Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 1N3Q


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 HIS 146 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  GLU*     3.3     8.7    +      -       -      -
    129A  PHE*     3.7     1.9    -      -       -      -
    130A  ASP*     2.9    49.7    +      -       +      +
    132A  PHE      4.9     0.2    -      -       -      -
    133A  TYR*     4.7     3.8    -      -       +      -
    141A  ASP*     3.1    17.7    +      -       +      -
    142A  PRO*     3.5    24.4    -      -       +      +
    144A  TYR*     2.7    26.9    +      -       +      +
    145A  PRO*     1.3    76.6    -      -       +      +
    147A  ILE*     1.3    63.7    +      -       -      +
    159A  THR*     4.0    17.0    -      -       +      -
    160A  VAL      3.3    16.2    -      -       -      +
    162A  TRP*     3.6    11.3    -      -       -      +
    271A   MN      2.3    35.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  VAL*     4.4     6.3    -      -       +      -
    128A  GLU      3.2    10.8    -      -       -      +
    129A  PHE*     3.8    31.9    -      -       +      -
    146A  HIS*     1.3    76.4    -      -       -      +
    148A  GLY*     1.3    61.5    +      -       -      +
    159A  THR*     3.2     4.5    -      -       -      -
    160A  VAL*     3.0    37.3    +      -       +      +
    162A  TRP*     3.6    36.1    -      -       +      +
    185A  VAL*     4.3    11.7    -      -       +      -
    187A  ALA*     4.0    10.1    -      -       +      -
    195A  TYR*     3.9    23.6    -      -       +      +
    197A  VAL*     4.2    18.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  VAL*     3.4     5.9    -      -       -      +
    128A  GLU*     2.8    45.1    +      -       -      +
    147A  ILE*     1.3    77.4    -      -       -      +
    149A  ILE*     1.3    65.7    +      -       -      +
    156A  SER*     3.7    13.0    -      -       -      -
    158A  LYS      3.3     9.9    -      -       -      -
    159A  THR*     3.9     3.6    -      -       -      -
    197A  VAL*     5.5     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  ILE*     5.2     4.7    -      -       +      -
    126A  ALA      3.5     5.8    -      -       -      +
    127A  VAL*     4.7     2.7    -      -       +      +
    148A  GLY*     1.3    73.5    -      -       -      +
    150A  ASP*     1.3    64.3    +      -       -      +
    151A  VAL*     4.3    12.8    -      -       +      -
    156A  SER*     3.3     2.4    -      -       -      -
    157A  VAL*     3.0    42.1    +      -       +      +
    158A  LYS*     2.9    13.1    +      -       +      +
    183A  LEU*     4.0    26.5    -      -       +      +
    185A  VAL*     4.4     9.0    -      -       +      -
    197A  VAL*     4.2    19.7    -      -       +      +
    198A  SER*     3.7    39.0    -      -       -      +
    199A  TYR*     3.8    13.5    -      -       +      +
    201A  VAL*     6.2     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  LEU*     4.9     1.6    -      -       -      +
    110A  LEU*     5.1     1.4    -      -       -      +
    111A  PHE*     4.6     9.9    -      -       +      -
    124A  VAL*     3.7     0.9    -      -       +      +
    125A  ILE*     3.2     7.4    -      -       -      +
    126A  ALA*     2.7    52.6    +      -       +      +
    128A  GLU*     2.5    36.1    -      -       -      +
    149A  ILE*     1.3    73.2    -      -       -      +
    151A  VAL*     1.3    62.7    +      -       -      +
    152A  ASN      4.0     0.9    -      -       -      -
    153A  SER      3.4    21.1    -      -       -      +
    154A  ILE*     4.3     9.3    -      -       -      +
    156A  SER*     2.7    32.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  THR*     4.3     6.6    -      -       -      +
    124A  VAL      3.7     2.7    -      -       -      +
    125A  ILE*     4.7     9.2    -      -       +      +
    149A  ILE*     4.1    12.0    +      -       +      -
    150A  ASP*     1.3    77.2    -      -       -      +
    152A  ASN*     1.3    69.1    +      -       -      +
    153A  SER*     3.0    16.0    +      -       -      +
    155A  ARG      5.6     0.2    +      -       -      -
    157A  VAL*     4.2    36.0    -      -       +      +
    199A  TYR*     4.5    10.8    -      -       +      -
    201A  VAL*     4.5    15.3    -      -       +      -
    206A  VAL*     4.0    31.0    -      -       +      -
----------------------------------------------------------
 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