Contacts of the strand formed by residues 267 - 271 (chain A) in PDB entry 1JS6


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 267 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ALA*     4.1     8.6    -      -       -      +
    158A  ALA*     3.7    31.4    -      -       +      -
    159A  ALA*     3.6    29.2    -      -       +      -
    162A  LYS*     4.4    13.0    -      -       +      -
    237A  PHE      3.1    15.6    +      -       -      +
    238A  PHE*     3.5    21.2    -      +       +      -
    239A  VAL      3.0    26.2    +      -       -      +
    265A  ASP      4.4     0.2    +      -       -      -
    266A  ILE*     1.3    73.9    -      -       -      +
    268A  LEU*     1.3    66.8    +      -       -      +
    295A  ASP*     3.3    32.4    -      -       +      +
    296A  SER*     2.9    34.0    +      -       -      -
    314A  MET*     5.6     0.9    -      -       +      -
    316A  VAL*     4.9     7.0    -      -       +      -
    321A  ASP*     3.9    39.0    -      -       +      -
    322A  LEU*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 268 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  VAL*     3.4    19.1    -      -       +      +
    241A  ALA*     4.1     8.7    -      -       +      -
    254A  LEU*     4.5    11.0    -      -       +      -
    257A  VAL*     3.8    14.1    -      -       +      -
    258A  GLY*     3.6    33.9    -      -       -      +
    261A  CYS*     3.8    29.4    -      -       +      -
    266A  ILE      3.2     0.8    +      -       -      -
    267A  TRP*     1.3    74.6    -      -       -      +
    269A  HIS*     1.3    65.8    +      -       -      +
    270A  VAL*     4.7     1.3    -      -       +      -
    290A  GLY      5.4     0.2    -      -       -      +
    293A  PHE*     4.3     4.3    -      -       +      +
    294A  ALA*     3.7    24.9    -      -       +      +
    295A  ASP*     2.8    40.4    +      -       -      +
    296A  SER      3.4     6.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 269 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  ALA      4.4     7.6    -      -       -      -
    152A  THR*     3.6    30.7    +      -       +      -
    155A  ALA*     3.6    13.4    -      -       +      +
    238A  PHE*     3.6    24.2    -      -       +      -
    239A  VAL      2.9     7.8    +      -       -      +
    240A  VAL*     3.2    19.4    -      -       +      -
    241A  ALA      2.9    24.6    +      -       -      -
    267A  TRP*     3.8     1.2    -      -       -      -
    268A  LEU*     1.3    74.7    -      -       -      +
    270A  VAL*     1.3    75.1    +      -       -      +
    271A  ASP*     4.2     3.4    +      -       +      +
    296A  SER*     2.8    34.5    +      -       -      +
    298A  ASN*     3.8    28.5    +      -       +      +
    314A  MET*     4.4     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  ALA*     3.5    10.5    -      -       +      +
    243A  LEU*     4.0    22.0    -      -       +      -
    254A  LEU*     3.8    31.2    -      -       +      -
    268A  LEU*     4.7     2.7    -      -       +      -
    269A  HIS*     1.3    81.7    +      -       -      +
    271A  ASP*     1.3    64.7    +      -       -      +
    291A  VAL*     4.9     0.9    -      -       +      -
    294A  ALA*     3.8    22.4    -      -       +      -
    296A  SER      2.9    12.0    +      -       -      +
    297A  PHE*     3.5    31.8    -      -       +      -
    298A  ASN      3.0    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  ALA*     4.6     5.2    -      -       -      +
    152A  THR*     4.5     7.9    +      -       -      +
    192A  HIS*     4.3     6.6    +      -       -      +
    194A  SER*     4.5     4.3    +      -       -      -
    195A  VAL*     5.2     3.3    -      -       -      +
    240A  VAL*     3.9    20.4    -      -       +      +
    241A  ALA      2.9     8.3    +      -       -      +
    242A  THR*     3.3    12.5    +      -       -      +
    243A  LEU      3.0    21.7    +      -       -      -
    269A  HIS*     3.9    11.9    +      -       +      +
    270A  VAL*     1.3    70.7    -      -       -      +
    272A  ALA*     1.3    58.4    +      -       -      +
    273A  ALA*     3.0    19.9    +      -       -      +
    298A  ASN*     4.1     4.7    -      -       -      +
    601A  PLP      2.8    37.6    +      -       -      +
----------------------------------------------------------
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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