Contacts of the strand formed by residues 581 - 589 (chain B) in PDB entry 1J1C


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 LEU 581 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    558B  ASP*     6.1     0.9    -      -       +      +
    572B  GLN*     3.4    36.3    -      -       -      +
    573B  ALA      3.4    18.8    -      -       -      +
    574B  LYS*     4.1    15.9    -      -       +      -
    579B  GLY      3.6     4.2    +      -       -      +
    580B  GLU*     1.3    79.9    -      -       -      +
    582B  VAL*     1.3    66.8    +      -       -      +
    613B  ARG*     4.3     4.9    +      -       -      -
    634B  TYR*     3.6    35.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 582 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556B  TYR*     5.8     0.4    -      -       +      -
    572B  GLN*     3.5     8.1    -      -       -      +
    573B  ALA*     2.9    47.4    +      -       +      +
    575B  LEU*     3.9    26.0    -      -       +      -
    581B  LEU*     1.3    82.2    -      -       -      +
    583B  ALA*     1.3    63.0    +      -       -      +
    584B  ILE*     4.4     5.8    -      -       +      -
    613B  ARG*     3.7    37.9    -      -       -      +
    631B  VAL*     3.9    19.7    -      -       +      -
    632B  LEU      3.2    12.3    -      -       -      +
    634B  TYR*     3.5     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 583 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562B  ILE*     4.2     5.6    -      -       +      -
    570B  VAL*     4.2     8.5    -      -       +      -
    571B  TYR      3.1    10.1    -      -       -      +
    582B  VAL*     1.3    75.6    -      -       -      +
    584B  ILE*     1.3    63.4    +      -       -      +
    585B  LYS      4.0     0.7    -      -       -      -
    630B  LEU      3.5     0.3    -      -       -      +
    631B  VAL*     3.4     3.8    -      -       -      +
    632B  LEU*     2.7    36.0    +      -       +      +
    634B  TYR*     4.1     1.3    -      -       +      +
    930B  ADP      3.6    44.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 584 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556B  TYR*     3.9    33.2    -      -       +      +
    559B  THR*     5.4     0.9    -      -       +      +
    569B  VAL      3.4     5.2    -      -       -      +
    570B  VAL*     4.3     1.8    -      -       -      -
    571B  TYR*     2.8    49.4    +      -       +      +
    573B  ALA*     3.9    25.4    -      -       +      -
    582B  VAL*     4.4     8.7    -      -       +      -
    583B  ALA*     1.3    78.8    -      -       -      +
    585B  LYS*     1.3    61.5    +      -       -      +
    586B  LYS      3.4     0.8    +      -       -      +
    616B  PHE*     4.7     4.5    -      -       +      -
    629B  ASN*     4.0    33.0    -      -       +      +
    630B  LEU      3.3     6.5    -      -       -      +
    631B  VAL*     4.3    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 585 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    567B  PHE*     5.8     1.8    -      -       -      -
    568B  GLY      6.4     0.2    -      -       -      -
    569B  VAL      3.9     3.6    -      -       -      -
    570B  VAL*     4.2    18.5    -      -       +      +
    583B  ALA      4.0     1.0    -      -       -      -
    584B  ILE*     1.3    69.8    -      -       -      +
    586B  LYS*     1.3    60.6    +      -       -      +
    587B  VAL*     3.8    20.2    +      -       +      +
    597B  GLU*     2.7    38.0    +      -       -      +
    628B  LEU      3.4     4.5    -      -       -      +
    629B  ASN*     3.5     0.2    -      -       -      -
    630B  LEU*     2.8    52.1    +      -       +      +
    632B  LEU*     4.5    14.3    -      -       +      +
    700B  ASP*     3.2    17.6    +      -       -      +
    702B  GLY*     4.8     0.8    -      -       -      -
    930B  ADP      3.0    48.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 586 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    526B  MET*     5.8     4.4    -      -       -      +
    568B  GLY*     3.1    26.2    -      -       -      -
    569B  VAL*     2.9    21.6    +      -       +      +
    571B  TYR*     4.1    28.9    +      -       +      +
    584B  ILE*     3.4     1.5    +      -       +      +
    585B  LYS*     1.3    72.9    -      -       -      +
    587B  VAL*     1.3    63.2    +      -       -      +
    618B  SER*     3.5    28.1    +      -       -      -
    619B  SER      5.9     1.4    +      -       -      -
    620B  GLY*     5.9     2.0    -      -       -      -
    627B  TYR*     3.6    36.9    -      -       +      -
    628B  LEU      3.5     3.1    -      -       -      -
    629B  ASN*     3.6    19.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 587 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    567B  PHE*     4.1    32.3    -      -       +      -
    568B  GLY*     4.7     1.1    -      -       -      +
    585B  LYS*     4.1    28.7    -      -       +      +
    586B  LYS*     1.3    80.0    -      -       -      +
    588B  LEU*     1.3    75.8    +      -       -      +
    589B  GLN*     5.3     1.6    -      -       -      +
    595B  ASN*     4.5    14.8    -      -       -      +
    597B  GLU*     4.8     7.4    -      -       -      +
    627B  TYR*     3.3     7.3    -      -       -      -
    628B  LEU*     2.7    46.8    +      -       +      +
    630B  LEU*     6.2     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 588 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  PRO*     5.3     8.1    -      -       +      -
    296A  ILE*     5.3    14.1    -      -       +      -
    567B  PHE      3.8    12.4    +      -       -      +
    587B  VAL*     1.3    85.2    -      -       +      +
    589B  GLN*     1.3    68.8    +      -       -      +
    590B  ASP*     3.9     1.7    +      -       -      -
    595B  ASN*     5.3     0.2    -      -       -      +
    625B  GLU*     3.9    25.1    -      -       +      -
    626B  VAL      4.2     3.1    -      -       -      +
    627B  TYR*     3.4    43.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 589 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    587B  VAL*     3.3     1.2    +      -       -      +
    588B  LEU*     1.3    82.6    +      -       -      +
    590B  ASP*     1.3    87.3    +      -       -      +
    591B  LYS*     3.5    16.5    +      -       +      +
    593B  PHE      3.2    12.1    -      -       -      +
    594B  LYS      4.3     0.5    -      -       -      -
    595B  ASN*     3.2    43.4    +      -       -      +
    617B  TYR*     4.0    22.7    -      -       +      -
    626B  VAL*     2.7    31.8    +      -       +      +
    628B  LEU*     4.1    21.2    -      -       +      +
----------------------------------------------------------
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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