Contacts of the strand formed by residues 115 - 119 (chain A) in PDB entry 2O6C


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 115 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  PRO*     4.0    20.2    -      -       +      -
     61A  GLN*     4.1     3.8    -      -       -      +
    113A  MSE      4.1     0.2    +      -       -      -
    114A  PHE*     1.3    75.6    -      -       -      +
    116A  PRO*     1.3    74.6    -      -       +      +
    117A  MSE      3.4    21.7    +      -       +      +
    125A  TYR*     3.4     4.8    -      -       -      -
    126A  GLY      2.9    27.3    +      -       -      -
    153B  SER*     5.5     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  PHE*     5.3     2.2    -      -       +      -
     95A  LEU      5.9     1.8    -      -       -      +
    114A  PHE      4.8     0.7    -      -       -      +
    115A  ALA*     1.3    86.1    -      -       +      +
    117A  MSE      1.3    66.1    +      -       -      +
    124A  HIS      3.4     8.5    -      -       -      +
    125A  TYR*     4.1    15.9    -      -       +      -
     94B  TYR*     3.5    32.1    -      -       +      +
    151B  GLU      3.4    24.2    -      -       -      +
    152B  TYR*     3.6    16.2    -      -       +      -
    153B  SER*     3.3    16.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with MSE 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  MSE      3.5    34.3    -      -       +      +
     58A  PRO*     4.1     6.3    -      -       +      -
     70A  HIS*     3.8    10.1    -      -       -      -
    115A  ALA*     3.4    33.9    -      -       +      +
    116A  PRO*     1.3    77.6    -      -       -      +
    118A  ASN*     1.3    63.0    +      -       -      +
    122A  GLY      3.9     0.3    -      -       -      +
    123A  PRO*     3.3     2.8    -      -       -      +
    124A  HIS*     2.9    52.4    +      -       +      +
    126A  GLY      3.5    15.0    -      -       -      +
    152B  TYR*     3.7     6.7    -      -       -      -
    153B  SER*     3.1    24.2    -      -       -      +
    155B  HIS*     3.5    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  MSE      1.3    73.0    -      -       -      +
    119A  ALA*     1.3    62.3    +      -       -      +
    122A  GLY      3.6     3.8    -      -       -      -
    123A  PRO*     3.2    19.8    -      -       -      +
     84B  LEU      2.8    31.1    +      -       -      +
     85B  GLY      4.0     3.0    -      -       -      -
     86B  TYR*     3.4    36.8    +      -       -      -
    152B  TYR*     2.6    30.2    +      -       -      -
    153B  SER      3.0     7.7    +      -       -      -
    154B  LEU*     3.5    11.3    -      -       +      +
    155B  HIS*     2.9    30.0    +      -       -      +
    162B  VAL*     4.5     1.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  PHE*     4.4     6.3    -      -       +      -
     72A  GLU*     5.8     0.2    -      -       -      +
    117A  MSE      4.2     0.4    +      -       -      -
    118A  ASN*     1.3    75.7    -      -       -      +
    120A  GLY*     1.3    67.4    +      -       -      +
    121A  ASP*     3.0    19.8    +      -       -      +
    122A  GLY*     3.0    16.7    +      -       -      +
    124A  HIS*     4.3     5.6    -      -       +      -
     85B  GLY*     3.6     7.1    -      -       -      -
    155B  HIS*     3.5    35.9    -      -       +      +
    160B  THR      3.5     7.4    -      -       -      +
    162B  VAL*     3.6    10.7    -      -       -      +
----------------------------------------------------------
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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