Contacts of the strand formed by residues 545 - 548 (chain A) in PDB entry 3A1B


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 545 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  EDO      3.1     5.2    +      -       -      +
    458A  THR*     4.3    21.3    +      -       +      +
    459A  LYS      3.4     7.6    -      -       -      +
    460A  GLN*     2.9    31.2    +      -       -      +
    544A  ARG*     1.3    80.8    -      -       +      +
    546A  VAL*     1.3    66.0    +      -       -      +
    547A  LEU*     5.4     0.2    -      -       +      -
    559A  CYS*     3.1     2.8    -      -       -      -
    560A  VAL*     3.0    48.8    +      -       +      +
    576A  ILE*     4.2    17.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 546 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458A  THR*     3.2     6.7    -      -       -      -
    459A  LYS*     2.9    67.1    +      -       +      +
    461A  THR*     3.5    24.7    -      -       +      -
    535A  SER      4.9     0.9    -      -       -      +
    536A  TYR      4.7     0.2    -      -       -      -
    537A  CYS      4.2    15.9    -      -       -      +
    542A  GLY      4.2     0.2    -      -       -      +
    545A  GLU*     1.3    80.9    -      -       -      +
    547A  LEU*     1.3    63.8    +      -       -      +
    548A  MET*     3.8     0.7    +      -       +      +
    557A  CYS*     3.8    23.8    -      -       +      -
    558A  PHE      3.5     4.5    -      -       -      +
    559A  CYS*     3.8    21.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 547 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456A  ALA*     4.3     5.6    -      -       +      -
    457A  ARG      3.6     3.6    -      -       -      -
    458A  THR*     3.8    11.9    -      -       +      -
    546A  VAL*     1.3    73.4    -      -       -      +
    548A  MET*     1.3    62.7    +      -       -      +
    549A  CYS      4.1     0.2    +      -       -      -
    556A  ARG      4.0     0.2    -      -       -      +
    557A  CYS*     3.1     6.4    -      -       -      -
    558A  PHE      2.7    40.6    +      -       -      +
    559A  CYS      5.3     1.3    -      -       -      -
    560A  VAL*     5.0     8.7    -      -       +      -
    563A  VAL*     4.4    14.4    -      -       +      -
    572A  ALA*     4.0    18.8    -      -       +      +
    575A  ALA*     3.5    32.8    -      -       +      -
    576A  ILE*     3.5    32.1    -      -       +      +
    581A  TRP*     4.0    24.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 548 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456A  ALA*     4.1     5.5    -      -       -      +
    457A  ARG*     2.8    59.9    +      -       +      +
    458A  THR*     3.0    48.0    -      -       -      +
    459A  LYS*     3.3    24.5    -      -       +      +
    531A  ASP*     4.0     6.7    -      -       -      +
    533A  TYR*     3.9    18.6    -      -       +      -
    546A  VAL      4.5     2.2    -      -       -      +
    547A  LEU*     1.3    72.5    -      -       -      +
    549A  CYS*     1.3    64.9    +      -       -      +
    550A  GLY*     3.5     1.6    +      -       -      -
    556A  ARG      3.7     3.8    -      -       -      -
    557A  CYS*     3.7    21.1    -      -       -      -
    581A  TRP*     3.5    13.5    -      -       -      -
----------------------------------------------------------
 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