Contacts of the strand formed by residues 82 - 90 (chain A) in PDB entry 1LGQ


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 82 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  HIS*     3.2    17.2    +      -       +      -
     61A  CYS*     3.9     9.5    -      -       -      +
     74A  LEU*     4.2    17.0    -      -       +      -
     76A  ASP*     2.6    28.8    +      -       -      +
     81A  GLY*     1.3    71.6    -      -       -      -
     83A  VAL*     1.3    68.4    +      -       -      +
     84A  ILE*     4.9     2.0    -      -       +      -
     89B  VAL*     3.7     1.6    -      -       -      +
     90B  VAL*     2.7    43.5    +      -       -      +
    103B  ILE*     3.8    24.7    -      -       +      -
    104B  TYR      3.8    13.5    -      -       -      +
    105B  LEU*     4.6     0.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  GLY      5.7     1.1    -      -       -      -
     82A  THR*     1.3    77.3    -      -       -      +
     84A  ILE*     1.3    70.9    +      -       -      +
     87B  LEU*     4.4    18.4    -      -       +      -
     88B  LYS      3.3    11.2    -      -       -      +
     89B  VAL*     4.5    18.4    -      -       +      -
    102B  VAL      3.7     0.2    -      -       -      +
    103B  ILE*     3.7     0.3    -      -       -      -
    104B  TYR*     2.7    64.4    +      -       +      +
    107B  TYR*     4.0    32.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LEU*     4.4    17.7    -      -       +      -
     82A  THR*     4.8     4.9    -      -       +      +
     83A  VAL*     1.3    83.4    -      -       -      +
     85A  ASN*     1.3    72.2    +      -       -      +
     86A  LYS*     3.8    20.6    +      -       +      +
     86B  LYS      3.5     1.4    -      -       -      +
     88B  LYS*     2.8    47.2    +      -       +      +
     90B  VAL*     3.8    25.1    -      -       +      -
     95B  CYS*     4.3    14.4    -      -       +      -
     96B  PRO      4.7     4.9    -      -       -      +
     97B  LEU*     4.8     2.0    -      -       +      -
    101B  ASP*     4.0    12.3    -      -       +      -
    102B  VAL      3.4     7.2    -      -       -      +
    103B  ILE*     3.8    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  VAL*     4.3     0.6    -      -       +      -
     84A  ILE*     1.3    73.2    -      -       -      +
     86A  LYS*     1.3    60.7    +      -       -      +
     87A  LEU*     4.2     8.5    -      -       -      +
     85B  ASN*     3.0    40.7    +      -       -      -
     86B  LYS      3.4     3.3    -      -       -      +
     87B  LEU*     3.2    19.8    -      -       +      +
    100B  GLY      5.5     2.0    +      -       -      -
    101B  ASP*     3.3    12.1    -      -       -      +
    102B  VAL*     2.9    43.7    +      -       +      +
    104B  TYR*     4.0    22.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ILE*     3.9    21.0    -      -       +      +
     85A  ASN*     1.3    73.1    -      -       -      +
     87A  LEU*     1.3    65.4    +      -       -      +
     88A  LYS*     3.6     9.6    -      -       +      +
     84B  ILE      3.5     0.7    -      -       -      +
     85B  ASN*     3.2    10.4    -      -       -      +
     86B  LYS*     2.6    51.0    +      -       +      +
     88B  LYS*     5.5    10.1    -      -       +      +
     95B  CYS*     4.3    10.0    -      -       -      -
     96B  PRO*     2.6    37.7    +      -       -      +
     97B  LEU*     4.3     0.2    -      -       -      +
     98B  GLN*     3.1    32.1    -      -       -      +
    101B  ASP*     2.9    19.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  ASN*     4.2     7.2    -      -       -      +
     86A  LYS*     1.3    74.7    -      -       -      +
     88A  LYS*     1.3    63.0    +      -       -      +
     89A  VAL*     4.0     6.2    +      -       -      +
    104A  TYR*     5.4     3.8    -      -       +      -
    107A  TYR*     4.3    27.8    -      -       +      +
     83B  VAL*     3.8    24.7    -      -       +      -
     84B  ILE      4.0     0.9    -      -       -      -
     85B  ASN*     3.2    30.3    -      -       +      +
     98B  GLN*     4.2    16.7    +      -       -      +
    100B  GLY*     5.5    11.7    -      -       -      +
    101B  ASP*     4.3     6.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LYS*     3.6    11.0    -      -       +      -
     87A  LEU*     1.3    74.4    -      -       -      +
     89A  VAL*     1.3    70.2    +      -       -      +
     90A  VAL*     4.0     7.0    -      -       +      -
     93A  GLN*     4.8    12.3    -      -       -      +
     94A  THR      5.1     1.6    +      -       -      -
     95A  CYS*     2.9    38.0    -      -       -      +
     96A  PRO*     4.8     4.8    -      -       -      +
     82B  THR      3.9     0.3    -      -       -      +
     83B  VAL*     3.2     6.2    -      -       -      +
     84B  ILE*     2.8    48.5    +      -       +      +
     86B  LYS*     5.0    13.6    -      -       +      +
     98B  GLN*     5.5     1.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  LEU      4.7     6.3    -      -       -      +
     88A  LYS*     1.3    80.8    -      -       -      +
     90A  VAL*     1.3    64.6    +      -       -      +
     91A  LYS*     3.6    36.3    +      -       +      +
     93A  GLN*     3.8    10.6    +      -       -      -
     80B  SER      5.0     3.6    -      -       -      +
     81B  GLY      5.3     0.2    -      -       -      -
     82B  THR      3.7     7.4    -      -       -      +
     83B  VAL*     4.4    19.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LYS*     4.7    10.1    -      -       +      +
     89A  VAL*     1.3    74.5    -      -       -      +
     91A  LYS*     1.3    60.2    +      -       -      +
     93A  GLN*     3.4    41.7    -      -       +      +
     95A  CYS*     4.1    22.7    -      -       +      -
     74B  LEU*     4.7     4.5    -      -       +      +
     76B  ASP*     3.2    16.0    -      -       +      +
     81B  GLY*     3.2     2.3    -      -       -      -
     82B  THR*     2.6    49.5    +      -       -      +
     84B  ILE*     3.6    28.7    -      -       +      -
----------------------------------------------------------
 Back to top of page


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