Contacts of the strand formed by residues 62 - 66 (chain J) in PDB entry 5XS0


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 62 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54J  SER*     3.6    34.3    -      -       -      +
     55J  ARG      3.8     4.7    -      -       -      -
     56J  MET*     4.2    15.0    -      -       +      +
     61J  GLN*     1.3    76.9    -      -       -      +
     63J  VAL*     1.3    59.2    +      -       -      +
     64J  CYS*     4.2    10.7    +      -       -      -
    176J  ASN*     4.3    19.4    -      -       -      +
    180J  ARG*     6.1     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 63 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54J  SER*     3.2     4.1    -      -       -      -
     55J  ARG*     3.1    35.2    +      -       +      +
     57J  ALA*     3.7    31.4    -      -       +      -
     59J  GLY*     5.1     5.8    -      -       -      +
     61J  GLN*     3.0    33.2    +      -       +      +
     62J  LYS*     1.3    74.5    -      -       -      +
     64J  CYS*     1.3    74.1    +      -       -      +
     65J  TYR*     4.0     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 64 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52J  ILE*     3.6    26.0    -      -       +      -
     53J  SER      3.2     8.1    -      -       -      -
     54J  SER*     4.9     6.5    -      -       -      -
     62J  LYS*     5.3     9.4    -      -       -      -
     63J  VAL*     1.3    87.1    -      -       -      +
     65J  TYR*     1.3    64.6    +      -       -      +
    166J  ILE*     3.9    18.8    -      -       +      +
    172J  LEU*     4.0    26.5    -      -       +      +
    175J  LEU*     5.5     2.0    -      -       -      -
    176J  ASN*     6.1     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 65 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52J  ILE*     3.8     4.7    -      -       -      -
     53J  SER*     3.1    44.4    +      -       -      -
     54J  SER      3.6    23.7    +      -       -      -
     55J  ARG*     3.7    56.8    -      -       +      +
     63J  VAL      4.0     0.9    -      -       -      -
     64J  CYS*     1.3    78.9    -      -       -      +
     66J  ILE*     1.3    74.6    +      -       -      +
     67J  GLU*     3.6    37.9    +      -       +      +
    152J  LYS*     4.3    11.2    -      -       -      +
    166J  ILE*     4.4     9.0    -      -       -      -
    169K  LYS*     5.0     4.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 66 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47J  LEU*     4.1    21.1    -      -       +      -
     51J  TYR*     4.1    15.3    -      -       +      +
     52J  ILE*     4.4    13.9    -      -       +      -
     65J  TYR*     1.3    80.6    -      -       -      +
     67J  GLU*     1.3    70.5    +      -       -      +
     70J  ARG*     3.8    15.0    -      -       +      -
     71J  VAL*     3.5    25.6    -      -       +      +
     74J  LEU*     4.7     7.0    -      -       +      -
    152J  LYS*     3.2    27.8    +      -       +      +
    162J  LEU      4.7     3.1    -      -       -      +
    163J  GLY*     3.7    30.5    -      -       -      +
    166J  ILE*     4.6    12.8    -      -       +      -
----------------------------------------------------------
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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