Contacts of the strand formed by residues 28 - 35 (chain A) in PDB entry 3EOV


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 LYS 28 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  VAL*     4.5     7.4    -      -       +      -
     27A  ALA*     1.3    82.7    -      -       -      +
     29A  VAL*     1.3    62.7    +      -       -      +
     44A  THR*     4.8     8.5    -      -       +      -
     45A  ILE      3.2     5.8    -      -       -      +
     47A  LEU*     5.4     0.2    -      -       -      -
    155A  LEU*     4.0    28.2    -      -       +      +
    186A  GLU*     3.6     6.6    -      -       -      +
    187A  LEU*     2.8    57.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  LYS*     1.3    79.1    -      -       -      +
     30A  TYR*     1.3    65.2    +      -       -      +
     44A  THR*     3.6     5.0    -      -       -      +
     45A  ILE*     2.8    52.7    +      -       +      +
     47A  LEU*     3.9    21.1    -      -       +      -
     59A  PHE*     3.9    22.2    -      -       +      -
     60A  ARG*     4.2    18.8    -      -       +      -
     63A  CYS*     3.8    18.2    -      -       +      -
    185A  GLY      3.5    17.9    -      -       -      +
    186A  GLU*     4.2     3.4    -      -       +      +
    187A  LEU*     4.9     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL*     1.3    78.8    -      -       -      +
     31A  PHE*     1.3    71.6    +      -       -      +
     32A  ASP*     3.4    23.3    -      -       -      -
     42A  ARG*     3.5    39.4    +      -       +      +
     43A  ILE      3.2    11.2    -      -       -      +
     44A  THR*     4.4     4.3    -      -       -      +
     45A  ILE*     5.5     1.3    -      -       -      -
     63A  CYS*     4.8     0.7    -      -       -      -
    183A  ALA*     4.2     3.8    -      -       +      +
    184A  SER*     3.2    12.9    +      -       -      -
    185A  GLY*     3.1    40.4    +      -       -      +
    186A  GLU      3.2    32.3    -      -       -      -
    187A  LEU*     3.5    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL*     6.1     0.2    -      -       +      -
     30A  TYR*     1.3    83.8    -      -       -      +
     32A  ASP*     1.3    63.3    +      -       -      +
     33A  VAL*     3.6    13.1    +      -       +      -
     42A  ARG*     3.3     1.9    -      -       -      -
     43A  ILE*     2.8    46.8    +      -       +      +
     45A  ILE*     3.9    25.1    -      -       +      -
     59A  PHE*     3.9    21.1    -      +       -      -
     63A  CYS*     3.8    14.4    -      -       -      -
     71A  TYR*     4.0    17.7    -      +       +      -
     76A  PHE*     4.5     7.6    -      +       -      -
    134A  PHE*     3.6    30.7    -      +       -      -
    136A  ILE*     5.4     1.3    -      -       +      -
    181A  ILE*     3.7    24.0    -      -       +      -
    183A  ALA      3.5     2.5    -      -       -      -
    184A  SER*     3.5    23.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  TYR*     3.4    11.7    -      -       -      -
     31A  PHE*     1.3    72.1    -      -       -      +
     33A  VAL*     1.3    60.1    +      -       -      +
     41A  GLY      3.5     4.5    -      -       -      +
     42A  ARG*     2.7    52.5    +      -       -      +
    181A  ILE*     3.5     5.2    -      -       -      -
    182A  VAL*     3.1    40.1    +      -       +      +
    183A  ALA*     2.6    26.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PHE*     4.2    12.8    -      -       +      +
     32A  ASP*     1.3    77.9    -      -       -      +
     34A  MET*     1.3    66.3    +      -       -      +
     39A  PRO*     3.8     1.9    -      -       -      +
     40A  LEU*     2.9    39.6    +      -       +      -
     41A  GLY      2.8    18.6    +      -       -      +
     43A  ILE*     3.8    29.4    -      -       +      -
     76A  PHE*     4.3    14.6    -      -       +      -
    160A  VAL*     4.5     8.1    -      -       +      -
    164A  ILE*     3.9     4.0    -      -       +      -
    179A  VAL*     3.7    28.9    -      -       +      -
    180A  LYS      3.5     6.7    -      -       -      +
    181A  ILE*     4.5     1.6    -      -       +      -
    182A  VAL*     4.8     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  VAL*     1.3    77.4    -      -       -      +
     35A  ILE*     1.3    61.1    +      -       -      +
     36A  ASP*     3.8     5.9    +      -       -      +
     37A  SER*     3.0    39.9    -      -       -      +
     38A  GLU      3.1    27.8    -      -       -      +
     39A  PRO*     3.7     7.4    -      -       +      -
     40A  LEU*     4.2     0.9    -      -       -      +
    179A  VAL      3.7     0.3    -      -       -      -
    180A  LYS*     2.8    55.4    +      -       +      +
    182A  VAL*     3.4    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  MET*     1.3    71.9    -      -       -      +
     36A  ASP*     1.3    74.5    +      -       +      +
     38A  GLU*     2.9    24.6    +      -       +      +
     40A  LEU*     3.2    43.0    -      -       +      +
    163A  ARG*     4.9     5.6    -      -       +      +
    164A  ILE*     4.9     5.8    -      -       +      -
    167A  THR*     4.2    17.5    -      -       -      +
    177A  LYS*     4.0    26.9    -      -       +      +
    178A  PRO      3.6    10.5    -      -       -      +
    179A  VAL*     3.8    23.1    -      -       +      -
----------------------------------------------------------
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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