Contacts of the strand formed by residues 108 - 115 (chain E) in PDB entry 4DOH


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 TYR 108 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45E  PHE*     5.2     2.2    -      -       +      -
     73E  TYR*     4.9     3.1    -      +       +      -
     74E  PHE      3.4    10.3    -      -       -      +
     75E  ILE*     3.7    31.0    -      -       +      -
    100E  GLU      3.6    18.1    +      -       -      -
    101E  THR*     3.3    40.5    -      -       +      -
    102E  SER      3.9     0.2    +      -       -      -
    103E  ASP*     2.8    50.1    +      -       -      +
    106E  HIS*     3.4    19.7    +      +       +      +
    107E  GLN*     1.3    78.0    -      -       -      +
    109E  TYR*     1.3    69.8    +      -       -      +
    128E  ARG*     3.6     5.5    -      -       -      +
    129E  PHE*     2.9    43.7    +      +       +      +
    131E  PRO*     3.7    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 109 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54C  GLN*     4.4     9.2    +      -       -      +
     57C  ASP*     4.6     2.6    +      -       -      -
     60C  ILE*     3.8    31.1    -      -       +      +
     45E  PHE*     4.6     3.6    -      -       -      -
     73E  TYR*     3.6     4.3    -      -       -      +
     74E  PHE*     3.0    45.4    +      +       +      +
     76E  TYR*     3.9    26.4    -      +       +      -
     81E  TRP*     4.1     7.9    -      -       +      -
    108E  TYR*     1.3    82.1    -      -       -      +
    110E  ALA*     1.3    65.3    +      -       -      +
    125E  GLU*     4.6    11.9    -      -       +      -
    126E  SER*     3.5    27.1    -      -       -      -
    127E  GLY*     4.1     1.1    -      -       -      -
    128E  ARG*     3.0    58.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 110 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43E  ILE*     5.7     0.7    -      -       -      -
     45E  PHE*     3.7    22.2    -      -       +      -
     54E  LEU*     4.1    20.9    -      -       +      -
     72E  GLN      3.2    13.5    -      -       -      +
     73E  TYR*     4.4     0.9    -      -       -      -
     81E  TRP*     3.9     4.0    -      -       -      -
     97E  LEU*     4.2     9.6    -      -       +      -
    109E  TYR*     1.3    76.9    -      -       -      +
    111E  ARG*     1.3    64.3    +      -       -      +
    125E  GLU*     3.6     3.5    -      -       -      +
    126E  SER*     2.8    33.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 111 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43E  ILE*     5.6     0.9    -      -       -      -
     54E  LEU*     5.3     0.9    -      -       -      -
     71E  VAL*     3.1     6.6    -      -       -      +
     72E  GLN*     2.7    61.4    +      -       +      +
     81E  TRP*     3.4    58.4    -      -       +      +
    110E  ALA*     1.3    75.3    -      -       -      +
    112E  VAL*     1.3    63.2    +      -       -      +
    123E  TRP*     3.5    51.0    -      -       +      +
    124E  ALA      2.7    24.0    -      -       -      +
    125E  GLU*     3.9     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 112 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40E  PRO*     3.9    12.3    -      -       +      +
     43E  ILE*     4.3    15.9    -      -       +      -
     54E  LEU*     4.9     1.1    -      -       +      -
     56E  TRP*     3.9    42.0    -      -       +      +
     69E  TYR*     3.9    15.0    -      -       +      -
     70E  THR      3.2    17.0    -      -       -      +
     71E  VAL*     4.0     7.4    -      -       +      -
    111E  ARG*     1.3    78.8    -      -       -      +
    113E  ARG*     1.3    62.9    +      -       -      +
    123E  TRP*     3.6     4.4    -      -       -      -
    124E  ALA*     2.7    51.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 113 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40E  PRO*     4.0     7.4    -      -       -      -
     69E  TYR*     3.1     4.4    -      -       -      -
     70E  THR*     2.9    54.0    +      -       -      +
    112E  VAL*     1.3    76.5    -      -       -      +
    114E  ALA*     1.3    60.2    +      -       -      +
    115E  ILE*     4.1     4.8    -      -       +      +
    120E  CYS*     4.2    32.0    -      -       -      +
    121E  SER      3.3     5.6    -      -       -      +
    122E  LYS      3.0    28.9    +      -       -      +
    123E  TRP*     3.6    37.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39E  LYS      4.2     7.6    -      -       -      +
     40E  PRO*     3.8     7.2    -      -       +      +
     59E  PRO*     3.8    20.0    -      -       +      -
     67E  VAL*     4.4    10.3    -      -       +      -
     68E  THR      3.1     6.1    -      -       -      +
     69E  TYR*     3.4    27.1    -      -       +      -
    113E  ARG*     1.3    75.4    -      -       -      +
    115E  ILE*     1.3    63.3    +      -       -      +
    119E  LYS      4.5     0.3    -      -       -      +
    120E  CYS*     3.6     3.3    -      -       -      +
    121E  SER*     3.3    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 115 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66E  LYS*     4.1     2.4    -      -       +      +
     67E  VAL*     3.3    11.1    -      -       -      +
     68E  THR*     2.5    56.4    +      -       -      +
     69E  TYR      4.3     0.4    -      -       -      +
     70E  THR*     4.4    15.5    -      -       +      +
     89E  ASN*     3.1    33.9    -      -       -      +
    113E  ARG*     4.1    13.5    -      -       -      +
    114E  ALA*     1.3    80.0    -      -       -      +
    116E  TRP*     1.3    72.9    +      -       -      +
    117E  GLY      5.1     4.0    -      -       -      +
    119E  LYS      4.0     3.8    -      -       -      -
    120E  CYS*     3.8    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