Contacts of the strand formed by residues 206 - 209 (chain B) in PDB entry 3ECS


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 ILE 206 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195B  VAL*     4.5     1.8    -      -       +      -
    196B  GLY      3.9    18.6    -      -       -      +
    197B  ALA*     4.1     7.2    -      -       +      -
    199B  GLY      3.2    13.5    -      -       -      +
    200B  VAL*     4.5     4.9    -      -       +      +
    201B  VAL*     4.6     1.8    -      -       -      +
    204B  GLY      4.4     2.0    -      -       -      +
    205B  GLY*     1.3    81.5    -      -       -      +
    207B  ILE*     1.3    65.4    +      -       -      +
    208B  ASN*     4.4     4.0    -      -       +      -
    212B  THR*     4.2    20.6    -      -       +      -
    226B  PHE*     4.8     2.5    -      -       +      -
    228B  VAL*     3.6    38.4    -      -       +      -
    274B  ASP      3.7     0.9    -      -       -      +
    275B  TYR*     3.3     8.0    -      -       -      -
    276B  THR*     2.9    43.5    +      -       -      +
    281B  ILE*     3.8    13.9    -      -       +      -
    284B  LEU*     4.5     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  VAL*     4.7    11.9    -      -       +      -
    197B  ALA*     3.9     0.7    -      -       -      -
    198B  GLU*     2.8    31.9    +      -       +      +
    199B  GLY*     3.0    14.4    +      -       -      +
    201B  VAL*     4.1    23.3    -      -       +      -
    206B  ILE*     1.3    75.4    -      -       -      +
    208B  ASN*     1.3    64.1    +      -       -      +
    236B  VAL*     5.0     4.3    -      -       +      -
    238B  LEU*     4.4    12.8    -      -       +      -
    240B  PRO*     5.8     0.9    -      -       +      -
    246B  VAL*     4.0    31.9    -      -       +      -
    247B  PRO*     5.1     0.4    -      -       +      -
    250B  PHE*     4.3    15.3    -      -       +      -
    273B  VAL*     3.6    33.0    -      -       +      -
    274B  ASP      3.4     6.1    -      -       -      +
    275B  TYR*     4.9     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  HIS*     4.5     5.2    -      -       -      +
    195B  VAL*     3.7     7.3    -      -       -      +
    196B  GLY      3.4    21.5    +      -       -      +
    197B  ALA*     3.3    24.7    -      -       -      +
    198B  GLU*     3.3    18.0    -      -       -      +
    206B  ILE*     4.1     4.7    +      -       +      -
    207B  ILE*     1.3    75.1    -      -       -      +
    209B  LYS*     1.3    66.1    +      -       -      +
    212B  THR*     3.0    30.3    +      -       +      +
    273B  VAL*     2.8    35.3    -      -       -      -
    274B  ASP      2.9    14.1    +      -       -      +
    502B  SO4      5.2     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 209 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  HIS*     3.3    16.3    +      -       +      +
    129B  ALA*     4.0     9.6    -      -       +      +
    155B  SER*     2.9    32.0    +      -       -      +
    156B  GLN      3.5    20.0    -      -       -      -
    157B  PRO*     4.4     1.6    -      -       -      -
    158B  ASP*     2.9    28.2    +      -       -      -
    160B  SER*     3.3    11.1    +      -       -      -
    198B  GLU*     4.3     7.2    +      -       -      +
    208B  ASN*     1.3    83.6    -      -       -      +
    210B  ILE*     1.3    74.5    +      -       +      +
    212B  THR*     2.9    25.3    +      -       -      -
    272B  TRP*     3.4    40.6    -      -       +      +
    273B  VAL*     4.5     0.9    -      -       -      -
    274B  ASP*     4.0     0.3    -      -       -      +
----------------------------------------------------------
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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