Contacts of the strand formed by residues 229 - 238 (chain H) in PDB entry 4BEI


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 THR 229 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189H  ASP*     4.2     6.2    +      -       -      +
    190H  LEU      3.4    10.6    +      -       -      -
    191H  ASN*     4.6     9.4    -      -       -      +
    224H  ILE*     4.7     1.6    -      -       -      -
    227H  GLY      5.1     2.7    -      -       -      +
    228H  ASP*     1.3    83.1    -      -       -      +
    230H  TYR*     1.3    69.2    +      -       -      +
    231H  SER*     3.6    17.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 230 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96G  VAL*     3.9    12.5    -      -       +      +
    188H  VAL*     3.7     7.8    -      -       +      +
    189H  ASP*     3.5     2.4    -      -       -      -
    190H  LEU*     2.9    63.1    +      -       +      -
    202H  PHE*     4.2    16.8    -      +       -      -
    220H  GLU*     2.5    27.8    +      -       -      -
    222H  TRP*     3.6    39.7    -      +       +      -
    224H  ILE*     4.1    19.3    -      -       +      +
    229H  THR*     1.3    70.1    +      -       -      +
    231H  SER*     1.3    63.0    +      -       -      +
    232H  LYS*     3.1    42.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 231 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188H  VAL      3.3     3.4    -      -       -      -
    189H  ASP*     2.6    25.6    +      -       -      -
    229H  THR*     3.6    16.3    +      -       -      -
    230H  TYR*     1.3    80.5    -      -       -      +
    232H  LYS*     1.3    67.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 232 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96G  VAL*     3.5    15.1    -      -       +      +
     97G  ASP      3.2    17.4    +      -       -      -
    187H  THR*     3.7     2.9    -      -       -      -
    188H  VAL*     2.8    47.6    +      -       +      +
    189H  ASP*     5.3     0.2    -      -       -      +
    202H  PHE*     4.6     3.6    -      -       -      -
    217H  ASN*     3.0    32.1    -      -       -      +
    220H  GLU*     3.2    17.4    +      -       -      -
    230H  TYR*     3.1    31.1    +      -       +      +
    231H  SER*     1.3    79.7    +      -       -      +
    233H  VAL*     1.3    71.8    +      -       -      +
    234H  ARG*     4.0    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 233 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171H  GLN*     3.9    24.2    -      -       -      +
    183H  PHE*     6.5     0.2    -      -       +      -
    185H  PRO*     4.0    14.6    -      -       +      -
    186H  PHE      3.4    10.8    -      -       -      +
    187H  THR*     4.4    16.6    -      -       +      -
    232H  LYS*     1.3    86.1    -      -       -      +
    234H  ARG*     1.3    68.2    +      -       -      +
    235H  GLY      4.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 234 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97G  ASP*     2.9    40.5    +      -       -      -
     98G  THR*     3.5    15.8    +      -       -      +
     99G  ALA      2.7    29.9    +      -       -      +
    100G  GLN*     3.7    14.1    +      -       -      +
    186H  PHE*     2.8    42.3    +      -       -      +
    188H  VAL*     4.4    11.4    -      -       +      +
    204H  MET*     4.5     9.0    -      -       -      +
    216H  VAL*     2.9    27.3    +      -       +      +
    217H  ASN*     3.6    24.1    -      -       +      +
    232H  LYS*     4.0    13.5    -      -       -      +
    233H  VAL*     1.3    80.0    -      -       -      +
    235H  GLY*     1.3    69.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 235 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100G  GLN*     4.6     4.2    -      -       -      +
    183H  PHE*     3.6    26.2    -      -       -      -
    184H  VAL      3.4    11.2    -      -       -      -
    185H  PRO*     3.7     5.1    -      -       -      +
    216H  VAL*     4.5     6.6    -      -       -      +
    233H  VAL*     4.3     1.4    -      -       -      +
    234H  ARG*     1.3    97.8    +      -       -      +
    236H  ILE*     1.3    62.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 236 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183H  PHE*     3.5     5.1    -      -       -      -
    184H  VAL      2.9    35.8    +      -       -      +
    186H  PHE*     3.7    19.3    -      -       +      -
    206H  ALA*     4.0    12.8    -      -       +      -
    214H  ILE*     4.7    13.0    -      -       +      -
    215H  PRO      5.6     0.4    -      -       -      +
    216H  VAL*     4.0    31.9    -      -       +      +
    235H  GLY*     1.3    75.4    -      -       -      +
    237H  ASN*     1.3    71.8    +      -       -      +
    238H  PHE*     3.6    44.6    +      -       +      -
    242H  TYR*     4.9     3.8    -      -       +      -
    249H  ILE*     4.4     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 237 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75G  LYS*     5.5     3.6    -      -       -      +
    100G  GLN*     5.5    10.3    +      -       +      +
    101G  GLN*     5.9     3.2    +      -       -      +
    182H  GLY      3.5    16.8    +      -       -      +
    183H  PHE*     3.9    21.2    -      -       +      +
    235H  GLY      4.4     0.4    +      -       -      -
    236H  ILE*     1.3    74.6    -      -       -      +
    238H  PHE*     1.3    62.9    +      -       -      +
    239H  ASP*     3.0    27.0    +      -       -      +
    242H  TYR*     3.4    16.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 238 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177H  VAL*     3.8    25.4    -      -       +      -
    181H  GLY*     3.1     4.7    -      -       -      -
    182H  GLY      2.7    39.3    +      -       -      +
    184H  VAL*     4.0    14.6    -      -       +      -
    236H  ILE*     3.7    41.5    -      -       +      -
    237H  ASN*     1.3    70.4    -      -       -      +
    239H  ASP*     1.3    67.4    +      -       -      +
    242H  TYR*     3.8    15.0    -      +       +      -
    247H  TYR*     3.6    42.2    -      +       +      -
    249H  ILE*     4.0    11.0    -      -       +      -
    268H  VAL*     3.7    33.2    -      -       +      -
    270H  LYS*     4.7     8.1    -      -       +      -
----------------------------------------------------------
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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