Contacts of the strand formed by residues 18 - 25 (chain B) in PDB entry 3EYF


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 LEU 18 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  GLY      2.8    29.6    -      -       -      +
      9B  GLY*     4.2     2.0    -      -       -      -
     10B  GLY*     4.3    14.1    -      -       -      +
     12B  VAL*     3.7    26.2    -      -       +      -
     17B  SER*     1.3    76.6    +      -       -      +
     19B  ARG*     1.3    67.9    +      -       -      +
     20B  LEU*     3.7    20.0    -      -       +      -
     81B  LEU      3.5     1.3    -      -       -      +
     82B  GLN*     3.4     6.4    +      -       -      -
     83B  MET*     2.5    47.9    +      -       +      -
     86B  LEU*     3.8    18.6    -      -       +      -
    121B  VAL*     4.1    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  GLY*     3.8    18.5    -      -       -      +
     18B  LEU*     1.3    76.5    -      -       -      +
     20B  LEU*     1.3    62.2    +      -       -      +
     21B  SER*     4.2     3.8    +      -       -      +
     71B  SER*     4.2    11.9    +      -       -      -
     80B  SER*     3.1    39.1    +      -       -      +
     81B  LEU      3.3     3.8    -      -       -      +
     82B  GLN*     3.2    41.3    +      -       -      +
    191C  LYS*     5.9     3.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  SER      3.5     4.5    -      -       -      +
      8B  GLY      3.6     4.0    -      -       -      -
      9B  GLY*     3.6    31.6    -      -       -      +
     18B  LEU*     3.7    11.9    -      -       +      -
     19B  ARG*     1.3    73.9    -      -       -      +
     21B  SER*     1.3    63.4    +      -       -      +
     36B  TRP*     4.0    22.2    -      -       +      -
     80B  SER*     3.0     6.9    +      -       -      -
     81B  LEU*     2.7    46.0    +      -       +      +
     83B  MET*     3.5    29.6    -      -       +      -
     94B  TYR*     3.7    34.3    -      -       +      -
    119B  THR*     4.1     7.0    -      -       +      -
    121B  VAL*     4.3     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLU*     3.1     6.9    -      -       -      +
      7B  SER*     2.9    47.4    +      -       -      -
     19B  ARG*     4.2     3.7    +      -       -      +
     20B  LEU*     1.3    79.0    +      -       -      +
     22B  CYS*     1.3    61.8    +      -       -      +
     23B  GLU*     6.3     0.7    -      -       -      -
     36B  TRP*     3.8     5.7    -      -       -      -
     78B  THR*     4.7     9.1    -      -       -      +
     79B  MET      3.3     9.9    +      -       -      -
     80B  SER*     3.8     8.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  LEU*     4.5    12.3    -      -       -      -
      5B  VAL      3.2     4.9    -      -       -      -
     21B  SER*     1.3    76.0    -      -       -      +
     23B  GLU*     1.3    62.5    +      -       -      +
     24B  GLY      4.1     0.8    +      -       -      -
     29B  PHE*     4.4     4.0    -      -       -      -
     34B  ILE*     4.2     8.7    -      -       -      -
     36B  TRP*     3.9     2.5    -      -       +      -
     77B  ASN      3.9     0.3    -      -       -      +
     78B  THR*     3.6     5.7    -      -       -      +
     79B  MET*     2.9    54.0    +      -       -      +
     96B  CYS*     2.0    50.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  ARG      3.8     0.7    -      -       -      +
      4B  LEU*     3.3     4.6    -      -       -      -
      5B  VAL*     2.6    50.2    +      -       +      +
      7B  SER*     5.9     1.8    -      -       -      +
     21B  SER*     6.3     0.4    -      -       -      -
     22B  CYS*     1.3    76.6    -      -       -      +
     24B  GLY*     1.3    69.6    +      -       -      +
     25B  SER*     5.3     3.9    -      -       -      -
     29B  PHE*     4.7     0.2    -      -       -      -
     76B  LYS      4.8     5.5    -      -       -      +
     77B  ASN*     3.5    10.1    -      -       -      +
     78B  THR*     4.6    10.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  ARG      3.4     8.1    -      -       -      -
      4B  LEU*     3.9     3.8    -      -       -      -
     23B  GLU*     1.3    80.9    -      -       -      +
     25B  SER*     1.3    64.1    +      -       -      -
     27B  PHE*     3.9    10.1    -      -       -      -
     29B  PHE*     3.6    22.1    -      -       -      -
     77B  ASN*     3.0    33.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  GLN*     3.3     4.2    +      -       -      +
      3B  ARG*     2.7    66.3    +      -       -      +
     23B  GLU*     5.3     4.3    -      -       -      -
     24B  GLY*     1.3    77.2    -      -       -      -
     26B  GLY*     1.3    60.1    +      -       -      +
     27B  PHE*     3.3    11.2    -      -       -      +
     77B  ASN*     4.9     5.6    -      -       -      -
----------------------------------------------------------
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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