Contacts of the strand formed by residues 60 - 64 (chain C) in PDB entry 2UX2


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 THR 60 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29C  THR*     3.3     5.7    -      -       -      +
     30C  LYS*     3.0    37.5    +      -       -      +
     47C  PHE*     4.8     7.2    -      -       +      -
     59C  LEU*     1.3    81.9    -      -       -      +
     61C  TYR*     1.3    61.1    +      -       -      +
     75C  LEU*     3.5    24.5    -      -       -      +
     76C  GLU      4.8     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 61 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  LEU*     4.0    14.6    -      -       +      -
     28C  ILE      3.3     6.5    -      -       -      -
     29C  THR*     3.5    17.7    -      -       -      +
     45C  CYS*     3.5    20.3    +      -       +      -
     46C  ASN*     3.3    23.2    -      -       -      -
     47C  PHE*     3.8    49.8    +      +       -      -
     50C  VAL*     4.2    11.2    -      -       +      -
     59C  LEU*     4.0     8.7    -      -       +      -
     60C  THR*     1.3    77.0    -      -       -      +
     62C  TYR*     1.3    68.0    +      -       -      +
     63C  CYS*     4.3    11.4    -      -       +      -
     75C  LEU*     3.9     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 62 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  CYS      3.8     0.7    -      -       -      +
     27C  LEU*     3.5     4.2    -      -       -      +
     28C  ILE*     2.9    42.7    +      -       +      +
     61C  TYR*     1.3    77.0    -      -       -      +
     63C  CYS*     1.3    70.6    +      -       -      +
     64C  CYS*     3.5    31.1    -      -       +      +
     74C  GLN*     3.4    55.3    +      -       +      -
     75C  LEU*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 63 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25C  ALA*     5.1     0.9    -      -       +      -
     26C  CYS      3.3     7.4    -      -       -      +
     27C  LEU*     3.8    23.8    -      -       -      -
     40C  TRP*     3.9     4.0    -      -       -      -
     42C  PHE*     4.8    11.0    -      -       +      -
     45C  CYS*     2.0    55.9    -      -       +      -
     61C  TYR*     4.3     8.5    -      -       +      -
     62C  TYR*     1.3    86.5    -      -       -      +
     64C  CYS*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 64 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25C  ALA*     3.4     5.3    -      -       -      +
     26C  CYS*     2.8    36.0    +      -       -      -
     42C  PHE*     6.0     1.1    -      -       -      -
     62C  TYR*     3.5    25.8    -      -       +      +
     63C  CYS*     1.3    76.7    -      -       -      +
     65C  LYS*     1.3    64.0    +      -       -      +
     66C  LYS*     5.8     1.1    -      -       +      -
     69C  CYS*     2.0    63.4    -      -       +      -
     70C  ASN*     3.7     3.8    -      -       -      -
----------------------------------------------------------
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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