Contacts of the strand formed by residues 557 - 565 (chain B) in PDB entry 2PMW


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 557 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533B  ASN      4.8     3.2    +      -       -      -
    535B  SER*     5.3     2.9    -      -       -      -
    552B  CYS*     4.3    13.2    -      -       +      +
    554B  GLN*     2.9    57.3    +      -       +      +
    555B  GLN      3.3     7.0    +      -       -      -
    556B  GLY*     1.3    84.3    +      -       -      +
    558B  VAL*     1.3    63.6    +      -       -      +
    586B  ASN*     2.9    23.6    +      -       -      -
    600B  CYS*     4.7     8.1    -      -       +      -
    601B  CYS*     3.2    11.4    -      -       -      +
    602B  HIS*     3.3    43.2    -      +       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 558 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552B  CYS*     4.1     3.6    -      -       -      -
    556B  GLY      4.7     6.3    -      -       -      +
    557B  HIS*     1.3    77.6    -      -       -      +
    559B  LEU*     1.3    60.3    +      -       -      +
    560B  THR*     3.7    12.4    +      -       +      +
    586B  ASN*     3.9     5.6    -      -       -      +
    600B  CYS*     3.5     2.4    -      -       -      -
    601B  CYS*     2.9    40.4    +      -       +      +
    603B  ALA*     5.2     6.3    -      -       +      +
    606B  LEU*     4.5    27.4    -      -       +      +
    607B  GLU*     5.6     0.2    -      -       -      -
    608B  CYS*     3.9    34.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 559 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    552B  CYS*     3.8     9.7    -      -       -      -
    558B  VAL*     1.3    72.7    -      -       -      +
    560B  THR*     1.3    60.1    +      -       -      +
    561B  GLY      3.4    20.9    -      -       -      +
    562B  CYS*     3.9     5.2    -      -       -      -
    586B  ASN*     3.4    36.3    +      -       -      +
    587B  GLN      3.8    16.6    -      -       -      +
    588B  CYS*     3.6    17.9    -      -       -      -
    598B  ALA*     3.4    23.3    -      -       +      -
    599B  SER      3.3    17.7    -      -       -      +
    608B  CYS*     4.4     9.7    -      -       -      +
    610B  VAL*     5.9     5.6    -      -       +      -
    677B  ILE*     3.6    24.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 560 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484B  LEU*     2.7    45.1    +      -       +      +
    558B  VAL*     4.0    22.7    -      -       +      +
    559B  LEU*     1.3    78.5    -      -       -      +
    561B  GLY*     1.3    58.1    +      -       -      +
    599B  SER*     3.1    18.8    +      -       -      -
    601B  CYS*     4.1    16.7    -      -       +      -
    606B  LEU*     5.2     3.8    -      -       +      -
    633B  THR*     2.7    40.5    +      -       -      +
    634B  GLY*     3.5     2.8    -      -       -      -
    677B  ILE*     3.6     7.7    -      -       -      +
    679B  CYS*     4.7     8.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 561 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    484B  LEU      3.3    10.3    +      -       -      -
    485B  SER*     3.8    11.9    -      -       -      -
    500B  MET*     4.2     2.6    -      -       -      +
    559B  LEU*     3.4     8.9    -      -       -      +
    560B  THR*     1.3    84.9    +      -       -      +
    562B  CYS*     1.3    65.2    +      -       -      -
    597B  HIS      3.9     0.2    -      -       -      +
    598B  ALA*     3.5     0.5    -      -       -      -
    599B  SER*     2.9    28.1    +      -       -      -
    634B  GLY*     4.6     1.3    -      -       -      -
    677B  ILE*     3.6     9.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 562 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    485B  SER*     5.0     1.4    -      -       -      -
    486B  CYS      3.8     8.7    +      -       -      +
    498B  GLU*     4.6     0.3    -      -       -      +
    559B  LEU*     3.9    11.4    -      -       -      -
    561B  GLY*     1.3    76.4    -      -       -      -
    563B  SER*     1.3    67.3    +      -       -      +
    587B  GLN      4.4     1.1    -      -       -      -
    588B  CYS*     2.0    52.3    -      -       +      -
    589B  VAL      5.1     1.6    -      -       -      +
    596B  ILE*     5.0     2.9    -      -       +      -
    597B  HIS      3.4     4.3    -      -       -      -
    634B  GLY*     5.7     0.6    -      -       -      -
    635B  CYS      5.1     1.9    -      -       -      +
    636B  SER*     4.4    28.1    +      -       -      +
    677B  ILE*     4.3     8.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 563 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    486B  CYS*     2.7    34.2    +      -       -      +
    498B  GLU*     3.3    24.5    -      -       -      -
    499B  ARG*     4.6     2.7    -      -       -      -
    500B  MET*     3.5    16.4    -      -       -      +
    562B  CYS*     1.3    73.0    +      -       -      +
    564B  SER*     1.3    62.1    +      -       -      +
    596B  ILE*     3.2    10.9    -      -       -      +
    597B  HIS*     2.9    38.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 564 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    497B  GLY*     3.2     6.8    -      -       -      -
    498B  GLU*     2.7    41.8    +      -       -      +
    563B  SER*     1.3    77.7    -      -       -      +
    565B  HIS*     1.3    54.1    +      -       -      +
    566B  TRP*     4.0    12.2    -      -       -      -
    590B  GLY*     4.9     6.2    -      -       -      -
    591B  HIS      5.1     0.9    +      -       -      -
    594B  ALA*     3.3    17.5    -      -       -      +
    595B  SER      3.0    18.9    +      -       -      -
    596B  ILE*     4.3     9.1    -      -       -      +
    597B  HIS*     4.0     1.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 565 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496B  ARG*     3.1    17.5    -      -       -      +
    497B  GLY      4.1     0.7    -      -       -      -
    498B  GLU      3.6    15.9    -      -       -      +
    499B  ARG*     3.7    32.0    +      -       +      +
    512B  HIS*     4.2    19.1    -      +       +      -
    564B  SER*     1.3    77.0    +      -       -      +
    566B  TRP*     1.3    69.9    +      -       -      +
    567B  GLU*     4.0    20.4    +      -       -      -
    595B  SER*     3.0    48.0    +      -       -      -
    597B  HIS*     2.8    34.3    +      +       -      -
----------------------------------------------------------
 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