Contacts of the strand formed by residues 80 - 86 (chain E) in PDB entry 3T0E


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 ASP 80 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  ASN*     3.9    13.0    +      -       -      +
     31E  SER*     2.9    44.2    +      -       -      -
     32E  ASN*     4.7     0.7    -      -       -      +
     77E  GLU      5.2     0.7    -      -       -      +
     78E  ASP      3.2     5.5    +      -       -      +
     79E  SER*     1.3    76.9    -      -       -      +
     81E  THR*     1.3    66.1    +      -       -      +
     82E  TYR*     3.6    20.8    +      -       +      -
     94E  GLN*     3.2    11.0    -      -       -      +
     95E  LEU*     2.8    32.6    +      -       -      +
     96E  LEU*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 81 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30E  ASN      3.8     0.5    -      -       -      -
     31E  SER*     3.1    36.1    +      -       -      +
     80E  ASP*     1.3    77.8    +      -       -      +
     82E  TYR*     1.3    63.3    +      -       -      +
     83E  ILE*     3.9     8.1    -      -       +      +
     92E  GLU*     3.7    28.9    -      -       +      +
     93E  VAL      3.6    12.1    -      -       -      +
     94E  GLN*     3.3    26.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 82 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14E  LEU*     4.5    15.7    -      -       +      -
     28E  TRP*     4.3     9.0    -      -       +      -
     29E  LYS      3.5     2.9    -      -       -      +
     30E  ASN*     4.0    23.8    -      -       +      -
     36E  ILE*     4.7     5.4    -      -       +      -
     51E  LEU*     3.9    22.1    -      -       +      +
     69E  LEU*     4.4    19.3    -      -       +      -
     71E  ILE*     3.9    23.7    -      -       +      +
     78E  ASP*     3.1    24.8    +      -       -      -
     80E  ASP*     3.6    22.7    +      -       +      +
     81E  THR*     1.3    81.0    -      -       -      +
     83E  ILE*     1.3    63.1    +      -       -      +
     92E  GLU*     3.7     4.9    -      -       -      +
     93E  VAL*     3.0    46.7    +      -       +      +
     95E  LEU*     4.6    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 83 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28E  TRP*     2.7    28.0    -      -       -      -
     29E  LYS*     2.8    41.2    +      -       +      +
     30E  ASN      4.4     2.0    -      -       -      +
     31E  SER*     4.4    15.3    -      -       -      +
     33E  GLN*     5.0     5.6    -      -       -      +
     81E  THR*     3.9    17.7    -      -       +      +
     82E  TYR*     1.3    79.5    -      -       -      +
     84E  CYS*     1.3    69.7    +      -       -      +
     85E  GLU*     3.6    33.4    -      -       +      +
     90E  LYS*     4.4    14.1    -      -       +      +
     91E  GLU      3.8     4.5    -      -       -      -
     92E  GLU*     4.8     8.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 84 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  CYS*     2.0    49.9    -      -       +      -
     26E  PHE*     5.5     4.3    -      -       -      -
     27E  HIS      3.8     7.6    -      -       -      -
     28E  TRP*     3.8    30.1    -      -       +      -
     67E  PHE*     4.8     0.9    -      -       -      -
     83E  ILE*     1.3    78.0    -      -       -      +
     85E  GLU*     1.3    69.9    +      -       -      +
     86E  VAL*     3.9     2.5    +      -       -      -
     89E  GLN*     2.9    14.4    -      -       -      +
     90E  LYS      3.6     1.2    -      -       -      -
     91E  GLU*     3.0    26.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 85 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26E  PHE*     3.3    24.0    -      -       -      -
     27E  HIS*     2.7    49.0    +      -       +      +
     29E  LYS*     3.6    23.9    +      -       -      +
     33E  GLN*     5.2     1.4    +      -       -      -
     83E  ILE*     3.6    17.6    -      -       +      +
     84E  CYS*     1.3    77.0    -      -       -      +
     86E  VAL*     1.3    59.6    +      -       -      +
     88E  ASP*     5.3     0.9    -      -       -      -
     89E  GLN      3.2    11.2    -      -       -      +
     90E  LYS*     5.1    12.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 86 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16E  CYS*     3.9    25.1    -      -       -      -
     17E  THR*     4.5     0.4    -      -       -      -
     18E  ALA*     3.8    22.9    -      -       +      +
     24E  ILE*     3.5    22.7    -      -       +      -
     25E  GLN      3.3    20.2    -      -       -      +
     26E  PHE*     4.0    10.8    -      -       +      -
     67E  PHE*     4.2     9.2    -      -       +      -
     84E  CYS      5.2     0.2    -      -       -      +
     85E  GLU*     1.3    74.1    -      -       -      +
     87E  GLU*     1.3    75.3    +      -       -      +
     88E  ASP      3.0     3.1    +      -       -      -
     89E  GLN*     3.1    30.5    +      -       +      +
----------------------------------------------------------
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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