Contacts of the strand formed by residues 108 - 114 (chain W) in PDB entry 5A0Q


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 PRO 108 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7W  VAL*     4.3    17.5    -      -       +      -
      8W  TYR      4.8     1.1    -      -       -      +
      9W  LYS      4.9     5.4    -      -       -      +
     10W  ASP      4.8     3.8    -      -       -      +
     11W  GLY*     3.8    22.4    -      -       -      +
     12W  ILE*     3.5    19.3    -      -       +      -
    102W  GLY      3.6     8.1    -      -       -      +
    103W  VAL*     3.7    10.3    -      -       +      -
    107W  GLY*     1.3    85.6    -      -       -      +
    109W  HIS*     1.3    71.9    +      -       -      +
    121W  LYS*     3.6    11.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 109 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7W  VAL*     4.7     0.4    -      -       -      -
     12W  ILE*     3.5     3.8    -      -       -      +
     76W  VAL*     3.3    30.3    -      -       +      +
     77W  VAL*     4.0    17.8    -      -       +      +
    101W  GLY*     3.4     2.3    -      -       -      -
    102W  GLY      3.0    30.4    +      -       -      +
    106W  THR*     3.3    35.8    +      -       -      -
    107W  GLY      3.3     8.7    +      -       -      -
    108W  PRO*     1.3    85.8    +      -       -      +
    110W  LEU*     1.3    60.9    +      -       -      +
    111W  TYR*     3.5    28.7    -      +       +      -
    121W  LYS*     3.8    22.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 110 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5W  GLY*     3.5    30.5    -      -       -      +
      6W  VAL*     3.6    15.9    -      -       -      +
      7W  VAL*     3.4    15.4    -      -       +      +
     12W  ILE*     3.8     7.6    -      -       +      -
     14W  LEU*     3.7    19.5    -      -       +      -
     99W  VAL*     3.4    32.8    -      -       +      -
    100W  LEU      3.3    10.5    -      -       -      +
    101W  GLY*     4.2     0.2    -      -       -      -
    109W  HIS*     1.3    75.5    -      -       -      +
    111W  TYR*     1.3    59.2    +      -       -      +
    112W  SER      4.0     0.3    +      -       -      -
    120W  ASP      4.0     0.3    -      -       -      +
    121W  LYS*     3.2    22.1    -      -       -      +
    122W  LEU      3.3    23.7    +      -       -      +
    123W  PRO      3.9     1.1    -      -       -      +
    125W  VAL*     4.1    11.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 111 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76W  VAL*     4.8     0.2    -      -       +      -
     77W  VAL*     3.6    23.2    -      -       +      +
     80W  ASN*     2.5    49.6    -      -       +      +
     99W  VAL*     4.6     2.7    -      -       -      -
    100W  LEU      2.9    31.3    +      -       -      -
    109W  HIS*     3.5    25.5    -      +       +      -
    110W  LEU*     1.3    77.5    -      -       -      +
    112W  SER*     1.4    67.0    +      -       -      +
    113W  ILE*     3.4     7.8    -      -       +      +
    119W  THR*     3.7    20.9    -      -       -      -
    120W  ASP*     3.5     8.5    -      -       -      +
    121W  LYS*     3.1    34.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 112 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98W  LEU      3.9     4.0    -      -       -      -
     99W  VAL*     4.5     1.6    -      -       -      +
    110W  LEU      4.0     1.8    +      -       -      -
    111W  TYR*     1.4    71.5    -      -       -      +
    113W  ILE*     1.3    59.0    +      -       -      +
    114W  TYR*     3.6    29.2    +      -       -      -
    118W  SER      3.5     1.4    -      -       -      +
    119W  THR*     3.5     2.3    -      -       -      -
    120W  ASP*     3.1    32.9    +      -       -      +
    125W  VAL*     3.8    35.0    -      -       -      +
    126W  THR      4.2     5.8    +      -       -      -
    127W  MET*     3.3    18.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 113 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80W  ASN*     3.6    16.8    -      -       -      +
     83W  LEU*     3.5    43.5    -      -       +      +
     84W  LYS*     4.9     0.2    -      -       -      -
     87W  LEU*     3.5    22.5    -      -       +      +
     97W  ALA*     3.4     4.3    -      -       -      +
     98W  LEU*     2.9    38.8    +      -       +      +
    100W  LEU*     4.3     4.7    -      -       +      -
    111W  TYR      3.4    13.9    -      -       -      +
    112W  SER*     1.3    79.9    +      -       -      +
    114W  TYR*     1.3    65.2    +      -       -      +
    117W  GLY*     4.7     2.2    -      -       -      -
    118W  SER      3.0    17.7    -      -       -      +
    119W  THR*     3.5    19.3    -      -       +      -
    127W  MET*     3.5     1.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 114 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22V  THR*     5.6     4.9    -      -       +      -
     25V  TYR*     5.5     3.1    -      -       -      -
     27V  ALA*     3.7    28.6    -      -       +      +
    300V  KNM      4.0    36.8    -      -       +      -
     87W  LEU*     3.9     2.1    -      -       -      +
     97W  ALA*     4.2     1.1    -      -       +      -
    112W  SER*     3.6    30.2    +      -       -      -
    113W  ILE*     1.3    78.8    -      -       -      +
    115W  PRO*     1.3    71.1    -      -       +      +
    116W  HIS      3.1     3.8    -      -       -      +
    117W  GLY*     2.9    21.5    +      -       -      -
    118W  SER*     3.2    23.0    +      -       -      -
    120W  ASP*     5.1    10.5    -      -       +      -
    126W  THR      4.5     7.6    +      -       -      -
    127W  MET*     4.6    16.4    -      -       +      -
    135W  MET*     5.0     8.3    -      -       -      +
----------------------------------------------------------
 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