Contacts of the strand formed by residues 102 - 107 (chain B) 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 102 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  ILE*     3.8     3.1    -      -       -      +
     88B  ARG*     3.0    27.2    +      -       +      -
     89B  VAL*     3.1    33.5    +      -       +      +
    100B  GLY      3.5     1.2    +      -       -      -
    101B  THR*     1.3    76.0    -      -       -      +
    103B  ARG*     1.3    62.1    +      -       -      +
    117B  VAL*     5.5     5.8    -      -       +      -
    118B  GLU      3.5     8.1    -      -       -      +
    119B  ILE*     3.9    15.9    -      -       +      -
    135B  LEU*     5.3     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 103 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  PHE*     3.0    74.6    +      -       +      +
     75B  PRO*     4.4     9.2    -      -       -      +
     79B  LYS*     3.9    22.8    -      -       -      +
     85B  CYS*     3.4    24.7    -      -       -      -
     86B  THR      3.5     7.4    -      -       -      +
     87B  ILE*     4.3     4.5    -      -       +      +
     88B  ARG*     5.0     2.7    -      -       -      -
    102B  ILE*     1.3    74.7    -      -       -      +
    104B  GLU*     1.3    61.4    +      -       -      +
    105B  VAL*     3.8    22.3    -      -       +      +
    116B  SER      3.9     0.2    -      -       -      +
    117B  VAL*     3.4     6.4    -      -       -      +
    118B  GLU*     3.0    50.6    +      -       +      +
    130B  LEU*     5.3     2.0    -      -       -      +
    132B  PHE*     4.1    19.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  SER      4.2     0.2    -      -       -      +
     85B  CYS*     3.5     2.6    -      -       -      -
     86B  THR*     2.8    37.0    +      -       -      -
     88B  ARG*     2.7    52.3    +      -       +      +
    103B  ARG*     1.3    73.2    -      -       -      +
    105B  VAL*     1.3    63.4    +      -       -      +
    106B  SER*     4.0     0.7    +      -       -      -
    115B  THR*     3.2    30.1    +      -       -      +
    116B  SER      3.3     8.3    -      -       -      +
    117B  VAL*     4.5    14.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  PRO*     4.6     3.8    -      -       +      -
     82B  ILE*     4.0    33.4    -      -       +      -
     84B  SER      3.7     4.7    -      -       -      -
     85B  CYS*     4.4     1.8    -      -       -      +
    103B  ARG*     3.8    34.1    -      -       +      +
    104B  GLU*     1.3    75.1    -      -       -      +
    106B  SER*     1.3    62.3    +      -       -      +
    107B  VAL*     5.2     3.4    -      -       +      -
    115B  THR*     2.9    24.3    +      -       -      -
    116B  SER*     2.7    36.9    +      -       -      +
    118B  GLU*     5.9     0.4    -      -       +      -
    301B  A9S      6.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  ILE      3.8     0.7    -      -       -      -
     83B  LYS*     2.9    31.4    +      -       -      +
     84B  SER*     2.7    40.4    +      -       -      +
    104B  GLU      4.0     1.1    +      -       -      -
    105B  VAL*     1.3    75.1    -      -       -      +
    107B  VAL*     1.3    62.6    +      -       -      +
    114B  SER      3.4     7.0    -      -       -      -
    115B  THR*     5.5     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  PHE      3.4    13.5    -      -       -      +
     82B  ILE*     4.6     2.7    -      -       +      +
     83B  LYS*     4.3     4.0    -      -       -      +
    105B  VAL*     4.8     7.0    -      -       +      +
    106B  SER*     1.3    77.3    -      -       -      +
    108B  VAL*     1.3    76.2    +      -       -      +
    109B  SER*     3.4     2.8    +      -       -      -
    111B  LEU*     4.2    12.8    -      -       +      -
    113B  ALA*     3.4    27.2    -      -       +      +
    114B  SER*     2.8    27.4    +      -       -      +
    115B  THR*     3.8    10.5    -      -       -      +
    116B  SER*     4.9     2.7    -      -       -      +
    301B  A9S      3.8    32.3    -      -       +      +
----------------------------------------------------------
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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