Contacts of the strand formed by residues 229 - 237 (chain A) in PDB entry 3IEU


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 TYR 229 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190A  GLN*     3.6    24.5    +      -       -      -
    221A  PHE*     3.9    24.0    -      +       -      -
    222A  VAL      3.3    14.6    -      -       -      +
    223A  SER*     3.7    19.9    -      -       -      +
    224A  ASN*     3.6     9.6    +      -       -      +
    227A  GLY      5.2     2.2    -      -       -      -
    228A  GLY*     1.3    75.8    -      -       -      -
    230A  ASP*     1.3    62.1    +      -       -      +
    231A  ILE*     4.2    10.8    -      -       +      -
    269A  PHE*     4.1    28.5    -      +       +      -
    271A  ALA*     3.9    27.1    -      -       +      -
    272A  PRO      2.7    15.3    +      -       -      +
    273A  VAL*     3.4    10.5    -      -       +      -
    274A  HIS*     2.9    26.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  ARG*     3.5    32.6    +      -       -      +
    222A  VAL*     2.8    43.8    +      -       +      +
    223A  SER*     4.9     0.2    -      -       -      +
    224A  ASN*     5.5     6.3    -      -       +      +
    229A  TYR*     1.3    73.9    -      -       -      +
    231A  ILE*     1.3    64.3    +      -       -      +
    232A  ASN*     3.9    10.6    -      -       -      +
    274A  HIS*     3.4    27.4    +      -       +      +
    276A  GLU*     5.1     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  ALA*     4.8     1.6    -      -       +      -
    218A  ILE*     3.9    28.5    -      -       +      -
    220A  ARG      3.3     8.3    -      -       -      +
    221A  PHE*     3.7    34.3    -      -       +      -
    222A  VAL      5.3     0.2    -      -       -      +
    229A  TYR*     4.5     6.5    -      -       +      -
    230A  ASP*     1.3    81.5    +      -       -      +
    232A  ASN*     1.3    70.3    +      -       -      +
    265A  MET*     3.7    23.1    -      -       -      -
    269A  PHE*     4.2     9.2    -      -       +      -
    273A  VAL*     3.9    15.9    -      -       +      -
    274A  HIS      2.9    10.8    +      -       -      +
    275A  LEU*     3.5    19.9    -      -       +      +
    276A  GLU      3.0    24.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 232 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  ILE*     3.7     4.2    -      -       -      +
    219A  GLU*     3.0    41.6    +      -       +      +
    220A  ARG*     2.9    41.3    +      -       +      +
    230A  ASP*     3.9     9.0    -      -       -      +
    231A  ILE*     1.3    81.2    -      -       -      +
    233A  GLY*     1.3    60.9    +      -       -      +
    276A  GLU*     3.4    35.0    +      -       -      +
    278A  TRP*     4.8     7.6    -      -       +      +
    293A  ARG*     5.8     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 233 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  ILE*     4.3    14.4    -      -       -      -
    217A  GLU      3.9     4.3    -      -       -      -
    218A  ILE*     4.7     2.9    -      -       -      -
    219A  GLU*     5.1     0.4    -      -       -      -
    231A  ILE      4.0     1.2    -      -       -      -
    232A  ASN*     1.3    74.4    -      -       -      +
    234A  LEU*     1.3    60.2    +      -       -      +
    235A  ILE*     4.2     0.7    -      -       -      -
    275A  LEU*     4.6     2.0    -      -       -      +
    276A  GLU      2.6    16.2    +      -       -      +
    277A  LEU*     3.3    18.4    -      -       -      +
    278A  TRP*     2.9    30.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 234 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  ARG*     5.9     4.3    -      -       -      +
    198A  ILE*     5.4     0.8    -      -       -      +
    215A  THR      3.9     1.0    -      -       -      +
    216A  VAL*     3.7     4.1    -      -       -      +
    217A  GLU*     2.9    50.3    +      -       -      +
    219A  GLU*     3.2    36.3    -      -       +      +
    233A  GLY*     1.3    73.8    -      -       -      +
    235A  ILE*     1.3    61.8    +      -       -      +
    236A  LEU*     3.9    26.1    +      -       +      +
    278A  TRP*     3.5    15.7    -      -       +      +
    280A  LYS*     4.0    18.2    -      -       +      +
    285A  TRP*     3.8    31.9    -      -       +      -
    293A  ARG*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 235 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  ILE*     4.3    17.7    -      -       +      -
    202A  LEU*     4.0    42.2    -      -       +      -
    214A  VAL*     4.1    12.8    -      -       +      -
    215A  THR      3.7     3.6    -      -       -      +
    216A  VAL*     4.8     2.7    -      -       +      -
    233A  GLY      5.5     0.4    -      -       -      -
    234A  LEU*     1.3    76.5    -      -       -      +
    236A  LEU*     1.3    62.3    +      -       -      +
    237A  VAL*     4.6     4.0    -      -       +      -
    246A  VAL*     4.5    10.1    -      -       +      -
    254A  ILE*     4.0    25.8    -      -       +      -
    257A  ILE*     5.0     0.2    -      -       +      -
    277A  LEU*     4.4    13.7    -      -       +      -
    278A  TRP      2.6    15.3    +      -       -      +
    279A  VAL*     3.3    16.8    -      -       +      +
    280A  LYS*     2.9    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 236 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  THR*     4.9     2.5    -      -       -      +
     38A  ARG*     5.9     4.7    -      -       -      +
    213A  SER      3.8     1.6    -      -       -      +
    214A  VAL*     3.3     8.3    -      -       -      +
    215A  THR*     2.8    58.1    +      -       -      +
    217A  GLU*     4.0    24.2    -      -       +      +
    234A  LEU*     4.1    21.8    -      -       +      +
    235A  ILE*     1.3    75.4    -      -       -      +
    237A  VAL*     1.3    62.8    -      -       -      +
    280A  LYS*     3.3    43.1    -      -       +      +
    282A  LYS*     4.2    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 237 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  PRO*     5.4     0.4    -      -       +      -
    213A  SER      4.5     3.6    -      -       -      -
    214A  VAL*     4.5    18.6    -      -       +      +
    235A  ILE*     4.6     2.7    -      -       +      -
    236A  LEU*     1.3    77.8    -      -       -      +
    238A  GLU*     1.3    58.7    +      -       -      +
    239A  ARG      3.6    18.4    -      -       -      +
    242A  GLN*     4.0    14.8    -      -       +      +
    243A  LYS*     3.9    19.5    -      -       +      +
    246A  VAL*     4.3    23.8    -      -       +      -
    279A  VAL*     4.5     9.4    -      -       +      -
    280A  LYS      3.0    12.0    +      -       -      +
    281A  VAL*     3.3     5.6    -      -       -      -
    282A  LYS*     2.9    29.5    +      -       -      +
----------------------------------------------------------
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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