Contacts of the strand formed by residues 204 - 209 (chain A) in PDB entry 2CXO


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 SER 204 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  ILE*     4.3     1.5    -      -       -      +
    151A  ASP*     3.4     6.5    +      -       -      +
    153A  ILE*     3.6    16.4    -      -       -      -
    199A  LEU*     3.5    27.5    -      -       -      +
    200A  SER      2.8    22.8    +      -       -      -
    201A  PRO*     3.9     3.4    +      -       -      +
    202A  GLU      3.7     0.8    -      -       -      -
    203A  THR*     1.3    79.3    -      -       -      +
    205A  LEU*     1.3    61.0    +      -       -      +
    206A  PHE*     4.1    17.9    +      -       -      -
    228A  TRP*     4.9     0.2    -      -       -      -
    229A  PHE*     5.6     0.2    -      -       -      -
    242A  HIS*     2.8    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  PHE*     3.6    37.5    -      -       +      -
    136A  VAL*     4.3    10.3    -      -       +      -
    141A  TRP*     4.6     4.5    -      -       +      +
    149A  ILE*     3.8    20.2    -      -       +      +
    151A  ASP      2.9     8.7    +      -       -      -
    152A  ILE*     3.3    29.5    -      -       +      +
    153A  ILE*     2.8    31.0    +      -       -      -
    204A  SER*     1.3    73.2    -      -       -      +
    206A  PHE*     1.3    64.5    +      -       -      +
    207A  ILE*     4.5     4.0    -      -       +      +
    241A  LYS      4.0     9.0    -      -       -      +
    242A  HIS*     3.6    27.1    -      -       -      +
    243A  PHE      4.1     2.2    -      -       -      +
    244A  VAL*     4.3     8.1    -      -       +      -
    286A  LEU*     4.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  ILE*     3.4    37.0    -      -       +      +
    155A  ILE*     3.7    17.7    -      -       +      -
    192A  ILE*     5.0     0.7    -      -       +      -
    196A  LEU*     3.7    18.6    -      -       +      -
    199A  LEU*     4.6     0.2    -      -       +      -
    204A  SER*     4.2    15.7    -      -       -      -
    205A  LEU*     1.3    74.8    -      -       -      +
    207A  ILE*     1.3    60.6    +      -       -      +
    208A  ILE*     4.0     5.8    -      -       +      -
    225A  ALA*     3.9    13.9    -      -       +      -
    228A  TRP*     3.7    34.8    -      +       -      -
    229A  PHE*     5.1     4.7    -      +       +      -
    242A  HIS*     2.8    17.1    +      -       +      +
    243A  PHE*     3.4    42.3    -      +       +      -
    244A  VAL*     2.9    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ILE*     3.3    35.0    -      -       +      -
    153A  ILE      2.7    13.8    +      -       -      +
    154A  ASN*     3.5    10.4    -      -       -      +
    155A  ILE      2.7    31.7    +      -       -      -
    205A  LEU*     4.5     5.4    -      -       +      +
    206A  PHE*     1.3    76.1    -      -       -      +
    208A  ILE*     1.3    58.3    +      -       -      +
    209A  ALA      3.4     2.6    +      -       -      -
    244A  VAL*     3.6    17.3    -      -       +      -
    246A  LEU*     3.4    44.4    -      -       +      -
    282A  LEU*     4.7     2.2    -      -       +      -
    283A  SER*     4.1    16.6    -      -       -      +
    286A  LEU*     3.7    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ILE*     3.6    24.9    -      -       +      -
    206A  PHE*     4.2     3.6    -      -       +      -
    207A  ILE*     1.3    75.4    -      -       -      +
    209A  ALA*     1.3    60.2    +      -       -      +
    210A  SER      3.9     0.2    -      -       -      -
    213A  PHE*     3.6    31.1    -      -       +      -
    218A  THR*     4.0    18.2    -      -       +      -
    219A  ILE*     5.0     2.7    -      -       +      -
    222A  ALA*     3.7    35.7    -      -       +      -
    243A  PHE*     4.2    21.5    -      -       +      -
    244A  VAL      2.9    16.0    +      -       -      +
    245A  ALA*     3.4     2.1    -      -       -      -
    246A  LEU      2.9    26.9    +      -       -      +
    256A  PHE*     4.5     1.6    -      -       +      -
    258A  ILE*     4.2    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  ASN*     3.7    17.3    -      -       -      +
    155A  ILE      2.8    18.8    +      -       -      +
    156A  GLY*     3.5     5.9    -      -       -      -
    160A  SER*     3.2    36.4    -      -       -      +
    207A  ILE      3.4     0.4    +      -       -      -
    208A  ILE*     1.3    70.2    -      -       -      +
    210A  SER*     1.3    64.1    +      -       -      +
    218A  THR*     3.6     2.6    +      -       -      +
    246A  LEU*     3.7    22.0    -      -       +      -
    280A  ILE*     3.9    10.8    -      -       +      -
   1601A  DER      4.4     0.2    +      -       -      -
----------------------------------------------------------
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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