Contacts of the strand formed by residues 60 - 67 (chain A) in PDB entry 2J3W


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 60 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  SER*     5.3     0.2    +      -       -      -
     58A  ASN*     3.3    19.4    +      -       +      +
     59A  MET*     1.3    78.6    -      -       -      +
     61A  LEU*     1.3    61.1    +      -       -      +
     62A  LYS*     3.5    52.0    -      -       +      +
     73A  SER*     4.7     3.4    +      -       -      -
     74A  ALA      3.6     8.5    -      -       -      -
     75A  PHE*     3.6    13.9    -      +       +      -
     92A  GLU*     2.9    42.5    +      -       +      +
     95A  ILE*     4.0     9.5    -      -       +      +
     96A  LYS*     3.6    47.8    +      -       +      -
     99A  PHE*     3.9    29.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  VAL*     4.0    19.5    -      -       +      +
     52A  ASN*     4.5    10.8    -      -       +      +
     53A  MET*     4.2    26.5    -      -       +      +
     56A  SER*     4.5    16.4    -      -       -      -
     58A  ASN      3.7    20.6    -      -       -      +
     59A  MET      4.0     7.2    -      -       -      +
     60A  TYR*     1.3    73.0    -      -       -      +
     62A  LYS*     1.3    73.4    +      -       -      +
     63A  THR      3.7     2.9    +      -       -      +
     64A  VAL*     3.8    19.8    -      -       +      +
     74A  ALA*     2.8    20.8    +      -       +      +
     76A  VAL*     3.8    23.3    -      -       +      -
     78B  ARG*     5.0     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     3.4    48.1    -      -       +      +
     61A  LEU*     1.3    84.5    -      -       -      +
     63A  THR*     1.3    65.4    +      -       +      +
     64A  VAL*     3.5     1.9    +      -       -      +
     73A  SER*     3.1     7.4    -      -       -      -
     74A  ALA      3.1    24.0    +      -       -      -
     92A  GLU*     3.1    37.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  TYR*     6.2     0.2    -      -       -      +
     61A  LEU      4.0     2.8    -      -       -      +
     62A  LYS*     1.3    80.1    -      -       +      +
     64A  VAL*     1.3    63.0    +      -       -      +
     65A  ASP      4.7     7.4    -      -       -      -
     71A  PHE*     4.8     5.4    -      -       +      -
     72A  VAL      3.2     9.9    -      -       -      -
     73A  SER*     3.6    13.0    -      -       -      +
     87A  HIS*     4.4    14.6    -      -       +      +
     90A  ARG*     4.0    34.3    +      -       +      +
     92A  GLU*     6.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ALA*     5.0     2.2    -      -       +      +
     48A  LEU*     3.4    22.4    -      -       +      +
     49A  VAL*     4.4    19.1    -      -       +      -
     52A  ASN*     3.9    24.3    -      -       +      +
     61A  LEU*     3.8    28.7    -      -       +      +
     62A  LYS      3.8     9.2    -      -       -      +
     63A  THR*     1.3    76.5    -      -       -      +
     65A  ASP*     1.3    65.7    +      -       +      +
     72A  VAL*     2.6    36.0    +      -       +      +
     74A  ALA*     4.5     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ALA*     6.1     3.7    -      -       +      -
     48A  LEU*     3.6    22.0    -      -       +      +
     63A  THR*     3.6     5.6    -      -       -      -
     64A  VAL*     1.3    87.7    -      -       +      +
     66A  LYS*     1.3    79.6    +      -       -      +
     67A  PHE*     4.6     8.1    +      -       -      +
     71A  PHE*     3.7     3.1    -      -       -      +
     72A  VAL*     2.8    40.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ASP*     1.3    95.4    +      -       -      +
     67A  PHE*     1.3    64.4    +      -       -      +
     68A  ASN      3.1    24.8    +      -       -      +
     69A  GLU*     4.2    12.7    -      -       -      +
     70A  TRP      3.3    11.7    -      -       -      +
     71A  PHE*     3.5    41.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LEU*     4.8    11.9    -      -       +      -
     41A  ILE*     3.5    51.4    -      -       +      -
     65A  ASP*     5.1     7.6    -      -       -      +
     66A  LYS*     1.3    73.1    -      -       -      +
     68A  ASN*     1.3    96.4    +      -       -      +
     70A  TRP*     2.9    35.6    +      -       -      +
     72A  VAL*     4.5     3.1    -      -       +      +
----------------------------------------------------------
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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