Contacts of the strand formed by residues 14 - 18 (chain B) in PDB entry 2JAJ


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 HIS 14 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  ALA*     3.5     6.6    -      -       -      +
     13B  THR*     1.3   111.8    +      -       -      +
     15B  ALA*     1.3    63.9    +      -       -      +
     59B  LEU*     4.0     4.8    -      -       -      +
     60B  GLN*     3.1    41.8    +      -       +      +
     62B  VAL*     4.9     7.9    -      -       +      -
    111B  LEU*     3.5    34.6    -      -       +      +
    276B  VAL      4.6     0.2    -      -       -      -
    277B  LEU*     3.6     3.3    -      -       -      -
    278B  ILE*     3.0    44.8    +      -       +      +
    280B  LYS*     4.2    15.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  HIS*     1.3    75.1    -      -       -      +
     16B  VAL*     1.3    63.7    +      -       -      +
     17B  VAL*     4.6     5.2    -      -       +      -
     53B  LEU*     4.0    20.9    -      -       +      -
     59B  LEU*     4.4     6.0    -      -       +      +
     60B  GLN      2.7    11.3    +      -       -      +
     61B  VAL*     3.3    12.3    -      -       +      +
     62B  VAL*     2.8    28.4    +      -       -      +
    275B  SER*     4.6     0.9    -      -       -      -
    276B  VAL      3.4     5.6    -      -       -      +
    277B  LEU*     3.7    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  HIS*     5.9     0.2    -      -       +      -
     15B  ALA*     1.3    74.9    -      -       -      +
     17B  VAL*     1.3    64.5    +      -       -      +
     62B  VAL*     3.5    13.2    -      -       +      +
     64B  LEU*     3.6    31.0    -      -       +      -
     76B  VAL*     3.6     5.6    -      -       +      +
    104B  MET*     4.1    13.9    -      -       -      -
    107B  ALA*     4.5     8.3    -      -       +      -
    108B  LEU*     4.3     9.4    -      -       +      -
    111B  LEU*     4.0    18.2    -      -       +      -
    275B  SER*     3.3     6.9    -      -       -      -
    276B  VAL*     2.8    41.3    +      -       +      +
    278B  ILE*     3.8    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ALA*     4.6     1.8    -      -       +      -
     16B  VAL*     1.3    79.1    -      -       -      +
     18B  ARG*     1.3    63.2    +      -       -      +
     46B  HIS*     4.4     7.4    -      -       +      -
     49B  TYR*     4.6     1.8    -      -       +      -
     50B  VAL*     3.8    26.9    -      -       +      -
     53B  LEU*     4.5    11.0    -      -       +      -
     61B  VAL*     3.6    28.9    -      -       +      -
     62B  VAL      2.7    12.8    +      -       -      +
     63B  GLU*     3.8    13.7    -      -       +      +
     64B  LEU*     2.9    30.5    +      -       -      +
     76B  VAL*     4.1     4.9    -      -       -      -
    274B  CYS      3.5    20.0    -      -       -      +
    275B  SER*     4.0    11.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  VAL*     1.3    80.2    -      -       -      +
     19B  ALA*     1.3    73.3    +      -       -      +
     46B  HIS*     3.3    18.2    +      -       -      -
     64B  LEU*     3.4    16.8    -      -       +      +
     65B  PRO*     2.7    26.2    +      -       -      +
     66B  ALA      4.6     0.2    -      -       -      -
     67B  ASP*     3.8    24.8    +      -       -      +
     70B  LEU*     4.4     3.6    -      -       -      +
     73B  CYS*     3.0    48.5    -      -       -      +
     74B  VAL*     3.4    16.3    +      -       -      +
     76B  VAL*     3.5    13.4    -      -       +      +
     99B  LYS      5.2     0.4    +      -       -      -
    100B  GLU*     3.8    23.0    +      -       -      +
    103B  MET*     3.5    38.2    -      -       -      +
    104B  MET      5.2     0.2    -      -       -      +
----------------------------------------------------------
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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