Contacts of the strand formed by residues 453 - 459 (chain A) in PDB entry 5J2P


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 GLY 453 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445A  ALA      3.2    12.1    -      -       -      -
    446A  ALA*     3.9     0.7    -      -       -      -
    452A  LEU*     1.3    76.2    -      -       -      +
    454A  LYS*     1.3    69.9    +      -       -      +
    468A  THR*     3.6     2.3    -      -       -      +
    469A  LEU*     2.9    34.0    +      -       -      +
    472A  THR*     3.7    17.5    -      -       -      +
    477A  THR*     4.2     0.4    -      -       -      -
    556A  ILE*     4.5     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 454 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444A  GLY*     3.3     3.5    -      -       -      -
    445A  ALA      2.9    30.3    +      -       -      +
    453A  GLY*     1.3    80.5    -      -       -      +
    455A  ALA*     1.3    60.6    +      -       -      +
    466A  VAL*     3.9    18.5    -      -       +      +
    467A  VAL      3.3    11.0    -      -       -      +
    468A  THR*     4.1    20.9    -      -       +      -
    469A  LEU*     4.7     0.9    -      -       -      +
    477A  THR*     3.6     6.3    -      -       -      +
    551A  LEU      4.1     8.0    +      -       -      +
    552A  VAL*     3.5    26.8    -      -       -      +
    554A  ALA*     2.6    34.7    +      -       -      +
    555A  GLY*     4.5     3.4    -      -       -      -
    556A  ILE*     4.2    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 455 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  ASP      3.6     5.8    -      -       -      -
    454A  LYS*     1.3    72.6    -      -       -      +
    456A  GLY*     1.3    57.9    +      -       -      +
    466A  VAL*     3.4     1.9    -      -       -      +
    467A  VAL*     2.7    45.9    +      -       +      +
    469A  LEU*     4.2     7.8    -      -       +      +
    477A  THR      3.3    24.2    -      -       -      +
    480A  GLN*     3.9    13.7    -      -       +      -
    481A  ALA*     3.6    14.6    -      -       -      +
    484A  LEU*     4.0     3.3    -      -       +      +
    552A  VAL*     3.9     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 456 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442A  VAL*     3.4     2.8    -      -       -      +
    443A  ASP      3.2    27.9    +      -       -      +
    455A  ALA*     1.3    77.8    -      -       -      +
    457A  TYR*     1.3    66.4    +      -       -      +
    465A  LYS      3.0    14.1    -      -       -      -
    466A  VAL*     4.3     2.2    -      -       -      -
    481A  ALA*     3.6     7.8    -      -       -      +
    484A  LEU*     3.8    11.4    -      -       -      -
    548A  VAL*     3.9     6.5    -      -       -      -
    552A  VAL*     3.8     3.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440A  PHE*     3.5    40.6    -      +       +      -
    441A  TYR      3.1    13.0    -      -       -      +
    442A  VAL*     3.9     9.4    -      -       +      -
    456A  GLY*     1.3    77.0    -      -       -      +
    458A  VAL*     1.3    67.2    +      -       -      +
    459A  THR*     3.7    14.6    -      -       +      -
    463A  ARG*     3.9    13.5    +      -       +      +
    464A  GLN*     3.3     9.9    -      -       -      +
    465A  LYS*     3.1    59.8    +      -       +      +
    466A  VAL*     5.5     0.2    -      -       -      +
    481A  ALA      4.9     0.2    -      -       -      -
    484A  LEU*     3.9    20.6    -      -       +      -
    485A  ALA*     4.1    10.1    -      -       -      -
    488A  ASP*     2.7    36.4    +      -       +      +
    548A  VAL*     3.8     5.3    -      -       -      +
    551A  LEU*     4.7     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    440A  PHE*     3.6     1.2    -      -       -      -
    441A  TYR*     2.7    40.9    +      -       +      +
    457A  TYR*     1.3    77.7    -      -       -      +
    459A  THR*     1.3    64.6    +      -       -      +
    463A  ARG      3.3     5.4    -      -       -      +
    464A  GLN*     3.7    24.5    -      -       +      +
    544A  GLY      3.5    25.1    -      -       -      +
    547A  GLN*     4.2    10.8    -      -       +      -
    548A  VAL*     3.8    15.5    -      -       +      +
    551A  LEU*     4.0    12.6    -      -       +      -
    286B  THR*     4.1    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 459 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438A  GLU*     2.8    30.1    +      -       -      +
    439A  THR      3.2     9.6    -      -       -      -
    440A  PHE*     3.5    36.1    -      -       +      -
    457A  TYR*     3.7     7.4    -      -       +      -
    458A  VAL*     1.3    80.1    -      -       -      +
    460A  ASN*     1.3    63.4    +      -       -      +
    461A  ARG      3.3     4.3    +      -       -      -
    462A  GLY*     3.1    12.0    +      -       -      -
    463A  ARG*     2.8    34.7    +      -       +      +
    286B  THR*     3.5    13.1    -      -       -      +
----------------------------------------------------------
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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