Contacts of the strand formed by residues 404 - 412 (chain B) in PDB entry 1JEQ


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 GLN 404 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    507A  THR*     5.9     0.2    -      -       -      -
    360B  GLN*     5.2     6.2    +      -       -      +
    394B  ARG*     3.1    10.4    -      -       -      +
    395B  TYR*     2.6    63.4    +      -       +      +
    402B  ASN      4.1     8.9    +      -       -      +
    403B  PRO*     1.3    79.3    -      -       -      +
    405B  VAL*     1.3    63.8    +      -       -      +
    421B  TYR*     3.0    26.0    +      -       -      +
    423B  GLN*     2.9    45.1    +      -       -      +
    426B  PHE*     4.4     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 405 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    473A  TYR*     5.4     0.4    -      -       +      -
    478A  PHE*     3.9    35.2    -      -       +      -
    507A  THR*     3.8    24.9    -      -       +      -
    343B  LEU*     4.6     4.7    -      -       +      -
    392B  ILE*     4.0    14.8    -      -       +      -
    393B  VAL      3.2     5.6    -      -       -      +
    394B  ARG*     5.1     1.1    -      -       -      -
    404B  GLN*     1.3    79.6    -      -       -      +
    406B  GLY*     1.3    61.1    +      -       -      +
    421B  TYR*     4.1     1.8    -      -       -      -
    423B  GLN*     3.8     3.9    -      -       -      +
    424B  LEU*     2.8    36.0    +      -       +      +
    425B  PRO      5.3     3.6    -      -       -      +
    426B  PHE*     3.7    30.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 406 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392B  ILE*     3.3     7.4    -      -       -      +
    393B  VAL*     2.7    35.6    +      -       -      -
    405B  VAL*     1.3    76.5    -      -       -      +
    407B  VAL*     1.3    58.2    +      -       -      -
    421B  TYR*     3.8    14.3    +      -       -      -
    422B  VAL      3.3    12.6    -      -       -      -
    423B  GLN*     3.9     0.4    -      -       -      -
    424B  LEU*     3.4    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 407 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  LYS*     5.9     0.9    -      -       -      +
    351B  VAL*     4.0    17.5    -      -       +      -
    356B  PHE*     4.0    26.5    -      -       +      -
    390B  VAL*     3.9    21.5    -      -       +      -
    391B  ALA      3.3     9.4    -      -       -      +
    392B  ILE*     4.6     1.3    -      -       +      +
    393B  VAL*     4.8     0.2    -      -       -      -
    406B  GLY*     1.3    73.9    -      -       -      -
    408B  ALA*     1.3    67.3    +      -       -      +
    409B  PHE*     3.8    20.4    -      -       +      -
    420B  VAL      3.3     0.7    -      -       -      +
    421B  TYR*     3.2     8.8    -      -       -      -
    422B  VAL*     2.9    47.7    +      -       +      +
    424B  LEU*     3.7     9.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 408 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  PHE*     4.5    12.6    -      -       +      -
    384B  LEU*     4.1     6.1    -      -       -      +
    390B  VAL*     3.9     1.0    -      -       -      +
    391B  ALA*     2.8    37.8    +      -       +      +
    393B  VAL*     4.2    18.2    -      -       +      -
    407B  VAL*     1.3    75.4    -      -       -      +
    409B  PHE*     1.3    60.3    +      -       -      +
    419B  LEU*     4.1    27.4    -      -       +      -
    420B  VAL      3.3     6.7    -      -       -      -
    421B  TYR*     4.9     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 409 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  LYS*     4.0    42.6    -      -       +      +
    359A  HIS*     4.1    18.8    -      -       +      -
    356B  PHE*     4.2    12.1    -      +       -      -
    390B  VAL*     3.2    25.4    -      -       +      -
    407B  VAL*     3.8    15.9    -      -       +      -
    408B  ALA*     1.3    73.5    -      -       -      +
    410B  PRO*     1.3    80.3    -      -       +      +
    411B  HIS*     5.5     0.7    -      -       +      -
    419B  LEU*     3.4     4.8    -      -       -      -
    420B  VAL*     3.0    66.4    +      -       +      +
    422B  VAL*     3.8    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 410 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381B  ILE*     3.3    30.1    -      -       +      +
    384B  LEU*     3.6    21.3    -      -       +      -
    385B  ASP*     3.6    31.2    -      -       +      +
    389B  MET      3.9     9.6    -      -       -      +
    390B  VAL*     4.2     0.4    -      -       +      -
    409B  PHE*     1.3   102.7    -      -       +      +
    411B  HIS*     1.3    60.1    +      -       -      +
    412B  ILE*     4.2     1.3    -      -       +      -
    418B  CYS      3.9     5.6    -      -       -      +
    419B  LEU*     3.9     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 411 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  LYS*     6.1     0.2    -      -       -      -
    359A  HIS*     3.4    40.3    +      +       -      -
    363B  LYS*     3.7    22.6    +      -       -      -
    381B  ILE*     4.6     0.2    -      -       -      +
    409B  PHE*     5.5     1.0    -      -       +      -
    410B  PRO*     1.3    74.8    +      -       -      +
    412B  ILE*     1.3    61.1    +      -       -      +
    413B  LYS*     3.7    28.0    +      -       +      +
    416B  TYR*     3.8    19.1    +      +       -      +
    417B  GLU*     3.6     2.8    -      -       -      -
    418B  CYS*     3.0    51.6    +      -       -      +
    420B  VAL*     3.9    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 412 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451A  LYS*     3.7    10.3    -      -       -      +
    381B  ILE*     3.8    19.1    -      -       +      -
    382B  HIS*     3.8    24.5    -      -       +      +
    385B  ASP*     3.6    41.1    -      -       +      +
    410B  PRO*     5.0     0.7    -      -       +      -
    411B  HIS*     1.3    78.9    +      -       -      +
    413B  LYS*     1.3    87.8    +      -       -      +
    416B  TYR      4.1     1.3    -      -       -      -
    417B  GLU*     3.6    22.9    -      -       +      +
----------------------------------------------------------
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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