Contacts of the strand formed by residues 102 - 109 (chain A) 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 102 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  VAL*     3.9    22.0    -      -       +      -
     87A  PHE      3.4     4.3    -      -       -      +
     88A  TYR*     4.4     1.1    -      -       +      -
     90A  THR*     4.0     0.2    +      -       -      -
     93A  ASP*     3.1     4.7    -      -       -      +
     94A  LYS      2.7    29.8    +      -       -      -
     95A  ASN*     3.3    12.9    +      -       -      +
     99A  PHE*     3.9     9.6    -      -       +      +
    100A  LYS      3.3     7.1    -      -       -      +
    101A  ASN*     1.3    84.5    -      -       -      +
    103A  TYR*     1.3    56.8    +      -       -      +
    104A  VAL*     4.9     0.4    -      -       +      -
    141A  TYR*     5.8     0.9    -      -       +      -
    142A  SER      6.0     0.4    -      -       -      +
    145A  GLU*     3.5    19.7    -      -       +      +
    146A  VAL*     3.4    50.5    -      -       +      +
    149A  VAL*     3.9    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  VAL*     3.4     1.3    -      -       -      -
     87A  PHE*     2.6    39.1    +      -       +      +
     90A  THR*     3.9     9.1    +      -       -      +
     92A  LYS*     3.7    37.6    +      -       +      +
     93A  ASP      4.6     0.7    -      -       -      -
     94A  LYS*     3.9    39.2    +      -       +      +
    102A  ILE*     1.3    72.8    -      -       -      +
    104A  VAL*     1.3    65.0    +      -       -      +
    105A  LEU*     3.1    29.0    +      -       +      -
    134A  MET*     4.7    11.6    +      -       -      +
    135A  MET*     3.6    50.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  VAL      3.9     2.5    -      -       -      -
     86A  VAL*     4.2    13.2    -      -       +      -
     94A  LYS*     2.9    42.0    +      -       +      +
     95A  ASN*     4.1     5.6    -      -       +      -
    102A  ILE*     4.9     0.7    -      -       +      -
    103A  TYR*     1.3    73.6    -      -       -      +
    105A  LEU*     1.3    61.8    +      -       -      +
    106A  GLN      4.0     4.3    -      -       -      +
    107A  GLU*     3.9    37.2    -      -       +      +
    149A  VAL*     3.7    29.6    -      -       +      -
    153A  LEU*     4.0    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  VAL*     2.9    35.3    +      -       +      +
     87A  PHE*     3.7    15.9    -      -       +      -
     94A  LYS*     5.6     2.8    +      -       -      -
    103A  TYR*     3.1    16.2    +      -       +      -
    104A  VAL*     1.3    74.8    -      -       -      +
    106A  GLN*     1.3    72.4    +      -       +      +
    118A  GLU*     3.9    26.8    -      -       -      +
    119A  LEU*     3.9    19.3    -      -       +      -
    122A  PHE*     3.9    20.6    -      -       +      -
    134A  MET*     4.7     4.5    -      -       -      -
    135A  MET*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  TYR*     2.7    40.0    +      -       -      +
     84A  ALA*     3.1     4.2    -      -       -      +
     85A  VAL*     2.8    41.7    +      -       +      +
    104A  VAL*     4.0     5.0    -      -       -      +
    105A  LEU*     1.3    86.7    -      -       +      +
    107A  GLU*     1.3    64.2    +      -       -      +
    115A  ARG*     3.1    55.5    +      -       +      +
    118A  GLU*     2.9    30.8    +      -       -      +
    119A  LEU*     3.9    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  LEU      3.2     1.4    -      -       -      +
     84A  ALA*     4.6     0.2    -      -       -      -
    104A  VAL*     3.9    19.9    -      -       +      +
    105A  LEU      4.3     0.2    -      -       -      -
    106A  GLN*     1.3    73.8    -      -       -      +
    108A  LEU*     1.3    64.7    +      -       -      +
    115A  ARG*     2.5    38.7    +      -       -      +
    153A  LEU*     4.0    16.7    -      -       +      +
    156A  ASP*     5.0    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  SER*     3.9     9.6    -      -       -      +
     38A  LEU      3.8    11.7    -      -       -      +
     39A  ILE*     4.3     3.8    -      -       +      -
     82A  LEU*     3.4    44.2    -      -       +      +
     83A  LEU      3.4     2.0    -      -       -      -
     84A  ALA*     3.6    23.3    -      -       +      +
    107A  GLU*     1.3    75.7    -      -       -      +
    109A  ASP*     1.3    62.7    +      -       -      +
    153A  LEU*     3.4    35.0    -      -       +      +
    154A  PHE*     3.6    31.4    -      -       +      -
    157A  VAL*     5.1     7.9    -      -       +      +
    158A  GLN*     5.3     5.0    -      -       -      +
    159A  PHE*     5.4     2.1    -      -       -      -
    161A  MET*     4.6     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  LEU*     3.8    16.0    -      -       -      +
     83A  LEU*     2.9    29.1    +      -       -      +
    107A  GLU*     3.1     0.6    +      -       +      -
    108A  LEU*     1.3    77.2    -      -       -      +
    110A  ASN*     1.3   101.1    +      -       -      +
    111A  PRO      3.6     0.7    -      -       -      -
    115A  ARG*     3.3    27.4    +      -       -      +
    159A  PHE*     4.6    10.3    -      -       -      -
    318B  SER*     5.3     3.4    +      -       -      -
----------------------------------------------------------
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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