Contacts of the strand formed by residues 235 - 239 (chain E) in PDB entry 1AXC


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 LEU 235 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160E  ILE*     4.7     8.7    -      -       +      -
    207E  PHE*     3.5    34.4    -      -       +      -
    212E  LEU*     3.7    20.4    -      -       +      -
    227E  LEU*     4.2    16.2    -      -       +      -
    228E  SER      3.7     9.2    -      -       -      +
    229E  MET*     3.2    40.2    -      -       +      +
    233E  VAL      3.6     3.0    +      -       -      -
    234E  PRO*     1.3    75.4    -      -       -      +
    236E  VAL*     1.3    61.2    +      -       -      +
    237E  VAL*     3.5    27.6    -      -       +      -
    249E  TYR      3.6     0.4    -      -       -      +
    250E  TYR*     3.0    26.0    -      -       -      -
    251E  LEU*     2.9    17.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 236 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133E  TYR*     3.2    38.4    -      -       +      +
    226E  THR      3.2     7.4    -      -       -      +
    227E  LEU*     3.3     1.0    -      -       -      -
    228E  SER*     3.0    38.6    +      -       -      +
    234E  PRO      3.8     3.6    -      -       -      +
    235E  LEU*     1.3    78.2    -      -       -      +
    237E  VAL*     1.3    63.4    +      -       -      +
    238E  GLU*     5.0     4.2    -      -       +      +
    248E  LYS*     4.2    22.7    -      -       +      +
    249E  TYR      3.4     6.5    -      -       -      +
    250E  TYR*     3.6    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 237 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144E  PHE*     3.6    16.4    -      -       +      -
    212E  LEU*     4.2     4.3    -      -       +      -
    215E  PHE*     3.9    25.1    -      -       +      -
    225E  VAL*     3.4    29.2    -      -       +      -
    226E  THR      3.5     2.9    -      -       -      -
    227E  LEU*     3.6    11.4    -      -       +      -
    235E  LEU*     3.5    30.1    -      -       +      -
    236E  VAL*     1.3    72.5    -      -       -      +
    238E  GLU*     1.3    57.8    +      -       -      +
    239E  TYR*     3.9    12.8    -      -       +      +
    248E  LYS*     3.6     1.0    -      -       -      -
    249E  TYR*     2.9    38.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 238 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224E  THR      4.6     0.2    -      -       -      +
    225E  VAL*     3.7     5.1    -      -       -      -
    226E  THR*     3.0    41.3    +      -       -      +
    236E  VAL*     3.8     5.3    +      -       +      +
    237E  VAL*     1.3    74.7    -      -       -      +
    239E  TYR*     1.3    71.1    +      -       -      +
    240E  LYS*     3.2    33.6    +      -       -      +
    246E  HIS*     3.2    27.6    +      -       +      +
    247E  LEU      3.5     5.2    -      -       -      +
    248E  LYS*     3.5    37.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 239 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141E  SER*     4.0     8.7    +      -       -      -
    144E  PHE*     3.8    13.5    -      -       -      -
    215E  PHE      3.7    10.0    -      -       -      -
    216E  THR*     3.6    20.1    +      -       -      -
    218E  ALA*     3.4    29.6    -      -       +      +
    219E  THR*     4.0    13.5    +      -       -      -
    221E  LEU*     4.5     7.9    -      -       +      -
    222E  SER*     4.4    12.3    -      -       -      -
    224E  THR      4.1    12.6    -      -       -      -
    225E  VAL*     3.6    25.0    -      -       +      +
    237E  VAL*     3.9    13.4    -      -       +      +
    238E  GLU*     1.3    72.8    -      -       -      +
    240E  LYS*     1.3    63.7    +      -       -      +
    241E  ILE*     3.2     1.7    +      -       -      +
    247E  LEU*     2.8    43.6    +      -       +      +
    249E  TYR*     3.5    38.1    -      +       -      -
----------------------------------------------------------
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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