Contacts of the strand formed by residues 247 - 253 (chain B) in PDB entry 1JEQ


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 TRP 247 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  HIS*     1.3    72.7    -      -       -      +
    248B  PRO*     1.3    66.4    -      -       +      +
    249B  CYS*     3.5    22.7    -      -       +      -
    261B  ILE*     3.9     4.4    -      -       +      +
    262B  ALA*     3.1     6.3    -      -       -      -
    263B  ALA*     2.7    61.9    +      -       +      +
    338B  LYS*     3.7    21.6    -      -       +      +
    339B  CYS      3.5    17.0    -      -       -      -
    340B  PHE*     4.0    14.6    -      +       +      -
    362B  LEU*     6.2     0.4    -      -       +      -
    395B  TYR*     3.4    31.6    -      +       -      -
    396B  ALA      3.6    20.2    -      -       -      -
    397B  TYR*     3.2    52.4    +      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 248 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246B  HIS*     3.3    34.5    -      -       +      +
    247B  TRP*     1.3    87.2    -      -       +      +
    249B  CYS*     1.3    61.1    +      -       -      +
    261B  ILE      3.6     7.0    -      -       -      +
    338B  LYS*     2.6    45.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 249 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247B  TRP*     3.5    40.7    +      -       +      -
    248B  PRO*     1.3    77.2    -      -       -      +
    250B  ARG*     1.3    71.4    +      -       -      +
    260B  ARG*     3.7     3.1    -      -       -      +
    261B  ILE*     2.7    42.7    +      -       +      +
    338B  LYS*     4.2    10.3    -      -       -      +
    339B  CYS*     3.8    26.7    -      -       -      -
    340B  PHE*     3.9     6.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 250 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536A  PRO      3.9     5.5    +      -       -      -
    537A  GLU*     3.1    63.0    +      -       -      +
    249B  CYS*     1.3    86.7    -      -       -      +
    251B  LEU*     1.3    64.2    +      -       -      +
    252B  THR*     3.3    15.5    +      -       +      +
    258B  SER*     3.4    25.4    -      -       -      +
    259B  ILE      3.4     3.6    -      -       -      +
    260B  ARG*     4.5    18.6    -      -       +      +
    261B  ILE*     4.4     1.3    -      -       -      -
    340B  PHE*     3.5    14.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 251 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  ARG*     1.3    71.6    -      -       -      +
    252B  THR*     1.3    60.0    +      -       -      +
    253B  ILE*     4.0    16.0    +      -       +      +
    257B  LEU      4.2     0.2    -      -       -      +
    258B  SER*     3.8     1.6    -      -       -      -
    259B  ILE*     2.7    45.3    +      -       +      +
    261B  ILE*     3.9    14.5    -      -       +      +
    340B  PHE*     3.3    35.2    -      -       +      +
    342B  VAL*     3.6    25.4    -      -       +      -
    364B  VAL*     5.3     0.4    -      -       +      -
    377B  LEU*     4.0    16.2    -      -       +      -
    380B  LEU*     4.0    11.0    -      -       +      -
    419B  LEU*     3.7    29.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 252 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250B  ARG*     3.5    20.4    -      -       +      +
    251B  LEU*     1.3    78.2    -      -       -      +
    253B  ILE*     1.3    62.3    +      -       -      +
    254B  GLY      4.0    12.0    +      -       -      -
    255B  SER*     5.9     0.7    -      -       -      -
    257B  LEU      3.6     8.1    -      -       -      +
    258B  SER*     4.0    14.6    -      -       -      +
    340B  PHE      3.3     6.3    +      -       -      -
    341B  SER*     3.2    22.9    -      -       -      -
    342B  VAL*     2.8    34.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 253 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462A  MET*     4.5    17.7    -      -       +      -
    465A  ILE*     4.3     9.4    -      -       +      -
    469A  LEU*     3.5    31.2    -      -       +      -
    514A  MET*     4.2     5.6    -      -       +      -
    518A  LEU*     4.3     9.9    -      -       +      +
    522A  VAL*     5.1     0.7    -      -       -      +
    251B  LEU*     4.0    12.8    -      -       +      +
    252B  THR*     1.3    75.6    -      -       -      +
    254B  GLY*     1.3    63.7    +      -       -      +
    256B  ASN      4.1     0.3    +      -       -      -
    257B  LEU*     3.2    52.2    +      -       +      +
    259B  ILE*     5.3     3.4    -      -       +      -
    342B  VAL*     3.6    16.4    -      -       +      -
    345B  PHE*     4.2    18.8    -      -       +      -
    380B  LEU*     4.6     7.6    -      -       +      -
----------------------------------------------------------
 Back to top of page


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