Contacts of the strand formed by residues 34 - 43 (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 GLU 34 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  TYR*     2.7    38.1    +      -       -      -
    291A  LEU      5.0     0.9    -      -       -      +
    292A  ARG*     4.8     5.5    -      -       -      -
    294A  VAL*     4.0     5.6    +      -       +      +
    295A  GLN*     3.0    34.9    +      -       -      +
      4B  GLU*     4.5    14.5    -      -       +      +
      5B  CYS      2.9    15.6    +      -       -      +
      6B  ARG*     3.3    39.4    +      -       +      +
      7B  VAL      2.9    23.5    +      -       -      +
     32B  GLY      3.8     1.7    +      -       -      +
     33B  PHE*     1.3    68.9    -      -       -      +
     35B  ILE*     1.3    59.8    +      -       -      +
     36B  ASP*     3.8     7.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  TYR*     4.8     1.9    +      -       -      -
     22A  ARG*     3.0    25.5    +      -       -      -
      7B  VAL*     3.3    20.6    -      -       +      +
      9B  SER*     3.6    24.2    -      -       -      +
     21B  ASN*     4.7     0.2    -      -       -      +
     24B  ALA      4.4     1.8    -      -       -      +
     25B  THR*     3.9    32.5    -      -       +      +
     28B  LEU*     3.7    34.5    -      -       +      -
     29B  GLN*     3.5    31.8    -      -       +      +
     33B  PHE      3.0     6.6    +      -       -      +
     34B  GLU*     1.3    73.1    -      -       -      +
     36B  ASP*     1.3    69.6    +      -       -      +
     37B  ALA      4.6     0.2    -      -       -      +
     81B  LEU*     5.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ILE*     3.0    34.4    -      -       +      +
     16A  ARG*     2.7    28.5    +      -       -      -
     17A  GLY      4.5     0.3    +      -       -      -
     22A  ARG*     3.4    12.5    +      -       -      +
      6B  ARG*     4.7     4.2    +      -       -      -
      7B  VAL      2.7    12.1    +      -       -      +
      8B  LEU*     3.5     4.8    -      -       +      +
      9B  SER*     2.7    31.7    +      -       -      -
     34B  GLU*     4.2     8.6    -      -       -      +
     35B  ILE*     1.3    74.5    -      -       -      +
     37B  ALA*     1.3    57.3    +      -       -      +
     38B  VAL      3.8     0.5    +      -       -      -
     77B  TYR*     2.6    32.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 37 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  HIS*     2.9    37.9    +      -       +      -
     15A  ILE*     3.8    11.0    +      -       -      +
     22A  ARG*     4.1    10.0    -      -       -      +
      9B  SER*     3.4     4.9    -      -       -      -
     21B  ASN*     3.6    24.5    -      -       +      +
     25B  THR*     4.0    14.6    -      -       +      +
     35B  ILE*     3.9     2.7    +      -       +      -
     36B  ASP*     1.3    72.3    -      -       -      +
     38B  VAL*     1.3    61.5    +      -       -      +
     39B  ASN*     3.7     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 38 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ILE*     3.8    21.5    -      -       +      -
     42A  GLN*     3.7     7.6    -      -       -      +
      8B  LEU*     3.8    28.5    -      -       +      -
      9B  SER      2.8     7.9    +      -       -      -
     10B  ILE*     3.3    23.7    -      -       +      -
     11B  GLN      3.1    15.4    +      -       -      +
     21B  ASN*     3.0    12.4    +      -       -      -
     36B  ASP      3.8     0.2    +      -       -      -
     37B  ALA*     1.3    71.4    -      -       -      +
     39B  ASN*     1.3    59.9    +      -       -      +
     40B  SER      3.3     0.3    +      -       -      -
     57B  LEU*     4.1    14.6    -      -       +      -
     62B  LEU*     3.8    28.0    -      -       +      -
     65B  LEU*     4.4     7.2    -      -       +      -
     69B  LEU*     5.6     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 39 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  HIS*     3.5    26.9    +      -       -      -
     39A  ASN*     3.1    29.6    -      -       -      +
     42A  GLN*     2.9    28.9    -      -       -      +
     11B  GLN      3.2     4.3    -      -       -      -
     13B  HIS*     3.5    31.7    +      -       +      +
     21B  ASN*     3.4    20.3    +      -       -      +
     37B  ALA*     4.0     5.5    -      -       -      +
     38B  VAL*     1.3    68.3    -      -       -      +
     40B  SER*     1.3    63.8    +      -       -      +
     41B  VAL*     3.2     5.7    +      -       -      +
     42B  GLN*     5.7     2.7    -      -       +      -
     57B  LEU*     3.3    11.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 40 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  ILE*     4.5     2.7    -      -       -      -
     11B  GLN*     2.8    35.2    +      -       -      -
     12B  SER*     3.2     6.8    +      -       -      -
     38B  VAL      3.3     2.2    +      -       -      -
     39B  ASN*     1.3    73.8    -      -       -      +
     41B  VAL*     1.3    67.6    +      -       -      +
     56B  VAL*     4.2     0.3    -      -       -      +
     57B  LEU*     2.8    36.5    +      -       -      +
     84B  TYR*     4.5     8.7    +      -       -      -
     85B  THR*     6.3     1.3    -      -       -      -
     90B  PHE*     3.6    27.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 41 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  SER*     3.2    28.7    -      -       -      +
     13B  HIS*     2.9    33.3    +      -       -      +
     14B  VAL*     6.0     0.7    -      -       +      -
     39B  ASN*     3.2     6.6    -      -       -      +
     40B  SER*     1.3    90.6    +      -       -      +
     42B  GLN*     1.3    61.9    +      -       -      +
     43B  PHE*     4.0    25.8    -      -       +      -
     55B  GLN      3.5    13.0    -      -       -      +
     56B  VAL*     4.0    19.5    -      -       +      +
     57B  LEU      4.4     0.4    -      -       -      +
     84B  TYR*     5.7     4.5    -      -       +      -
     86B  ARG*     4.3    17.0    -      -       +      -
    500B  PLP      4.9     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 42 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  VAL*     3.7     0.2    -      -       -      -
     39A  ASN*     2.8    51.4    +      -       -      +
     57A  LEU*     4.0    18.4    -      -       -      +
     65A  LEU*     3.6    15.3    -      -       +      +
     13B  HIS*     3.3    19.3    -      -       +      -
     15B  ILE*     3.5    23.8    -      -       +      +
     39B  ASN*     5.7     2.5    -      -       +      -
     41B  VAL*     1.3    74.3    -      -       -      +
     43B  PHE*     1.3    61.2    +      -       -      +
     54B  GLY*     3.1     3.5    -      -       -      -
     55B  GLN*     2.9    37.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 43 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LEU*     3.9     4.7    -      -       -      -
     13B  HIS      3.0    10.2    +      -       -      +
     14B  VAL*     3.1     7.3    -      -       +      -
     15B  ILE*     2.8    28.1    +      -       -      +
     41B  VAL*     4.0    17.7    -      -       +      -
     42B  GLN*     1.3    87.1    -      -       -      +
     44B  SER*     1.3    62.5    +      -       -      +
     45B  ASN      3.2    15.9    -      -       -      +
     46B  HIS*     5.8     0.4    -      -       -      -
     47B  THR*     4.0    13.9    -      -       +      -
     52B  TRP*     3.6    33.7    -      +       +      -
     53B  LYS      3.2     7.6    -      -       -      +
     54B  GLY*     3.5    20.4    -      -       -      -
     55B  GLN      3.4    20.9    -      -       -      -
     56B  VAL*     4.1    15.3    -      -       +      -
    500B  PLP      5.7     7.0    -      -       +      -
    536B  SO4      3.9    20.9    -      -       -      -
----------------------------------------------------------
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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