Contacts of the strand formed by residues 281 - 290 (chain A) in PDB entry 2JEF


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 PRO 281 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273A  TYR*     4.3     6.7    -      -       +      +
    276A  LEU*     3.8    14.1    -      -       +      -
    279A  ARG      3.7     8.5    -      -       -      +
    280A  ILE*     1.3    88.5    -      -       +      +
    282A  LYS*     1.3    60.9    +      -       -      +
    283A  ALA      4.0     2.9    -      -       -      +
    305A  GLY*     3.3     1.7    -      -       -      -
    306A  ILE*     2.8    39.9    +      -       +      +
    337A  PHE*     3.7    39.9    -      -       +      -
    338A  SER      3.4    16.4    -      -       -      +
    339A  LYS      4.1     0.7    -      -       -      +
    340A  PHE*     3.7    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  PRO*     1.3    73.3    -      -       -      +
    283A  ALA*     1.3    57.0    +      -       -      +
    301A  THR*     4.4     5.6    -      -       +      -
    302A  PHE*     2.7    54.3    +      -       -      +
    303A  PRO      4.8     2.5    -      -       -      -
    304A  HIS*     3.6    22.2    -      -       -      +
    306A  ILE*     3.6     6.9    -      -       -      +
    338A  SER      3.2     0.2    +      -       -      -
    339A  LYS*     2.8    45.9    +      -       +      +
    340A  PHE      4.1    10.1    +      -       -      -
    341A  ILE*     3.7    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  PRO*     4.0     2.1    -      -       -      +
    282A  LYS*     1.3    81.1    -      -       -      +
    284A  ILE*     1.3    60.8    +      -       -      +
    285A  HIS*     4.4    10.5    -      -       +      -
    300A  ARG      3.5     5.2    -      -       -      +
    301A  THR*     3.8    12.3    -      -       -      +
    306A  ILE*     3.8     2.0    -      -       -      -
    336A  ARG      4.6     0.2    -      -       -      -
    337A  PHE*     3.4     8.1    -      -       -      -
    338A  SER*     3.0    48.2    +      -       -      +
    339A  LYS*     3.8    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269A  ILE*     5.0     1.3    -      -       +      -
    283A  ALA*     1.3    74.9    -      -       -      +
    285A  HIS*     1.3    74.5    +      -       -      +
    286A  VAL*     5.3     0.4    -      -       +      -
    299A  GLY*     3.2     1.9    -      -       -      -
    300A  ARG      3.0    32.6    +      -       -      +
    302A  PHE*     4.2     1.1    -      -       +      -
    306A  ILE*     3.8    18.6    -      -       +      -
    311A  ALA*     3.8    27.1    -      -       +      +
    314A  GLU*     4.0    23.6    -      -       +      -
    315A  SER*     4.4    17.0    -      -       -      +
    318A  LEU*     4.1     5.3    -      -       +      +
    335A  VAL*     5.0     4.0    -      -       +      -
    336A  ARG      3.4     5.8    -      -       -      +
    337A  PHE*     3.4    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283A  ALA*     4.4    16.4    -      -       +      -
    284A  ILE*     1.3    84.0    +      -       -      +
    286A  VAL*     1.3    66.2    +      -       -      +
    287A  VAL*     3.9     6.0    +      -       +      -
    297A  SER*     4.8    11.4    -      -       -      -
    298A  ARG      3.6     5.4    -      -       -      +
    299A  GLY*     3.5    23.4    -      -       -      -
    300A  ARG      4.6     2.9    -      -       -      -
    301A  THR*     5.4     0.9    -      -       -      -
    335A  VAL*     3.2     5.2    -      -       -      +
    336A  ARG*     2.8    50.2    +      -       +      +
    338A  SER*     4.6     9.3    +      -       -      -
    339A  LYS*     6.2     2.0    -      -       -      -
      7P    A      5.2    14.2    +      -       -      +
      8P    G      4.9    12.9    +      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  LEU*     4.2     4.0    -      -       +      -
    284A  ILE*     5.3     1.1    -      -       +      -
    285A  HIS*     1.3    74.3    -      -       -      +
    287A  VAL*     1.3    61.5    +      -       -      +
    297A  SER*     3.3     7.1    -      -       -      -
    298A  ARG      2.9    27.7    +      -       -      +
    315A  SER*     3.5    42.8    -      -       -      +
    318A  LEU*     3.8    18.8    -      -       +      +
    319A  LEU*     4.3    11.9    -      -       +      -
    322A  ILE*     3.8    20.0    -      -       +      +
    333A  ILE*     3.9    17.3    -      -       +      -
    334A  GLY      3.5     8.5    -      -       -      +
    335A  VAL*     4.2    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  ILE*     4.1    20.1    -      -       +      +
    285A  HIS*     4.4    11.9    -      -       +      +
    286A  VAL*     1.3    77.6    -      -       -      +
    288A  ALA*     1.3    62.9    +      -       -      +
    295A  ILE*     3.7    27.1    -      -       +      -
    296A  VAL      3.8     4.3    -      -       -      +
    297A  SER*     4.3     9.9    -      -       -      -
    332A  ARG      3.9     0.2    -      -       -      +
    333A  ILE*     3.4     5.1    -      -       -      +
    334A  GLY      2.8    44.2    +      -       -      +
    335A  VAL      5.0     0.9    -      -       -      -
    336A  ARG*     4.6    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  VAL      4.2     0.4    +      -       -      -
    287A  VAL*     1.3    75.4    -      -       -      +
    289A  VAL*     1.3    62.5    +      -       -      +
    290A  THR      3.9     0.4    -      -       -      -
    294A  ASP      3.7     0.2    -      -       -      +
    295A  ILE*     3.4     5.4    -      -       -      +
    296A  VAL*     2.9    54.4    +      -       +      +
    322A  ILE*     3.9    14.6    -      -       +      -
    330A  ILE*     3.7    22.0    -      -       +      -
    332A  ARG      3.3     4.5    -      -       -      +
    333A  ILE*     4.0    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  ILE*     3.6    28.5    -      -       +      -
    288A  ALA*     1.3    74.6    -      -       -      +
    290A  THR*     1.3    61.7    +      -       -      +
    293A  LEU*     4.1    17.5    -      -       +      -
    294A  ASP      3.2    10.3    -      -       -      +
    295A  ILE*     4.4    20.0    -      -       +      -
    330A  ILE*     3.8     1.4    -      -       -      +
    331A  ARG*     2.7    31.6    +      -       +      +
    332A  ARG*     2.6    58.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  VAL*     1.3    75.3    -      -       -      +
    291A  GLU*     1.3    56.5    +      -       -      +
    292A  ASP*     2.4    25.5    +      -       -      -
    293A  LEU*     2.6    33.6    +      -       -      +
    294A  ASP*     2.8    25.7    +      -       +      +
    296A  VAL*     4.3    14.6    -      -       +      -
    326A  ASP*     3.8    22.0    -      -       -      +
    328A  ARG*     3.5    10.7    +      -       +      +
    329A  LYS      3.4     9.4    -      -       -      +
    330A  ILE*     3.8    22.2    -      -       +      +
    331A  ARG*     3.9     2.7    -      -       -      +
----------------------------------------------------------
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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