Contacts of the strand formed by residues 54 - 57 (chain Y) in PDB entry 1JJ2


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 ILE 54 (chain Y).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   16540    U      5.5     3.1    -      -       -      +
     45A  ILE*     3.8    25.1    -      -       +      +
     46A  GLU*     3.8    28.5    -      -       -      +
     47A  HIS*     3.9    11.4    -      -       +      +
     54A  PRO*     3.9     4.0    -      -       +      -
     49Y  ARG*     3.5     4.3    -      -       -      +
     50Y  ALA*     2.6    46.5    +      -       +      -
     51Y  GLY*     3.1    20.6    +      -       -      +
     52Y  THR      3.7    10.1    -      -       -      +
     53Y  GLY*     1.3    79.7    -      -       -      +
     55Y  TRP*     1.3    59.8    +      -       -      +
     63Y  LYS*     3.9    27.6    -      -       +      -
     64Y  ILE      3.7     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 55 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33Y  HIS*     3.7    10.8    -      -       -      -
     37Y  HIS*     3.8    25.1    -      +       -      -
     47Y  LEU*     4.9     4.5    -      -       +      -
     48Y  LYS*     3.6     7.2    -      -       -      -
     49Y  ARG*     3.4    51.6    -      -       +      -
     50Y  ALA*     5.0     0.4    -      -       -      -
     53Y  GLY      3.7     5.3    -      -       -      -
     54Y  ILE*     1.3    77.5    -      -       -      +
     56Y  MET*     1.3    60.3    +      -       -      +
     63Y  LYS*     3.2     6.9    -      -       -      +
     64Y  ILE*     2.6    60.3    +      -       +      -
     65Y  ALA      4.5     0.7    -      -       -      -
     66Y  GLY*     3.7    22.2    -      -       -      -
     67Y  GLY      3.0    21.8    +      -       -      +
     68Y  CYS      4.1     0.2    -      -       -      -
     69Y  TYR*     3.5    20.6    -      -       -      -
     70Y  GLN*     3.2    33.0    +      -       -      -
     71Y  PRO*     3.6    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 56 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46Y  LYS      3.5     0.9    -      -       -      +
     47Y  LEU*     3.3     6.0    -      -       -      -
     48Y  LYS*     2.8    40.9    +      -       -      +
     50Y  ALA*     4.5    14.6    -      -       +      -
     55Y  TRP*     1.3    75.6    -      -       -      +
     57Y  CYS*     1.3    63.4    +      -       -      +
     58Y  GLY*     3.8     1.5    +      -       -      -
     61Y  GLY*     3.3    32.5    -      -       -      +
     62Y  TYR      3.1     7.6    -      -       -      +
     63Y  LYS*     3.4    40.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 57 (chain Y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39Y  CYS*     3.8    13.0    -      -       -      -
     42Y  CYS*     4.2     2.2    -      -       -      -
     46Y  LYS*     3.2    15.3    -      -       -      -
     47Y  LEU*     3.5    13.6    -      -       +      +
     56Y  MET*     1.3    73.6    -      -       -      +
     58Y  GLY*     1.3    57.6    +      -       -      +
     59Y  HIS*     3.0    28.3    -      -       -      -
     60Y  CYS*     3.6     9.0    -      -       -      -
     61Y  GLY*     2.6    34.1    +      -       -      -
     62Y  TYR      2.9    12.0    +      -       -      +
   8403Y   CD      2.5    31.0    -      -       -      -
----------------------------------------------------------
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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