Contacts of the strand formed by residues 129 - 135 (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 GLU 129 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5B  ILE*     3.3    31.8    -      -       +      +
      6B  PRO      2.6    12.4    +      -       -      +
      7B  VAL*     3.3     7.9    -      -       +      +
      8B  VAL*     2.9    24.8    +      -       -      -
     39B  TYR*     3.5    17.7    +      -       -      -
    127B  VAL      4.9     3.6    -      -       -      +
    128B  PRO*     1.3    72.7    -      -       -      +
    130B  LEU*     1.3    59.3    +      -       -      +
    131B  LYS*     3.1    31.9    +      -       -      +
    160B  PHE      5.4     3.4    -      -       -      +
    188B  ASN*     5.6     2.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  VAL*     3.6    32.3    -      -       +      +
     10B  LEU*     4.2    18.6    -      -       +      -
     45B  ILE*     5.6     1.1    -      -       +      -
     97B  LEU*     3.1    43.7    -      -       +      +
    100B  HIS*     3.9    14.1    -      -       +      +
    101B  HIS*     3.6    25.4    +      -       +      +
    104B  LEU*     3.9    15.5    -      -       +      -
    128B  PRO      3.7     1.8    +      -       -      -
    129B  GLU*     1.3    72.9    -      -       -      +
    131B  LYS*     1.3    59.9    +      -       -      +
    160B  PHE*     3.0    39.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  VAL*     3.8    22.9    -      -       +      -
      8B  VAL      3.0    10.3    +      -       -      +
      9B  LEU*     3.5     7.6    -      -       +      -
     10B  LEU*     2.9    26.9    +      -       -      +
     33B  LEU*     4.7     2.9    -      -       +      -
     39B  TYR*     3.8    19.9    +      -       -      -
     97B  LEU*     4.6     3.8    -      -       -      -
    129B  GLU*     3.1    30.3    +      -       -      +
    130B  LEU*     1.3    78.8    -      -       -      +
    132B  LEU*     1.3    60.6    +      -       -      +
    160B  PHE      3.7    13.7    +      -       -      +
    161B  GLY*     3.4    19.8    -      -       -      +
    163B  VAL*     4.1    26.9    -      -       +      -
    188B  ASN*     4.7     8.7    -      -       -      +
    190B  HIS*     3.9    20.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LEU*     3.5    15.0    -      -       +      +
     12B  CYS*     4.4    16.2    -      -       +      +
     93B  THR*     3.9    31.2    -      -       +      -
     97B  LEU*     4.3    24.8    -      -       +      +
    131B  LYS*     1.3    70.7    -      -       -      +
    133B  LEU*     1.3    66.7    +      -       -      +
    134B  CYS*     5.1     6.1    -      -       +      -
    138B  VAL*     5.8     2.5    -      -       +      -
    142B  PHE*     5.2     4.9    -      -       +      -
    148B  TRP*     5.4     4.9    -      -       +      -
    156B  ILE*     4.1    19.5    -      -       +      -
    161B  GLY      2.8    15.5    +      -       -      +
    162B  LEU*     3.5    23.5    -      -       +      +
    163B  VAL*     2.9    26.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  LEU*     4.4    13.5    -      -       +      -
     10B  LEU      2.6    25.3    +      -       -      +
     11B  ALA*     3.6    12.6    -      -       -      +
     12B  CYS      4.4     4.0    +      -       -      +
     25B  MET*     3.9    25.7    -      -       +      +
     26B  PHE*     3.6    55.6    -      -       +      -
     29B  ALA*     3.6    27.4    -      -       +      -
    131B  LYS      3.6     0.6    +      -       -      -
    132B  LEU*     1.3    74.8    -      -       -      +
    134B  CYS*     1.3    70.9    -      -       -      +
    163B  VAL*     3.4    17.5    -      -       +      +
    165B  VAL*     4.1     4.7    -      -       +      -
    502B  APC      4.3     2.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  CYS      6.0     0.4    -      -       -      +
     25B  MET*     3.9     8.8    -      -       -      +
    132B  LEU*     5.1     5.6    -      -       +      -
    133B  LEU*     1.3    78.5    -      -       -      +
    135B  GLY*     1.3    71.1    +      -       -      +
    138B  VAL*     3.8    25.6    -      -       +      -
    139B  LEU*     4.6     6.3    -      -       -      -
    142B  PHE*     5.6     0.4    -      -       -      -
    162B  LEU*     3.7    31.4    -      -       -      -
    163B  VAL      3.0     9.1    +      -       -      +
    164B  CYS*     3.2    12.5    -      -       -      -
    165B  VAL*     2.9    23.9    +      -       -      +
    502B  APC      3.2    13.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  MET*     4.0     2.1    -      -       -      -
    134B  CYS*     1.3    78.8    -      -       -      +
    136B  ALA*     1.3    67.2    +      -       -      +
    137B  ASP*     3.1     5.8    -      -       -      -
    138B  VAL*     2.9    18.9    +      -       -      +
    139B  LEU      3.6     2.6    +      -       -      -
    164B  CYS*     4.0     1.6    -      -       -      -
    165B  VAL      3.5     9.0    -      -       -      -
    167B  ARG*     4.3     6.5    -      -       -      -
    502B  APC      3.0    31.7    +      -       -      -
----------------------------------------------------------
 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