Contacts of the strand formed by residues 444 - 449 (chain A) in PDB entry 2JED


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 MET 444 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429A  LYS*     3.6    19.5    -      -       +      +
    432A  LEU*     3.6    45.0    +      -       +      +
    433A  SER*     3.8     7.6    -      -       -      +
    435A  ALA*     5.1     0.2    -      -       -      +
    436A  TRP*     5.1     3.6    -      -       -      +
    442A  THR      3.8     2.0    +      -       -      -
    443A  HIS*     1.3    73.6    -      -       -      +
    445A  PHE*     1.3    63.1    +      -       -      +
    446A  CYS      3.8    26.5    -      -       -      +
    447A  THR*     3.8    16.6    -      -       -      +
    456A  PHE*     4.8     2.2    -      -       +      -
    457A  VAL      3.7     8.3    -      -       -      +
    458A  MET*     3.7    22.9    -      -       +      -
    696A  PHE*     3.9    26.1    -      -       +      -
    698A  ASN*     3.2    21.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 445 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    406A  PHE*     3.5    37.2    -      +       +      -
    443A  HIS*     4.5    14.8    -      -       +      -
    444A  MET*     1.3    74.8    -      -       -      +
    446A  CYS*     1.3    64.8    +      -       -      +
    457A  VAL*     2.7    18.7    +      -       +      +
    458A  MET      3.8     2.0    -      -       -      -
    459A  GLU*     3.3    46.2    -      -       +      -
    697A  MET*     3.4    10.5    -      -       +      +
    698A  ASN*     2.9    46.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 446 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  LEU*     3.5    34.3    -      -       +      -
    444A  MET*     3.8     8.2    -      -       -      +
    445A  PHE*     1.3    84.9    -      -       -      +
    447A  THR*     1.3    62.8    +      -       -      +
    448A  PHE*     4.5     4.0    -      -       -      -
    455A  PHE      4.1     0.2    -      -       -      +
    456A  PHE*     3.6     2.1    -      -       -      -
    457A  VAL*     2.7    55.4    +      -       -      +
    696A  PHE      3.4    13.9    -      -       -      +
    697A  MET*     3.7    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 447 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429A  LYS*     4.0     5.7    -      -       +      +
    444A  MET*     3.8    17.6    -      -       -      +
    446A  CYS*     1.3    76.6    +      -       -      +
    448A  PHE*     1.3    66.2    +      -       -      +
    455A  PHE      3.5     9.8    +      -       -      -
    456A  PHE*     3.8    16.5    -      -       -      -
    694A  PHE*     2.3    48.9    -      -       +      +
    695A  SEP      3.4     8.5    -      -       -      +
    696A  PHE*     3.0    28.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 448 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  LEU*     3.4    43.1    -      -       +      +
    376A  LYS*     4.0     8.7    -      -       -      -
    377A  ILE*     3.7    32.3    -      -       +      -
    380A  PHE*     4.4     5.4    -      +       -      -
    446A  CYS*     4.5    10.1    -      -       +      -
    447A  THR*     1.3    78.9    -      -       -      +
    449A  GLN*     1.3    68.4    +      -       -      +
    450A  THR*     5.4     2.5    -      -       -      -
    455A  PHE*     2.9    68.3    +      +       +      +
    457A  VAL*     3.8    24.9    -      -       +      -
    694A  PHE*     3.5     5.6    -      -       -      -
    695A  SEP      4.0    11.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 449 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413A  LYS*     2.8    29.2    +      -       -      +
    448A  PHE*     1.3    82.4    -      -       -      +
    450A  THR*     1.3    65.1    +      -       -      +
    453A  ASN      3.4    12.6    -      -       -      +
    454A  LEU*     3.8    13.0    -      -       +      -
    455A  PHE*     5.1     0.7    -      -       -      -
    691A  PHE*     2.7    28.3    +      -       -      +
    692A  ARG*     2.8    28.6    +      -       -      +
    694A  PHE*     3.7     9.7    -      -       +      +
    695A  SEP      3.3    36.4    +      -       -      +
----------------------------------------------------------
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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