Contacts of the strand formed by residues 182 - 185 (chain B) in PDB entry 3KEU


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 182 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  ASP      3.0     3.9    +      -       -      +
    146B  ILE*     3.3    38.0    -      -       +      +
    147B  ILE*     2.9    27.2    +      -       -      +
    180B  PRO*     3.9     1.4    -      -       -      +
    181B  ASP*     1.3    80.6    -      -       -      +
    183B  VAL*     1.3    66.1    +      -       -      +
    184B  VAL*     4.2    10.8    -      -       +      -
    204B  SER      3.5     7.4    -      -       -      +
    205B  GLN*     3.1    31.9    +      -       +      +
    241B  LEU*     4.9     1.8    -      -       +      -
    245B  THR*     5.2     2.0    -      -       +      -
    252B  LEU*     4.1    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  ILE*     3.7    16.2    -      -       +      -
    149B  PRO*     4.6     3.1    -      -       +      -
    172B  MET*     3.8    28.0    -      -       +      +
    175B  LEU*     3.8    40.4    -      -       +      -
    176B  HIS*     3.7    29.6    -      -       +      +
    180B  PRO*     4.2     4.9    -      -       +      +
    182B  THR*     1.3    77.4    -      -       -      +
    184B  VAL*     1.3    68.6    +      -       -      +
    185B  ILE*     4.3     2.4    +      -       +      -
    202B  LEU      4.0     0.3    -      -       -      +
    203B  GLY*     3.6     1.2    -      -       -      -
    204B  SER*     2.9    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  ILE      3.0     9.8    +      -       -      +
    148B  THR*     3.2     9.6    -      -       +      -
    149B  PRO*     3.2    21.3    -      -       -      +
    182B  THR*     4.3    12.1    -      -       +      -
    183B  VAL*     1.3    80.1    -      -       -      +
    185B  ILE*     1.3    65.0    +      -       -      +
    186B  THR*     3.3     2.5    +      -       +      -
    201B  VAL*     4.0    11.9    -      -       +      -
    202B  LEU      3.3    11.0    -      -       -      +
    203B  GLY*     4.2     9.4    -      -       -      -
    237B  PHE*     3.8    30.3    -      -       +      -
    241B  LEU*     3.7    29.8    -      -       +      -
    252B  LEU*     4.5     2.2    -      -       +      -
    256B  CYS*     4.2    15.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  PRO*     3.0     8.7    -      -       +      +
    150B  ASN      4.0     0.9    -      -       -      -
    151B  GLN*     3.8    17.3    -      -       +      +
    154B  ALA*     4.2    23.8    -      -       +      -
    162B  ILE*     4.3     4.0    -      -       +      -
    168B  ALA*     4.2    15.3    -      -       +      -
    171B  VAL*     4.3     5.2    -      -       +      -
    172B  MET*     3.7    40.2    -      -       +      -
    183B  VAL*     4.2     2.2    -      -       +      -
    184B  VAL*     1.3    70.8    -      -       -      +
    186B  THR*     1.3    61.6    +      -       -      +
    187B  SER      3.4    23.6    +      -       -      +
    188B  SER*     4.4     8.3    -      -       -      -
    200B  ILE      4.9     0.9    -      -       -      +
    201B  VAL*     3.4     5.9    -      -       -      +
    202B  LEU*     2.8    37.9    +      -       +      +
----------------------------------------------------------
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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