Contacts of the strand formed by residues 581 - 588 (chain A) in PDB entry 2FBW


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 581 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  LEU*     3.6    12.4    -      -       -      +
    542A  ARG*     2.7    31.2    +      -       -      -
    575A  PHE*     3.0    54.6    +      -       +      +
    576A  GLU*     3.9    14.1    +      -       -      +
    578A  HIS*     3.1    21.4    +      -       +      +
    579A  TRP*     2.8    28.9    +      -       +      +
    580A  ARG*     1.3    74.6    -      -       -      +
    582A  HIS*     1.3    53.7    +      -       -      +
    598A  TYR*     3.6    37.6    -      -       +      +
    599A  ARG      3.5    13.0    -      -       -      +
    601A  VAL*     4.0     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 582 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  LEU*     3.0    30.4    +      -       +      +
     92A  ASP*     2.9    26.2    +      -       -      -
    245A  GLN*     3.4    23.2    -      -       +      +
    246A  ASP*     2.5    34.7    +      -       -      +
    402A  SER*     4.0    15.9    -      -       -      -
    581A  LYS*     1.3    70.4    -      -       -      +
    583A  THR*     1.3    59.8    +      -       -      +
    584A  LEU      3.7     0.2    +      -       -      -
    598A  TYR*     3.2    11.6    -      -       -      -
    599A  ARG*     2.9    52.3    +      -       +      +
    600A  PRO      3.8    17.9    -      -       -      -
    601A  VAL*     3.9     7.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 583 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  CYS      3.7     0.2    -      -       -      +
    245A  GLN*     3.1    10.7    -      -       -      +
    246A  ASP*     3.0    33.1    +      -       -      +
    247A  LEU      5.8     0.2    -      -       -      +
    248A  GLU*     2.7    38.0    +      -       -      +
    534A  GLN      6.0     0.2    -      -       -      +
    538A  GLY*     4.5     7.8    +      -       -      -
    542A  ARG*     3.0    12.3    +      -       -      +
    579A  TRP*     5.2     0.2    -      -       -      -
    582A  HIS*     1.3    71.0    -      -       -      +
    584A  LEU*     1.3    71.3    +      -       -      +
    585A  SER*     4.7     3.6    -      -       -      +
    596A  LEU*     4.1    19.5    -      -       +      -
    598A  TYR*     3.5    23.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 584 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  PRO*     4.1    17.7    -      -       +      -
    244A  CYS      3.3    11.4    -      -       -      +
    245A  GLN*     3.7    26.9    -      -       +      +
    371A  PRO*     4.5     7.4    -      -       +      -
    381A  HIS*     3.5    34.8    -      -       +      -
    582A  HIS      4.5     0.4    -      -       -      +
    583A  THR*     1.3    75.0    -      -       -      +
    585A  SER*     1.3    59.9    +      -       -      +
    586A  TYR*     4.4    10.2    -      -       +      +
    595A  THR      3.9     0.3    -      -       -      +
    596A  LEU*     3.3     6.4    -      -       -      +
    597A  LYS*     2.7    52.3    +      -       -      +
    598A  TYR      4.4     5.4    -      -       -      +
    599A  ARG*     3.8    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 585 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  LEU      4.2     0.9    -      -       -      +
    243A  PRO*     3.3     7.1    -      -       -      +
    244A  CYS*     3.0    38.8    +      -       -      +
    245A  GLN*     5.4     0.5    -      -       -      -
    246A  ASP      5.8     0.2    +      -       -      -
    247A  LEU*     4.3     4.7    +      -       -      +
    534A  GLN*     2.7    47.3    +      -       -      +
    583A  THR*     4.2     4.9    +      -       -      -
    584A  LEU*     1.3    74.1    -      -       -      +
    586A  TYR*     1.3    63.6    +      -       -      +
    594A  VAL*     4.7     0.9    -      -       -      -
    595A  THR      3.4     4.0    -      -       -      -
    596A  LEU*     3.6    20.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 586 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  THR*     5.5     0.4    -      -       -      -
    241A  GLY*     3.8    21.1    -      -       -      -
    242A  LEU      4.2     4.7    -      -       -      -
    243A  PRO*     3.7    45.7    -      -       +      +
    380A  THR*     4.2     3.8    +      -       -      -
    381A  HIS      4.0     5.7    +      -       -      -
    534A  GLN*     4.4     1.3    -      -       -      -
    584A  LEU*     4.4     7.6    -      -       +      +
    585A  SER*     1.3    75.9    -      -       -      +
    587A  VAL*     1.3    68.9    +      -       -      +
    594A  VAL*     3.3     7.4    -      -       -      +
    595A  THR*     2.8    51.2    +      -       +      +
    597A  LYS*     2.7    49.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 587 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  THR*     3.7    27.0    +      -       +      +
    241A  GLY*     5.7     2.3    -      -       -      -
    530A  LEU*     4.0    24.0    -      -       +      +
    533A  LEU*     4.7     4.3    -      -       +      -
    534A  GLN*     3.3    36.6    -      -       +      +
    586A  TYR*     1.3    83.6    -      -       -      +
    588A  ASP*     1.3    73.7    +      -       -      +
    589A  VAL*     3.4    10.2    +      -       +      +
    592A  GLY*     4.0    17.5    -      -       -      +
    593A  LYS      3.3     9.6    -      -       -      +
    594A  VAL*     4.4     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 588 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    587A  VAL*     1.3    68.1    -      -       -      +
    589A  VAL*     1.3    56.7    +      -       -      +
    590A  LYS*     3.3    10.0    +      -       -      +
    591A  SER*     2.9    32.1    +      -       -      +
    592A  GLY*     2.6    34.3    +      -       -      -
    593A  LYS*     2.8    20.5    +      -       +      +
----------------------------------------------------------
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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