Contacts of the strand formed by residues 82 - 89 (chain A) in PDB entry 4JDA


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 82 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  PRO*     4.4     8.3    -      -       +      -
     76A  ASN*     3.7    21.0    -      -       +      +
     79A  LYS*     3.7    37.3    -      -       +      +
     80A  HIS      3.1     7.2    -      -       -      +
     81A  PHE*     1.3    80.5    -      -       -      +
     83A  LYS*     1.3    66.4    +      -       -      +
     84A  SER      3.8    16.8    -      -       -      +
    105A  VAL*     3.7    40.4    -      -       +      -
    106A  SER      3.8     4.5    -      -       -      +
    107A  VAL*     5.8     0.4    -      -       +      -
    108A  VAL*     4.4     1.1    -      -       -      +
    301A  A9S      5.1    11.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  ASN*     4.3     8.7    -      -       -      +
     82A  ILE*     1.3    75.9    -      -       -      +
     84A  SER*     1.3    67.7    +      -       -      +
    106A  SER*     2.9    23.0    +      -       -      +
    107A  VAL      4.2    13.9    -      -       -      +
    108A  VAL*     3.9    17.2    -      -       +      +
    109A  SER*     5.2     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  ASN*     4.9     5.8    -      -       -      +
     82A  ILE*     3.4     7.7    -      -       -      +
     83A  LYS*     1.3    88.3    -      -       -      +
     85A  CYS*     1.3    64.0    +      -       -      +
     86A  THR*     5.4     2.3    +      -       -      -
    104A  GLU      4.2     0.2    -      -       -      +
    105A  VAL*     3.6     1.6    -      -       -      -
    106A  SER*     2.7    48.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ALA*     3.4    33.8    -      -       -      +
     75A  PRO*     3.9    20.0    -      -       +      -
     76A  ASN*     4.5     5.7    -      -       -      +
     84A  SER*     1.3    79.8    -      -       -      +
     86A  THR*     1.3    66.1    +      -       -      +
     87A  ILE*     4.4     0.5    +      -       -      +
    103A  ARG*     3.9    31.9    -      -       -      -
    104A  GLU      3.4     6.1    -      -       -      -
    105A  VAL*     3.8    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  SER*     5.4     2.1    +      -       -      -
     85A  CYS*     1.3    77.5    +      -       -      +
     87A  ILE*     1.3    76.4    +      -       -      +
     88A  ARG*     3.7    29.3    +      -       -      +
    103A  ARG*     3.3     5.0    -      -       -      +
    104A  GLU*     2.9    35.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  PHE*     5.7     0.9    -      -       +      -
     73A  ALA*     3.8    31.0    -      -       +      -
     85A  CYS*     4.4     0.4    +      -       -      -
     86A  THR*     1.3    85.3    -      -       -      +
     88A  ARG*     1.3    63.5    +      -       -      +
     89A  VAL      3.8    17.0    -      -       -      +
     90A  ASN*     3.2    32.2    +      -       -      +
     97A  ILE*     5.7     3.1    -      -       +      -
    101A  THR*     4.5    12.6    -      -       +      -
    102A  ILE      3.8     6.7    -      -       -      +
    103A  ARG*     4.8     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  THR*     4.2    22.1    +      -       -      +
     87A  ILE*     1.3    79.6    +      -       -      +
     89A  VAL*     1.3    69.1    +      -       +      +
     90A  ASN*     5.5     1.5    -      -       -      +
    102A  ILE*     2.9    22.1    +      -       +      +
    103A  ARG      4.4     0.9    -      -       -      -
    104A  GLU*     2.9    58.4    +      -       +      +
    117A  VAL*     6.0     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  ILE*     3.8     4.2    -      -       -      +
     88A  ARG*     1.3    85.3    -      -       +      +
     90A  ASN*     1.3    64.7    +      -       -      +
    100A  GLY      3.8     8.7    -      -       -      +
    101A  THR*     3.6     7.8    -      -       -      +
    102A  ILE*     3.3    59.1    +      -       +      +
----------------------------------------------------------
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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