Contacts of the strand formed by residues 225 - 229 (chain A) in PDB entry 3IE7


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 225 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217A  VAL*     4.1    13.6    -      -       -      +
    218A  VAL      3.4    14.6    -      -       -      -
    219A  SER*     3.9     7.2    -      -       -      -
    220A  LEU*     4.1     5.9    -      -       -      +
    223A  LYS      3.9     1.6    +      -       -      -
    224A  GLY*     1.3    76.6    -      -       -      -
    226A  ILE*     1.3    68.1    +      -       -      +
    227A  CYS      4.3     0.2    -      -       -      -
    235A  GLN*     3.8     1.6    -      -       -      +
    236A  VAL*     2.8    50.3    +      -       -      +
    253A  PHE*     4.2    15.4    -      -       -      -
    271A  LEU*     4.8     1.7    -      -       -      +
    275A  THR*     4.7     0.5    +      -       -      -
    900A  ATP      4.0     5.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 226 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202A  LEU*     4.3    13.9    -      -       +      -
    203A  GLU*     5.2     8.1    -      -       +      -
    206A  ILE*     3.9    28.0    -      -       +      +
    216A  LEU      3.8     0.3    -      -       -      +
    217A  VAL*     3.5     2.3    -      -       -      -
    218A  VAL*     2.9    33.2    +      -       +      +
    220A  LEU*     3.9    21.5    -      -       +      -
    225A  SER*     1.3    80.8    -      -       -      +
    227A  CYS*     1.3    64.2    +      -       -      +
    233A  LEU*     3.7    31.6    -      -       +      -
    234A  TYR      3.1    12.3    -      -       -      +
    235A  GLN*     4.8    11.9    -      -       +      +
    307A  LEU*     4.7    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 227 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215A  TYR*     5.4     0.4    -      -       -      -
    216A  LEU      3.1    13.0    -      -       -      +
    217A  VAL*     4.0    14.8    -      -       +      -
    225A  SER      4.3     0.2    -      -       -      -
    226A  ILE*     1.3    75.2    -      -       -      +
    228A  ALA*     1.3    71.2    +      -       -      +
    229A  HIS*     4.4     2.2    -      -       -      -
    233A  LEU*     3.4     4.1    -      -       -      -
    234A  TYR*     2.8    44.9    +      -       +      +
    236A  VAL*     5.0     1.5    -      -       +      +
    257A  PHE*     4.8     2.2    -      -       -      -
    267A  ILE*     4.2    18.6    -      -       -      -
    271A  LEU*     3.8    42.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  ILE*     4.0    11.8    -      -       +      +
    207A  ARG*     5.5     0.2    -      -       -      -
    210A  ALA*     3.6    30.1    -      -       +      -
    213A  ILE      4.7     0.7    -      -       -      +
    214A  PRO      3.6     3.6    -      -       -      +
    215A  TYR*     3.9     0.3    -      -       -      -
    216A  LEU*     2.8    36.9    +      -       +      +
    226A  ILE      4.3     0.2    -      -       -      -
    227A  CYS*     1.3    73.9    -      -       -      +
    229A  HIS*     1.3    64.9    +      -       -      +
    232A  LYS      3.3     7.4    -      -       -      +
    233A  LEU*     3.7    17.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214A  PRO*     3.0    26.9    -      -       +      +
    215A  TYR*     3.3    44.9    +      +       +      -
    227A  CYS*     4.1     5.3    +      -       -      -
    228A  ALA*     1.3    75.9    -      -       -      +
    230A  ASN*     1.3    87.1    +      -       +      +
    231A  GLY      3.2     2.6    -      -       -      +
    232A  LYS*     3.0    26.7    +      -       -      +
    234A  TYR*     4.4     6.7    +      -       +      -
    267A  ILE*     4.0    36.1    -      -       +      +
----------------------------------------------------------
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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