Contacts of the strand formed by residues 78 - 83 (chain E) in PDB entry 2X4O


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 78 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23E  LEU*     3.6    30.5    -      -       +      -
     40E  LEU      3.2    14.1    -      -       -      +
     41E  LYS*     3.6    43.1    +      -       +      +
     46E  ILE*     4.3     9.2    -      -       +      -
     70E  PHE*     3.6    36.3    -      +       +      +
     71E  THR      4.0    12.0    +      -       -      -
     72E  PRO*     5.0     3.1    -      -       +      -
     73E  THR      5.3     0.2    -      -       -      -
     76E  ASP*     3.7    27.7    +      -       +      -
     77E  GLU*     1.3    76.7    -      -       -      +
     79E  ALA*     1.3    63.0    +      -       -      +
     94E  LYS*     3.7     3.8    -      -       -      +
     95E  TRP*     2.7    59.0    +      +       +      +
----------------------------------------------------------
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Residues in contact with ALA 79 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9E  VAL*     4.7     5.2    -      -       -      -
     23E  LEU*     5.0     0.5    -      -       -      +
     39E  LEU*     3.5     7.4    -      -       -      +
     40E  LEU*     2.8    45.8    +      -       +      +
     43E  GLY      6.3     0.2    -      -       -      +
     78E  TYR*     1.3    77.2    -      -       -      +
     80E  CYS*     1.3    59.3    +      -       -      +
     81E  ARG      4.2     0.2    -      -       -      -
     92E  ILE*     3.9    21.8    -      -       +      -
     93E  VAL      3.2    14.1    -      -       -      +
     94E  LYS*     4.1     9.0    -      -       +      +
     95E  TRP      4.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 80 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7E  ILE*     4.7     1.6    -      -       +      -
      9E  VAL*     3.4    19.5    -      -       +      -
     25E  CYS*     2.0    53.6    -      -       +      -
     37E  VAL*     3.8    16.6    -      -       -      -
     38E  ASP      3.4     5.4    -      -       -      -
     39E  LEU*     4.1     3.8    -      -       +      -
     79E  ALA*     1.3    75.4    -      -       -      +
     81E  ARG*     1.3    60.0    +      -       -      +
     82E  VAL*     3.8     8.7    +      -       -      +
     91E  LYS      3.4     2.6    -      -       -      +
     92E  ILE*     3.4     3.9    -      -       -      -
     93E  VAL*     2.8    38.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 81 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36E  GLU      3.8     0.7    -      -       -      +
     37E  VAL*     3.4     3.6    -      -       -      -
     38E  ASP*     2.7    64.3    +      -       -      +
     40E  LEU*     3.9    33.7    -      -       +      +
     43E  GLY      5.4     3.0    +      -       -      -
     45E  ARG*     4.2    13.1    -      -       -      +
     79E  ALA      4.2     0.6    -      -       -      -
     80E  CYS*     1.3    72.1    -      -       -      +
     82E  VAL*     1.3    63.7    +      -       -      +
     83E  ASN*     4.3     1.1    +      -       +      +
     90E  PRO*     4.3    20.9    -      -       +      -
     91E  LYS      3.2     5.4    -      -       -      +
     92E  ILE*     3.6    28.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5E  PRO*     4.3    12.1    -      -       +      -
      7E  ILE*     3.7    37.2    -      -       +      -
     27E  VAL*     3.9    11.4    -      -       +      -
     35E  ILE*     3.8    28.5    -      -       +      -
     36E  GLU      3.3     4.0    -      -       -      +
     37E  VAL*     4.2     4.5    -      -       +      -
     80E  CYS*     3.8    22.7    -      -       -      +
     81E  ARG*     1.3    80.7    -      -       -      +
     83E  ASN*     1.3    63.8    +      -       -      +
     87E  LEU*     3.4     8.0    -      -       +      +
     90E  PRO*     3.5     2.0    -      -       -      +
     91E  LYS      2.7    37.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 83 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35E  ILE*     3.2     9.8    -      -       -      +
     36E  GLU*     2.8    67.9    +      -       +      +
     81E  ARG*     5.4     0.9    -      -       +      +
     82E  VAL*     1.3    74.8    -      -       -      +
     84E  HIS*     1.3    77.0    +      -       -      +
     87E  LEU*     4.4     3.5    -      -       -      +
     89E  GLN*     4.2     3.6    -      -       -      -
     90E  PRO*     3.8    35.9    -      -       +      +
----------------------------------------------------------
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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