Contacts of the strand formed by residues 443 - 447 (chain A) in PDB entry 3NKO


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 LEU 443 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391A  ARG*     3.6     3.8    -      -       -      +
    392A  ILE*     3.1    49.3    +      -       +      +
    402A  TYR*     4.0    24.0    +      -       -      +
    404A  PRO*     4.8     6.3    -      -       +      +
    407A  ILE*     3.6    32.8    -      -       +      -
    408A  ILE*     3.6    34.8    -      -       +      -
    411A  LEU*     4.7     1.3    -      -       +      -
    422A  PRO*     4.4     9.9    -      -       +      -
    423A  TYR      3.8     6.1    -      -       -      +
    424A  MET*     4.5     5.6    -      -       -      -
    441A  GLU*     3.2     7.5    -      -       -      +
    442A  ASP*     1.3    79.4    -      -       +      +
    444A  HIS*     1.3    74.2    -      -       -      +
    445A  LEU*     4.7     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 444 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  TYR*     2.7    32.6    +      +       -      -
    389A  LEU*     4.3     7.8    -      -       +      +
    390A  GLY      3.3    13.5    +      -       -      -
    391A  ARG*     3.7    18.2    -      -       +      +
    422A  PRO*     3.4     4.0    -      -       -      +
    423A  TYR*     2.8    38.8    +      -       -      +
    425A  LYS*     5.0     2.5    -      -       +      -
    428A  LEU*     4.0    34.3    -      -       +      -
    434A  TYR*     3.6    29.1    -      +       -      -
    440A  ILE*     5.0     3.0    -      -       -      +
    441A  GLU      5.0     3.3    +      -       -      +
    442A  ASP      3.8     2.4    +      -       -      +
    443A  LEU*     1.3    75.2    +      -       -      +
    445A  LEU*     1.3    86.8    +      -       -      +
    446A  LEU*     4.0     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 445 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  LEU*     4.1    13.7    -      -       +      -
    384A  LEU*     4.2    10.8    -      -       +      -
    389A  LEU*     3.8     1.9    -      -       -      -
    390A  GLY*     2.7    47.7    +      -       -      +
    392A  ILE*     4.2    12.1    -      -       +      -
    411A  LEU*     3.9    16.6    -      -       +      -
    420A  PHE*     4.2    20.9    -      -       +      -
    421A  LYS      3.6     2.9    -      -       -      -
    422A  PRO*     3.9    21.5    -      -       +      -
    443A  LEU*     4.7     2.0    -      -       +      -
    444A  HIS*     1.3    92.3    +      -       -      +
    446A  LEU*     1.3    60.3    +      -       -      +
    447A  VAL*     3.6     5.3    +      -       +      -
    453A  VAL*     3.8    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 446 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  TYR*     3.5    35.7    -      -       +      +
    420A  PHE*     3.2     2.1    -      -       -      -
    421A  LYS      2.8    39.5    +      -       -      +
    423A  TYR*     3.8    19.9    -      -       +      -
    428A  LEU*     3.9    18.8    -      -       +      -
    429A  PRO*     4.5     7.0    -      -       +      -
    432A  LEU*     4.3    13.2    -      -       +      -
    444A  HIS*     4.0     2.5    -      -       +      -
    445A  LEU*     1.3    71.4    -      -       -      +
    447A  VAL*     1.3    61.0    +      -       -      +
    477A  ASP*     4.4    17.5    -      -       +      +
    817A  MET*     4.3    17.5    -      -       -      -
   1016A  EDO      3.2    26.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 447 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  TYR*     5.3     0.2    +      -       -      -
    387A  GLY      3.8     4.5    -      -       -      +
    388A  THR      3.6    14.0    +      -       -      +
    389A  LEU*     3.6    23.5    -      -       -      +
    419A  HIS      3.6    11.2    -      -       -      +
    420A  PHE*     4.0     6.5    -      -       +      -
    445A  LEU*     3.6     3.5    +      -       +      +
    446A  LEU*     1.3    79.4    -      -       -      +
    448A  GLU*     1.3    71.5    +      -       -      +
    449A  ARG      3.5     0.7    +      -       -      -
    451A  TRP*     3.5    31.4    -      -       +      +
    452A  HIS      4.4     5.4    -      -       -      +
    453A  VAL*     3.6    29.6    -      -       +      -
    476A  PHE*     3.5    15.2    -      -       +      +
    477A  ASP*     5.3     4.4    +      -       -      +
   1016A  EDO      3.6     4.8    -      -       -      -
----------------------------------------------------------
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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