Contacts of the strand formed by residues 243 - 246 (chain B) in PDB entry 2CXU


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 PHE 243 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  LEU*     4.5     0.2    -      -       -      +
    206B  PHE*     3.4    42.0    -      +       +      -
    208B  ILE*     4.0    11.2    -      -       +      -
    222B  ALA      4.0    17.5    -      -       -      -
    225B  ALA*     3.8     7.0    -      -       +      -
    226B  LYS*     3.6    25.8    -      -       -      -
    229B  PHE*     4.1    26.7    -      +       +      -
    239B  VAL*     2.9    28.0    +      -       +      +
    240B  ALA      4.0     9.9    -      -       -      +
    241B  LYS      3.8     0.2    -      -       -      -
    242B  HIS*     1.3    86.6    -      -       +      +
    244B  VAL*     1.3    68.0    +      -       -      +
    256B  PHE*     3.5    17.5    -      +       -      -
    258B  ILE*     3.5    32.2    -      -       +      +
    262B  ASN*     5.1     0.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 244 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  PHE*     3.8    28.7    -      -       +      -
    141B  TRP*     4.4     8.3    -      -       +      -
    205B  LEU*     4.1     9.6    -      -       +      -
    206B  PHE      3.0    14.7    +      -       -      +
    207B  ILE*     3.9    24.9    -      -       +      -
    208B  ILE*     2.9    31.1    +      -       -      +
    243B  PHE*     1.3    79.7    -      -       -      +
    245B  ALA*     1.3    61.6    +      -       -      +
    258B  ILE*     3.9     7.4    -      -       -      -
    262B  ASN*     3.5    31.6    -      -       +      +
    264B  PHE*     4.3    10.1    -      -       +      -
    282B  LEU*     4.4     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 245 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208B  ILE      3.4     4.5    -      -       -      -
    213B  PHE*     3.6    25.6    -      -       +      -
    244B  VAL*     1.3    78.2    -      -       -      +
    246B  LEU*     1.3    64.3    +      -       -      +
    247B  SER*     3.7     3.6    -      -       -      -
    253B  VAL*     3.7    30.7    -      -       +      -
    258B  ILE*     4.0     2.6    -      -       +      +
    262B  ASN      3.1     6.6    +      -       -      +
    263B  MET*     3.3     4.8    -      -       +      -
    264B  PHE*     2.8    29.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 246 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154B  ASN*     4.4     2.5    -      -       -      +
    207B  ILE*     3.6    27.1    -      -       +      -
    208B  ILE      2.9     9.7    +      -       -      +
    209B  ALA*     3.8    19.1    -      -       +      -
    210B  SER      2.9    28.9    +      -       -      +
    244B  VAL*     5.2     0.2    -      -       +      -
    245B  ALA*     1.3    77.6    -      -       -      +
    247B  SER*     1.3    58.1    -      -       -      +
    264B  PHE*     3.4    18.2    -      -       +      +
    266B  PHE*     3.8     8.8    -      -       +      -
    279B  ALA      3.4    28.0    -      -       -      +
    280B  ILE*     3.6    28.0    -      -       +      +
    282B  LEU*     3.7    28.7    -      -       +      -
    283B  SER      5.6     0.4    -      -       -      +
----------------------------------------------------------
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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