Contacts of the strand formed by residues 195 - 198 (chain A) in PDB entry 1J1C


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 VAL 195 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  CYS      4.3     3.4    -      -       -      +
    108A  ASN*     4.7     0.2    -      -       -      +
    135A  VAL*     5.3     0.9    -      -       -      +
    164A  GLN*     3.5     9.0    -      -       -      +
    189A  LEU*     3.4     5.9    -      -       -      +
    190A  ASP*     3.0    31.6    +      -       +      -
    193A  THR*     3.1    23.0    +      -       -      +
    194A  ALA*     1.3    78.1    -      -       -      +
    196A  LEU*     1.3    67.3    +      -       -      +
    197A  LYS*     3.7    33.8    -      -       +      +
    357A  PRO*     3.4    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  ASN*     3.1    29.2    -      -       -      +
    139A  VAL*     4.0    20.0    -      -       +      -
    161A  TYR*     3.3    35.9    -      -       +      +
    164A  GLN*     3.1    26.2    -      -       +      +
    165A  LEU*     4.0    26.5    -      -       +      +
    187A  LEU*     4.1    21.5    -      -       +      -
    188A  LEU      3.2    10.1    -      -       -      +
    189A  LEU*     3.9     7.6    -      -       +      -
    195A  VAL*     1.3    75.0    -      -       -      +
    197A  LYS*     1.3    77.9    +      -       -      +
    198A  LEU*     4.0     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  CYS*     2.6    35.8    +      -       -      +
    108A  ASN      3.5     3.6    -      -       -      -
    109A  ILE      4.3     5.1    +      -       -      +
    110A  VAL*     3.8    26.7    -      -       +      +
    111A  ARG      5.2     1.3    -      -       -      +
    133A  ASP*     5.1    11.9    -      -       +      -
    135A  VAL*     4.0    22.9    -      -       +      -
    188A  LEU*     2.8    50.2    +      -       +      +
    195A  VAL*     3.7    18.9    -      -       +      +
    196A  LEU*     1.3    80.6    -      -       -      +
    198A  LEU*     1.3    63.6    +      -       -      +
    199A  CYS      3.6     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  ASN      2.8    17.3    +      -       -      +
    109A  ILE*     3.6     9.6    -      -       +      +
    110A  VAL*     2.9    24.9    +      -       -      +
    165A  LEU*     4.6     0.9    -      -       +      -
    168A  SER*     3.5    25.1    -      -       -      +
    169A  LEU*     4.3    16.2    -      -       +      -
    172A  ILE*     4.4     6.7    -      -       +      -
    179A  HIS*     3.7    26.7    -      -       +      +
    182A  ILE*     3.7    23.3    -      -       +      -
    186A  ASN*     3.6    13.9    -      -       +      +
    187A  LEU*     3.8    16.2    -      -       +      -
    196A  LEU*     4.0     3.3    -      -       +      +
    197A  LYS*     1.3    71.8    -      -       -      +
    199A  CYS*     1.3    64.1    +      -       -      +
    201A  PHE*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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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