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 158 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46S  THR*     6.2     3.1    -      -       -      -
     47S  ILE      5.4     0.4    -      -       -      +
     48S  GLY*     4.0    12.6    -      -       -      +
     49S  HIS*     3.0    28.7    +      -       -      +
     50S  VAL*     5.1    10.2    -      -       +      -
     54S  LYS*     5.5     9.2    -      -       +      -
    156S  LEU*     3.3     9.0    +      -       +      +
    157S  LEU*     1.3    68.4    -      -       -      +
    159S  ILE*     1.3    62.6    +      -       -      +
    188S  LEU*     3.6    11.4    -      -       +      +
    190S  ASN*     5.8     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 159 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49S  HIS*     5.0     4.9    -      -       -      +
    157S  LEU*     3.0    10.4    +      -       +      +
    158S  LEU*     1.3    75.3    -      -       -      +
    160S  ALA*     1.3    63.4    +      -       -      +
    168S  PRO*     5.4    10.5    -      -       +      -
    187S  ILE*     5.9     3.8    -      -       +      -
    188S  LEU      2.9    22.5    +      -       -      +
    189S  GLN*     3.4     3.7    -      -       +      -
    190S  ASN*     3.2    17.5    +      -       -      +
    206S  GLN*     6.4     2.2    -      -       +      -
----------------------------------------------------------
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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