Contacts of the strand formed by residues 5166 - 5168 (chain b) in PDB entry 2AXT


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 MET5166 (chain b).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   5068b  ARG*     3.1    16.4    -      -       +      +
   5069b  LEU*     5.3     0.4    -      -       +      -
   5158b  LEU*     4.1    24.5    -      -       +      +
   5165b  GLY*     1.3    75.5    -      -       -      +
   5167b  TRP*     1.3    68.7    +      -       -      +
   5168b  VAL*     3.0     9.4    +      -       +      +
   5178b  VAL*     3.8     6.6    -      -       -      +
   5179b  GLN      2.9    22.4    +      -       -      +
   5181b  VAL*     3.4    31.2    -      -       +      -
   5195b  PRO*     4.1    15.3    -      -       +      +
   5198b  VAL*     4.2    27.4    -      -       +      -
   5199b  VAL*     4.8     0.2    -      -       -      -
   5261b  ALA      3.9    22.0    -      -       -      +
   5262b  THR*     4.9     2.2    -      -       -      +
   5513b  CLA      4.0    18.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP5167 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   5067b  ALA      4.1     5.6    -      -       -      +
   5068b  ARG*     2.8    19.2    +      -       +      +
   5072b  THR*     4.2     6.5    -      -       +      -
   5080b  ILE*     3.8    27.8    -      -       +      -
   5081b  THR*     3.7    24.5    -      -       +      -
   5166b  MET*     1.3    76.0    -      -       -      +
   5168b  VAL*     1.3    65.8    +      -       -      +
   5169b  SER*     4.1     3.6    -      -       -      -
   5176b  GLY*     3.4    12.7    -      -       -      -
   5177b  SER*     3.3    26.5    -      -       -      -
   5178b  VAL*     3.9    10.9    -      -       +      +
   5195b  PRO*     5.5     0.7    -      -       -      +
   5261b  ALA      4.2     8.8    -      -       -      +
   5264b  PRO*     3.2    41.2    -      -       +      +
   5266b  GLU*     3.3    42.4    +      -       +      +
   5267b  LEU*     3.5    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL5168 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   5166b  MET*     3.0    17.7    +      -       +      +
   5167b  TRP*     1.3    78.8    -      -       -      +
   5169b  SER*     1.3    72.7    +      -       -      +
   5175b  THR      4.8     0.2    -      -       -      +
   5176b  GLY*     3.4     0.9    -      -       -      -
   5177b  SER*     2.8    31.7    +      -       -      +
   5179b  GLN*     4.7    13.8    -      -       +      +
   5181b  VAL*     3.6    28.0    -      -       +      -
   5195b  PRO*     4.1    23.1    -      -       +      -
   5065h  LEU*     4.7    10.5    -      -       +      -
----------------------------------------------------------
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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