Contacts of the strand formed by residues 44 - 53 (chain A) in PDB entry 1WSQ


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 GLN 44 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLY*     3.4     1.4    -      -       -      -
     41A  ILE*     2.7    49.6    +      -       +      +
     43A  ARG*     1.3   107.6    -      -       -      +
     45A  GLN*     1.3    62.0    +      -       -      +
     46A  VAL*     5.2     3.4    -      -       +      -
     66A  SER*     5.2     1.2    +      -       -      -
    108A  ASP*     4.9     7.6    -      -       -      +
    140B  GLN*     3.0    26.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  VAL*     3.6    26.2    -      -       +      +
     39A  PHE      3.3     4.3    -      -       -      +
     40A  GLY*     4.7     5.8    -      -       -      -
     43A  ARG      4.4     4.5    -      -       -      +
     44A  GLN*     1.3    76.3    -      -       -      +
     46A  VAL*     1.3    65.6    +      -       -      +
     47A  THR*     5.5     0.2    -      -       -      -
     65A  THR*     4.0     1.0    -      -       -      -
     66A  SER*     3.9    17.6    +      -       -      -
    131B  GLY      4.6     7.9    +      -       -      -
    132B  GLY*     5.9     0.2    -      -       -      -
    133B  GLN      4.8     0.6    +      -       -      -
    136B  ASN*     3.3    46.2    +      -       +      +
    137B  LEU*     3.1    31.5    -      -       -      +
    140B  GLN*     2.8    25.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ARG      3.7     0.7    -      -       -      +
     38A  VAL*     3.1     5.5    -      -       -      -
     39A  PHE*     2.8    54.1    +      -       +      +
     41A  ILE*     4.4    19.3    -      -       +      -
     44A  GLN*     4.9     4.0    -      -       +      +
     45A  GLN*     1.3    80.0    -      -       -      +
     47A  THR*     1.3    63.5    +      -       -      +
     63A  VAL*     3.9    21.8    -      -       +      -
     64A  ARG      3.4     7.2    -      -       -      +
     65A  THR*     4.2    23.8    -      -       +      -
     73A  LEU*     4.1    13.7    -      -       +      -
    125A  LEU*     4.3    15.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  GLY*     4.2    15.5    -      -       -      +
     37A  ARG      3.4     7.9    -      -       -      +
     38A  VAL*     3.6    16.1    -      -       +      +
     45A  GLN*     5.5     0.3    -      -       -      +
     46A  VAL*     1.3    74.9    -      -       -      +
     48A  VAL*     1.3    72.9    +      -       -      +
     49A  ASP*     3.4     9.9    +      -       -      +
     63A  VAL*     3.0     7.0    -      -       -      -
     64A  ARG*     3.0    45.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  TYR*     3.3    29.8    -      -       +      +
     35A  ILE*     3.8     4.5    -      -       +      +
     36A  GLY*     2.8    27.2    +      -       -      -
     37A  ARG      2.8    19.2    +      -       -      +
     39A  PHE*     3.6    31.4    -      -       +      -
     47A  THR*     1.3    72.6    -      -       -      +
     49A  ASP*     1.3    65.4    +      -       -      +
     50A  GLU      3.7    15.9    -      -       -      +
     51A  VAL      4.8     0.2    -      -       -      +
     61A  PHE*     3.6    33.2    -      -       +      -
     62A  LEU      3.7     4.0    -      -       -      +
     63A  VAL*     4.0     6.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ILE*     3.9    22.9    -      -       -      +
     47A  THR*     3.4     6.6    +      -       -      +
     48A  VAL*     1.3    79.1    -      -       -      +
     50A  GLU*     1.3    68.4    +      -       +      +
     62A  LEU*     2.8    29.8    +      -       +      +
     63A  VAL      4.7     0.5    -      -       -      -
     64A  ARG*     2.5    63.1    +      -       -      +
     70A  LYS*     4.5     5.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  ILE*     4.8     6.5    -      -       +      -
     48A  VAL*     3.7     8.1    -      -       -      +
     49A  ASP*     1.3    88.3    -      -       +      +
     51A  VAL*     1.3    66.7    +      -       -      +
     52A  LEU*     4.8     9.7    -      -       +      +
     61A  PHE*     3.5     3.8    -      -       -      -
     62A  LEU*     2.9    55.7    +      -       +      +
    128A  PHE*     6.1     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  LEU*     3.7    53.4    -      -       +      +
     31A  GLY*     4.6     5.8    -      -       -      +
     34A  TYR*     4.2     4.5    -      -       +      -
     35A  ILE*     5.2     3.4    -      -       +      +
     48A  VAL*     5.1     1.1    -      -       +      -
     50A  GLU*     1.3    75.9    -      -       -      +
     52A  LEU*     1.3    64.5    +      -       -      +
     53A  ALA*     4.2     7.6    -      -       -      +
     59A  ILE*     3.7    26.9    -      -       +      -
     60A  VAL      4.0     2.7    -      -       -      +
     61A  PHE*     3.8    20.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLU*     4.8    11.4    -      -       +      +
     51A  VAL*     1.3    76.4    -      -       -      +
     53A  ALA*     1.3    61.0    +      -       -      +
     60A  VAL*     2.7    25.6    +      -       +      +
     61A  PHE      3.8     8.1    -      -       -      +
     62A  LEU*     3.7    31.6    -      -       +      +
     72A  ALA*     4.3     4.3    -      -       +      -
    128A  PHE*     3.9    32.3    -      -       +      -
    133A  GLN*     5.1     1.6    +      -       -      -
    405A  KSA      3.9    51.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  LEU*     5.7     0.2    -      -       -      -
     51A  VAL*     3.7     5.1    -      -       -      -
     52A  LEU*     1.3    82.4    -      -       -      +
     54A  GLU*     1.3    61.2    +      -       -      +
     55A  GLY      3.8     1.7    +      -       -      +
     59A  ILE*     3.5     4.6    -      -       -      +
     60A  VAL*     2.8    28.5    +      -       -      +
    133A  GLN*     4.5     4.5    -      -       -      +
    405A  KSA      3.3    48.0    -      -       +      +
----------------------------------------------------------
 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