Contacts of the strand formed by residues 310 - 316 (chain B) in PDB entry 1JEY


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 ILE 310 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  LYS*     3.6    28.3    -      -       +      -
    288A  LEU      3.0    15.9    -      -       -      +
    296A  VAL*     4.5     7.9    -      -       +      -
    295B  TYR*     3.3    52.7    -      -       +      -
    305B  VAL*     4.0    17.7    -      -       +      +
    306B  LEU      4.3     4.5    -      -       -      +
    307B  LYS*     3.7    14.6    +      -       -      +
    308B  GLU      3.8     0.6    -      -       -      -
    309B  ASP*     1.3    82.9    -      -       -      +
    311B  ILE*     1.3    71.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  LYS*     3.7     3.3    -      -       -      +
    288A  LEU*     3.0    44.5    +      -       +      +
    290A  ARG*     4.0    44.9    -      -       +      +
    293A  ASN*     3.4    26.0    -      -       -      +
    310B  ILE*     1.3    83.1    -      -       -      +
    312B  GLN*     1.3    62.9    +      -       -      +
    322B  PRO*     3.7    22.4    -      -       +      -
    324B  SER*     6.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 312 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  PRO*     3.3    29.5    -      -       +      +
    286A  ILE      4.0     3.4    -      -       -      -
    287A  LYS*     5.3     0.7    -      -       -      +
    288A  LEU*     4.5     0.4    -      -       -      -
    311B  ILE*     1.3    81.0    -      -       -      +
    313B  GLY*     1.3    64.0    +      -       -      +
    314B  PHE*     3.6    10.7    -      -       +      -
    322B  PRO*     3.4     8.1    -      -       -      +
    323B  PHE      3.0    39.7    +      -       -      +
    324B  SER*     3.9     9.9    +      -       -      +
    325B  LYS*     3.0    49.9    -      -       +      +
    328B  GLU*     3.3    17.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  PRO*     3.6     2.8    -      -       -      +
    286A  ILE*     3.0    37.8    +      -       -      -
    288A  LEU*     3.9    14.8    -      -       -      -
    312B  GLN*     1.3    79.4    -      -       -      +
    314B  PHE*     1.3    70.1    +      -       -      -
    320B  ILE*     5.8     0.4    -      -       -      -
    321B  VAL      3.3    11.4    -      -       -      -
    323B  PHE      3.9     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  LYS*     4.7     2.9    -      -       -      -
    283A  PRO*     3.7    23.8    -      -       +      -
    284A  PRO      4.0     3.6    -      -       -      -
    285A  PRO*     3.5    30.3    -      -       +      -
    286A  ILE*     5.1     3.1    -      -       -      +
    288A  LEU*     5.2     0.4    -      -       -      +
    486A  HIS*     3.9    17.9    -      +       -      +
    490A  LEU*     4.0    23.8    -      -       +      -
    312B  GLN*     3.6    24.5    -      -       -      -
    313B  GLY*     1.3    78.1    -      -       -      -
    315B  ARG*     1.3    65.0    +      -       -      +
    320B  ILE*     3.5     4.6    -      -       -      +
    321B  VAL*     2.7    34.7    +      -       -      +
    323B  PHE*     3.6    36.3    -      +       +      -
    328B  GLU*     3.1    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283A  PRO*     5.5     7.7    -      -       +      +
    284A  PRO      5.8     0.4    +      -       -      -
    286A  ILE*     3.5    36.4    -      -       +      +
    295A  PRO*     4.5    18.0    -      -       -      +
    487A  PHE*     4.4     8.0    -      -       -      -
    490A  LEU*     3.9    11.9    -      -       -      +
    314B  PHE*     1.3    76.9    -      -       -      +
    316B  TYR*     1.3    60.8    +      -       -      +
    317B  GLY      3.8    15.9    +      -       -      +
    318B  SER*     5.3     5.3    +      -       -      +
    319B  ASP      3.3     7.8    +      -       -      +
    320B  ILE*     4.1    26.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  ILE*     4.8     3.9    -      -       +      +
     75A  ILE*     3.4    28.4    -      -       +      +
     76A  ILE*     6.0     0.2    -      -       +      -
    112A  GLY*     4.0     1.7    -      -       -      -
    113A  ALA*     3.6    39.3    -      -       +      -
    116A  ILE*     3.6    17.5    -      -       +      +
    487A  PHE*     3.7    34.5    -      +       +      -
    490A  LEU*     3.8    18.6    -      -       +      -
    491A  GLU*     2.5    43.8    +      -       +      +
    494A  ALA*     5.3     1.3    -      -       +      -
    314B  PHE      4.0     0.2    +      -       -      -
    315B  ARG*     1.3    73.1    -      -       -      +
    317B  GLY*     1.3    58.4    +      -       -      +
    318B  SER      3.1     0.7    +      -       -      -
    319B  ASP*     2.9    39.2    +      -       +      +
    321B  VAL*     4.3    13.0    -      -       +      -
----------------------------------------------------------
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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