Contacts of the strand formed by residues 409 - 416 (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 TYR 409 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  LEU*     3.4    27.4    -      -       +      -
    399A  ARG*     3.7     1.5    -      -       -      -
    400A  TYR*     2.8    38.9    +      -       +      +
    407A  PRO*     4.0     6.5    +      -       +      +
    408A  PRO*     1.3    80.4    -      -       -      +
    410A  PHE*     1.3    64.2    +      -       -      +
    411A  VAL*     4.8     0.4    -      -       +      -
    436A  PHE*     4.4    25.1    -      +       +      -
    437A  LEU      3.4    22.0    -      -       -      -
    439A  PHE*     3.6    22.7    -      +       -      -
    442A  ASP*     2.9    27.9    +      -       -      -
    269B  GLN*     3.6    27.1    +      -       -      +
    484B  ASN*     3.8    18.6    +      -       -      -
    486B  ARG*     6.3     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    348A  MET*     3.9    20.0    -      -       +      -
    397A  LEU*     4.4     3.1    -      -       +      -
    398A  CYS      3.4    13.2    -      -       -      -
    399A  ARG*     4.2    14.4    -      -       +      -
    408A  PRO*     6.5     0.4    -      -       +      -
    409A  TYR*     1.3    77.3    -      -       -      +
    411A  VAL*     1.3    60.7    +      -       -      +
    436A  PHE*     4.1     0.2    -      -       -      -
    437A  LEU*     2.9    36.3    +      -       +      +
    439A  PHE*     3.6    33.9    -      +       -      -
    477B  PHE*     3.9    13.2    -      +       -      -
    479B  THR*     3.7    39.5    -      -       +      +
    482B  ILE*     4.5     8.7    -      -       +      -
    516B  LEU*     3.5    46.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345A  LEU*     4.0    15.9    -      -       +      -
    397A  LEU*     3.1     5.9    -      -       -      +
    398A  CYS*     2.9    43.9    +      -       +      +
    400A  TYR*     3.8    28.7    -      -       +      -
    409A  TYR      3.9     2.2    -      -       -      +
    410A  PHE*     1.3    80.1    -      -       -      +
    412A  ALA*     1.3    59.3    +      -       -      +
    413A  LEU*     4.4     5.4    -      -       +      -
    434A  LEU*     3.7    30.7    -      -       +      -
    435A  VAL      3.2    10.3    -      -       -      +
    436A  PHE*     3.9    20.2    -      -       +      -
    437A  LEU*     3.9     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LEU*     3.7    32.5    -      -       +      -
    395A  ALA*     4.4     5.4    -      -       +      -
    396A  ALA      3.7     4.9    -      -       -      -
    397A  LEU*     4.6     3.1    -      -       +      +
    411A  VAL*     1.3    73.6    -      -       -      +
    413A  LEU*     1.3    61.9    +      -       -      +
    414A  VAL*     3.2     5.4    +      -       +      +
    433A  GLN      3.0     3.8    -      -       -      +
    435A  VAL*     2.8    39.5    +      -       +      +
    437A  LEU*     4.0    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  LEU*     4.1    26.9    -      -       +      -
    345A  LEU*     4.8     6.7    -      -       +      -
    368A  VAL*     4.1    16.6    -      -       +      -
    395A  ALA*     3.5     5.4    -      -       -      +
    396A  ALA*     2.8    47.3    +      -       +      +
    398A  CYS*     4.2    15.5    -      -       -      -
    411A  VAL*     4.1     7.8    -      -       +      -
    412A  ALA*     1.3    70.6    -      -       -      +
    414A  VAL*     1.3    62.5    +      -       -      +
    415A  PRO*     3.5     2.8    -      -       -      +
    432A  PHE*     3.7    29.2    -      -       +      -
    433A  GLN      3.4     2.0    -      -       -      -
    434A  LEU*     3.9    36.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  LEU*     4.2    13.0    -      -       +      -
    356A  LEU*     4.2    24.9    -      -       +      -
    395A  ALA*     4.5     2.2    -      -       +      -
    412A  ALA      3.7     4.9    -      -       -      +
    413A  LEU*     1.3    73.1    -      -       -      +
    415A  PRO*     1.3    81.8    -      -       +      +
    416A  GLN*     3.3     0.6    +      -       +      +
    432A  PHE*     3.3     2.3    -      -       -      -
    433A  GLN*     2.6    55.9    +      -       +      +
    435A  VAL*     3.7    24.2    -      -       +      -
    353B  ARG*     6.0     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 415 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353A  LEU*     4.2    16.7    -      -       +      +
    386A  LEU*     4.0     5.2    -      -       +      -
    389A  CYS*     4.0    21.5    -      -       +      +
    390A  LEU*     3.7    32.5    -      -       +      +
    394A  VAL      3.3    27.4    -      -       -      +
    395A  ALA*     4.2     0.2    -      -       -      -
    413A  LEU      3.5     6.7    -      -       -      +
    414A  VAL*     1.3    97.0    -      -       +      +
    416A  GLN*     1.3    58.8    +      -       -      +
    431A  GLY      3.8     1.3    -      -       -      +
    432A  PHE*     3.7    14.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  PHE*     3.6    14.5    -      -       -      -
    386A  LEU*     4.0     8.1    -      -       -      +
    414A  VAL*     4.0     5.6    -      -       +      +
    415A  PRO*     1.3    75.0    -      -       -      +
    417A  GLU*     1.3    61.5    +      -       -      +
    428A  THR*     3.4    27.4    -      -       +      +
    429A  PRO*     2.8    35.1    +      -       -      +
    430A  PRO*     3.3     3.1    -      -       -      +
    431A  GLY      2.7    44.8    +      -       -      +
    433A  GLN*     4.1    19.5    -      -       +      +
    354B  ARG*     3.2    29.1    -      -       -      +
----------------------------------------------------------
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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