Contacts of the strand formed by residues 20 - 24 (chain D) in PDB entry 6JBQ


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 20 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1323C  PHE*     4.3    18.4    -      -       +      -
   1327C  LEU*     5.8     0.2    -      -       +      -
   1337C  ILE*     3.8    30.5    -      -       +      -
   1338C  GLU      3.5    15.0    -      -       -      +
   1339C  LEU*     3.8    26.2    -      -       +      +
     17D  PHE*     4.9     4.7    -      -       +      -
     18D  ASP      4.4     5.4    -      -       -      +
     19D  ALA*     1.3    74.8    -      -       -      +
     21D  LYS*     1.3    62.8    +      -       -      +
     22D  ILE      4.1     0.2    +      -       -      -
   1319D  PHE*     4.9     5.3    -      -       +      -
   1320D  ILE*     4.1    23.8    -      -       +      -
   1340D  LYS      4.0     1.0    -      -       -      +
   1341D  ARG*     3.7    13.4    -      -       -      -
   1342D  ASP*     3.3    26.9    +      -       -      +
   1344D  LEU*     5.3     7.0    -      -       +      -
   1353D  VAL*     4.4    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 21 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1337C  ILE*     3.6     2.9    -      -       -      +
   1338C  GLU*     3.0    35.9    +      -       +      +
   1340C  GLU*     3.5    33.8    -      -       +      +
     19D  ALA      3.8     1.4    +      -       -      -
     20D  ILE*     1.3    74.5    -      -       -      +
     22D  ILE*     1.3    65.6    +      -       -      +
     23D  ALA*     5.1    11.0    -      -       +      +
    230D  SER*     5.9     3.8    -      -       -      -
   1339D  GLY*     3.9    23.4    +      -       -      -
   1340D  LYS      4.1     5.4    -      -       -      +
   1341D  ARG*     4.7    18.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 22 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1330C  ILE*     5.3     3.1    -      -       +      -
   1335C  ILE*     3.8    23.1    -      -       +      -
   1336C  ASN      3.3    13.5    -      -       -      +
   1337C  ILE*     4.5    12.1    -      -       +      -
     20D  ILE      5.1     0.2    -      -       -      +
     21D  LYS*     1.3    76.1    -      -       -      +
     23D  ALA*     1.3    67.4    +      -       -      +
   1319D  PHE*     3.7    50.0    -      -       +      -
   1332D  LEU*     4.2    13.0    -      -       +      -
   1335D  ALA*     3.7    23.0    -      -       +      +
   1336D  ALA*     4.5     4.7    -      -       +      -
   1339D  GLY*     3.4    20.4    -      -       -      -
   1340D  LYS      3.4    16.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 23 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1335C  ILE*     3.8     7.1    -      -       -      +
   1336C  ASN*     2.8    37.6    +      -       -      +
     21D  LYS*     5.1    13.0    -      -       +      +
     22D  ILE*     1.3    75.9    -      -       -      +
     24D  LEU*     1.3    66.9    +      -       -      +
    231D  GLY      5.7     0.9    -      -       -      +
    232D  ASN*     4.0    12.8    -      -       -      +
   1336D  ALA*     3.6    17.5    -      -       -      +
   1339D  GLY*     4.6     7.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 24 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1334C  GLY      4.0    13.5    -      -       -      +
   1335C  ILE*     4.5     4.9    -      -       +      -
   1336C  ASN*     3.3    14.0    +      -       -      +
     23D  ALA*     1.3    84.2    -      -       -      +
     25D  ALA*     1.3    61.6    +      -       -      +
     26D  SER      4.0     1.2    +      -       -      -
    116D  PHE*     4.0    30.5    -      -       +      -
    227D  PHE*     5.4     3.1    -      -       +      -
    232D  ASN*     3.9    14.7    +      -       +      +
    233D  LYS      4.0    12.1    -      -       -      +
    236D  TRP*     3.7    54.2    -      -       +      +
    237D  MET*     4.6    12.3    -      -       +      -
   1336D  ALA*     3.7    13.6    +      -       +      +
   1337D  VAL*     5.0    11.0    -      -       +      -
----------------------------------------------------------
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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