Contacts of the strand formed by residues 189 - 192 (chain B) in PDB entry 1NUS


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 189 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  LEU*     5.2     2.0    -      -       +      -
    157B  VAL*     3.9    29.6    -      -       +      -
    162B  LEU*     3.2    21.8    -      -       +      +
    164B  CYS*     5.4     0.7    -      -       +      -
    176B  ILE*     3.6    32.5    -      -       +      -
    182B  LEU*     3.7    39.5    -      -       +      +
    185B  HIS      3.8     9.9    -      -       -      +
    186B  GLN*     3.0    21.8    +      -       -      +
    187B  HIS      3.4     0.2    -      -       -      -
    188B  ASN*     1.3    84.0    -      -       -      +
    190B  HIS*     1.3    66.7    +      -       -      +
    191B  LEU*     4.1    11.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  HIS*     4.0    20.8    +      -       +      +
     33B  LEU*     3.8    15.8    -      -       +      +
     36B  THR*     5.1     5.5    -      -       -      +
     38B  MET*     4.9     4.0    -      -       +      -
     39B  TYR*     3.4    37.7    +      +       -      -
    131B  LYS*     3.9    17.2    +      -       +      -
    162B  LEU      2.8    14.7    +      -       -      +
    163B  VAL*     3.4    18.5    -      -       +      +
    164B  CYS      2.9    27.5    +      -       -      -
    187B  HIS      3.7    15.0    +      -       -      -
    188B  ASN*     3.7    20.4    +      -       -      -
    189B  ILE*     1.3    75.6    +      -       -      +
    191B  LEU*     1.3    65.2    +      -       -      +
    192B  ALA      3.6     1.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  HIS*     3.3    21.0    +      -       -      -
    139B  LEU*     4.6     0.7    -      -       +      -
    164B  CYS*     3.7    17.5    -      -       +      +
    172B  PRO*     4.0    18.2    -      -       +      -
    173B  LYS*     3.7    36.8    -      -       +      +
    176B  ILE*     3.5    33.9    -      -       +      -
    189B  ILE*     4.1     6.7    +      -       +      +
    190B  HIS*     1.3    78.3    -      -       -      +
    192B  ALA*     1.3    59.9    +      -       -      +
    193B  LYS*     3.7     8.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  VAL*     4.0    17.3    -      -       +      -
     29B  ALA*     4.2     8.1    -      -       -      -
     32B  HIS*     3.7    30.7    -      -       +      -
    163B  VAL*     4.7     3.6    -      -       +      -
    164B  CYS      2.8    15.1    +      -       -      +
    165B  VAL*     3.4    10.9    -      -       +      +
    166B  GLY*     3.0    26.0    +      -       -      -
    190B  HIS      3.6     1.4    +      -       -      -
    191B  LEU*     1.3    73.0    -      -       -      +
    193B  LYS*     1.3    60.8    +      -       -      +
    194B  GLU      3.8     0.2    +      -       -      -
----------------------------------------------------------
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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