Contacts of the strand formed by residues 44 - 49 (chain B) in PDB entry 3ANX


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 GLY 44 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  GLU*     3.6    13.2    -      -       -      -
     40B  SER*     3.0    36.9    +      -       -      -
     41B  LYS      4.7     0.8    -      -       -      -
     42B  GLY      3.6     2.0    +      -       -      -
     43B  PHE*     1.3    75.6    -      -       -      +
     45B  LYS*     1.3    65.4    +      -       -      -
     57B  GLU*     3.3    13.5    -      -       -      -
     58B  ARG*     3.9     8.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 45 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23B  ARG*     5.6     1.1    -      -       -      +
     25B  ILE*     3.7    28.3    -      -       +      -
     37B  LEU*     4.2    11.9    -      -       +      -
     38B  PHE      3.2     7.4    -      -       -      +
     39B  GLU*     3.5    17.7    -      -       -      +
     43B  PHE      3.5     0.7    +      -       -      +
     44B  GLY*     1.3    72.2    -      -       -      -
     46B  VAL*     1.4    56.8    -      -       -      +
     56B  THR*     3.5     0.3    -      -       -      -
     57B  GLU*     2.6    46.0    +      -       -      +
    120B  HIS      2.6    30.4    +      -       -      +
    122B  PRO*     4.1     3.4    -      -       -      +
    123B  GLU*     2.8    35.0    +      -       -      +
    124B  TRP*     3.5    18.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 46 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  GLU*     6.0     0.4    -      -       -      +
     19B  ARG*     4.5    13.9    -      -       +      +
     36B  PHE      3.5     1.6    -      -       -      +
     37B  LEU*     3.3     7.0    -      -       -      +
     38B  PHE*     2.8    66.9    +      -       +      -
     40B  SER*     3.3    26.9    -      -       -      +
     43B  PHE*     4.4     3.8    -      -       +      -
     44B  GLY      3.6     2.7    -      -       -      +
     45B  LYS*     1.4    71.6    -      -       -      +
     47B  LEU*     1.3    62.8    +      -       -      +
     48B  ILE*     4.3     7.2    -      -       +      -
     53B  VAL*     4.3    13.2    -      -       +      -
     55B  SER      3.8     7.6    -      -       -      +
     56B  THR*     3.8    16.8    -      -       -      +
    124B  TRP*     5.4     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 47 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  TYR*     4.7     7.6    -      -       +      -
     36B  PHE      3.7    15.0    -      -       -      +
     37B  LEU*     3.9    20.9    -      -       +      -
     46B  VAL*     1.3    74.4    -      -       -      +
     48B  ILE*     1.3    64.0    +      -       -      +
     49B  LEU*     2.9    34.5    -      -       +      -
     53B  VAL*     3.2     4.9    -      -       -      -
     54B  GLN*     2.5    49.0    +      -       +      -
     55B  SER*     2.8    20.9    +      -       -      +
     88B  GLU*     5.2     2.9    -      -       +      +
    113B  LEU*     5.0     8.5    -      -       +      -
    116B  VAL*     6.4     2.7    -      -       +      -
    121B  MET*     4.0    26.2    -      -       +      -
    124B  TRP*     5.3     0.8    -      -       +      -
    315B  MTA      5.3     1.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 48 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  PHE*     3.3    53.8    -      -       +      -
      9B  GLU*     5.0     2.2    -      -       +      -
     19B  ARG*     4.8     4.5    -      -       -      -
     35B  TYR*     3.3    16.6    -      -       -      +
     36B  PHE*     2.8    24.9    +      -       +      +
     38B  PHE*     3.4    29.4    -      -       +      -
     46B  VAL*     4.3     4.3    -      -       +      -
     47B  LEU*     1.3    78.9    -      -       -      +
     49B  LEU*     1.3    75.7    +      -       -      +
     50B  ASP      3.7    15.5    -      -       -      +
     52B  ASP      3.0    23.3    -      -       -      +
     53B  VAL*     3.8    12.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 49 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  GLN*     3.3    41.7    -      -       +      +
     34B  ASP      3.6     3.1    -      -       -      +
     35B  TYR*     4.2     9.6    -      -       +      -
     47B  LEU*     2.9    25.4    -      -       +      -
     48B  ILE*     1.3    97.0    -      -       -      +
     50B  ASP*     1.3    56.8    +      -       -      +
     51B  LYS      2.7    18.9    +      -       -      -
     52B  ASP*     2.6    23.1    +      -       -      +
     54B  GLN*     3.3    38.6    +      -       +      +
    113B  LEU*     4.5    10.1    -      -       +      -
    160B  THR*     6.3     1.3    -      -       +      -
    315B  MTA      3.8    16.2    -      -       +      -
----------------------------------------------------------
 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