Contacts of the strand formed by residues 312 - 316 (chain B) 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 SER 312 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144B  ILE*     3.3     6.1    -      -       -      +
    145B  GLN*     2.7    43.8    +      -       -      -
    147B  SER*     3.5    24.7    +      -       -      -
    148B  ALA      3.4     7.6    +      -       -      -
    151B  ALA*     4.4     0.3    -      -       -      +
    298B  ASN*     2.9    24.5    +      -       -      -
    299B  PHE      3.9     1.3    -      -       -      -
    300B  ASN*     2.6    27.0    +      -       -      -
    302B  HIS*     4.4     0.2    -      -       -      -
    311B  CYS*     1.3    74.9    -      -       -      +
    313B  ALA*     1.3    57.7    +      -       -      +
    314B  MET      3.9     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  MET*     3.6    27.1    -      -       +      -
    122B  LEU*     3.9    13.0    -      -       +      -
    143B  VAL      4.0     0.4    -      -       -      -
    144B  ILE*     4.9     0.2    -      -       -      +
    298B  ASN*     2.6    24.4    +      -       -      -
    299B  PHE*     2.9    26.6    +      -       +      +
    301B  PRO*     3.6     8.4    -      -       +      +
    311B  CYS*     5.7     0.2    -      -       -      -
    312B  SER*     1.3    69.4    +      -       -      +
    314B  MET*     1.3    56.3    +      -       -      +
    315B  TRP*     3.7    21.7    -      -       +      -
    362B  MET*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  MET*     3.5     0.8    -      -       -      +
    142B  GLY*     3.1     2.3    -      -       -      -
    143B  VAL*     2.7    49.8    +      -       +      +
    145B  GLN*     4.0    24.0    -      -       +      -
    151B  ALA*     3.8    35.2    -      -       -      +
    154B  VAL*     4.5     8.1    -      -       +      -
    155B  ALA*     3.9    16.8    -      -       +      +
    267B  TRP*     5.6     0.4    -      -       +      -
    269B  HIS*     4.5     2.2    -      -       +      -
    296B  SER*     3.7    25.4    -      -       -      -
    297B  PHE      3.4     9.6    -      -       -      +
    298B  ASN*     3.9    13.5    -      -       +      +
    312B  SER      3.9     0.4    +      -       -      -
    313B  ALA*     1.3    74.3    -      -       -      +
    315B  TRP*     1.3    66.5    +      -       -      +
    316B  VAL*     4.3    11.2    -      -       +      -
    322B  LEU*     5.1     6.1    -      -       +      -
    349B  TRP*     5.1     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  MET*     3.1    50.0    +      -       +      +
    120B  ASP*     5.1     0.8    +      -       -      +
    122B  LEU*     3.5    31.9    -      -       +      -
    123B  GLY*     3.5    14.1    -      -       -      -
    126B  LEU*     3.9    11.7    -      -       +      -
    128B  LEU*     3.6    14.7    -      -       +      +
    132B  PHE*     3.5    44.6    -      -       +      -
    133B  LEU*     4.5     2.8    -      -       -      +
    141B  GLY      3.4     3.8    -      -       -      -
    142B  GLY*     3.7    12.0    -      -       -      +
    296B  SER*     3.1     6.4    -      -       -      -
    297B  PHE*     2.9    53.6    +      +       +      +
    299B  PHE*     4.0    13.2    -      +       -      -
    313B  ALA*     3.7    20.4    -      -       +      -
    314B  MET*     1.3    72.5    -      -       -      +
    316B  VAL*     1.3    66.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  PHE*     3.7    11.5    -      -       -      -
    140B  GLY*     3.3     1.7    -      -       -      -
    141B  GLY      3.2    29.2    +      -       -      +
    267B  TRP*     4.8     6.5    -      -       +      -
    295B  ASP      3.3    15.5    -      -       -      +
    296B  SER*     3.8    11.9    -      -       -      -
    314B  MET*     4.3     8.5    -      -       +      -
    315B  TRP*     1.3    82.2    -      -       -      +
    317B  LYS*     1.3    58.6    +      -       -      +
    318B  ARG      4.2     6.1    -      -       -      +
    319B  ARG*     4.1    22.9    -      -       -      +
    321B  ASP*     6.1     0.2    -      -       +      -
    322B  LEU*     4.2    24.9    -      -       +      -
    349B  TRP*     4.0    18.6    -      -       +      -
----------------------------------------------------------
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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