Contacts of the strand formed by residues 443 - 447 (chain B) in PDB entry 2JGN


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 THR 443 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434B  LEU*     4.2    11.9    -      -       +      +
    441B  SER*     3.2    17.7    +      -       -      -
    442B  LEU*     1.3    72.7    +      -       -      +
    444B  LEU*     1.3    60.7    +      -       -      +
    445B  VAL*     4.0     9.8    +      -       +      -
    486B  PHE*     3.4     5.2    -      -       -      -
    492B  PRO      2.9    10.3    +      -       -      -
    493B  ILE*     3.5    12.4    -      -       -      +
    494B  LEU      3.0    23.9    +      -       -      +
    511B  HIS*     3.3    22.7    +      -       +      +
    513B  ILE*     3.5    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 444 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    442B  LEU      4.3     0.6    +      -       -      -
    443B  THR*     1.3    73.5    -      -       -      +
    445B  VAL*     1.3    60.0    +      -       -      +
    446B  PHE*     3.5    35.3    +      -       +      -
    486B  PHE*     4.3     6.5    -      -       +      -
    494B  LEU*     3.5    39.7    -      -       +      +
    496B  ALA*     4.0    16.6    -      -       +      -
    506B  ILE*     4.1    17.9    -      -       +      -
    509B  VAL*     4.3    10.3    -      -       +      +
    511B  HIS      2.9    10.8    +      -       -      +
    512B  VAL*     3.4     6.4    -      -       +      +
    513B  ILE      2.9    24.4    +      -       -      +
    530B  ARG*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 445 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430B  LEU*     4.5    11.2    -      -       +      -
    434B  LEU*     5.4     0.7    -      -       +      -
    443B  THR*     4.1    13.9    -      -       +      -
    444B  LEU*     1.3    76.0    -      -       -      +
    446B  PHE*     1.3    64.6    +      -       -      +
    447B  VAL*     4.6     0.2    -      -       +      -
    456B  LEU*     4.0    20.4    -      -       +      -
    460B  LEU*     5.2     0.2    -      -       +      -
    493B  ILE*     3.9    25.4    -      -       +      -
    494B  LEU      2.9     9.8    +      -       -      +
    495B  VAL*     3.5     9.5    -      -       +      +
    496B  ALA*     2.8    28.4    +      -       -      +
    513B  ILE*     3.3    20.6    -      -       +      +
    515B  PHE*     3.8    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 446 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444B  LEU*     3.5    33.9    -      -       +      -
    445B  VAL*     1.3    73.3    -      -       -      +
    447B  VAL*     1.3    59.8    +      -       -      +
    496B  ALA*     3.1    29.8    -      -       +      -
    497B  THR      4.4    12.3    -      -       -      -
    498B  ALA*     4.5     6.3    -      -       -      -
    500B  ALA      5.3     4.0    -      -       -      -
    506B  ILE*     6.4     1.3    -      -       +      -
    512B  VAL*     3.8    16.4    -      -       +      -
    513B  ILE      2.7    11.1    +      -       -      +
    514B  ASN*     3.8    16.2    -      -       -      +
    515B  PHE*     3.1    25.8    +      -       -      +
    516B  ASP      3.3     7.1    +      -       -      +
    527B  ARG*     3.6    58.8    -      -       +      +
    530B  ARG*     4.1    16.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 447 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445B  VAL*     4.6     0.7    -      -       +      -
    446B  PHE*     1.3    80.0    -      -       -      +
    448B  GLU*     1.3    62.5    +      -       -      +
    449B  THR      3.8     4.3    -      -       -      +
    452B  GLY*     4.5     7.9    -      -       -      +
    453B  ALA*     3.5    41.7    -      -       +      +
    456B  LEU*     3.6    31.2    -      -       +      -
    495B  VAL*     4.0     6.7    -      -       +      -
    496B  ALA      2.8    14.7    +      -       -      +
    497B  THR*     3.6    16.9    -      -       +      -
    498B  ALA      4.3     3.1    +      -       -      -
    515B  PHE*     3.9    17.9    -      -       +      -
    516B  ASP*     3.6    10.5    -      -       -      +
    527B  ARG*     4.5     7.5    +      -       -      -
----------------------------------------------------------
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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