Contacts of the strand formed by residues 120 - 128 (chain A) in PDB entry 1QST


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 PHE 120 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  TYR*     2.9    53.8    +      +       +      +
    118A  GLN*     3.3    35.2    -      -       +      -
    119A  ARG*     1.3    80.2    -      -       -      +
    121A  ALA*     1.3    61.6    +      -       -      +
    154A  ILE*     3.8     4.7    -      -       -      +
    156A  TYR*     3.1    26.9    -      -       +      +
    158A  LEU*     4.8     2.0    -      -       +      -
    180A  MET*     3.9    20.6    -      -       +      -
    184A  LYS*     3.5    25.8    -      -       +      +
    185A  TRP*     3.7    21.1    -      -       +      -
    188A  TYR*     3.7    17.0    -      +       +      -
    189A  ILE*     3.8    22.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  PHE*     5.0     3.6    -      -       +      -
    113A  ARG      3.4    13.0    -      -       -      +
    114A  GLN*     4.0    11.2    -      -       +      -
    115A  TYR*     4.5     0.2    -      -       -      -
    120A  PHE*     1.3    77.7    -      -       -      +
    122A  GLU*     1.3    63.2    +      -       -      +
    123A  VAL      4.1     0.3    +      -       -      -
    145A  PHE*     5.2     0.9    -      -       +      -
    149A  MET*     3.9    27.6    -      -       -      -
    154A  ILE*     4.1     2.2    -      -       +      -
    156A  TYR      2.8     6.3    +      -       -      -
    157A  LEU*     3.3    13.6    -      -       +      +
    158A  LEU*     2.8    26.0    +      -       -      +
    189A  ILE*     4.7     5.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  PHE*     3.2     6.1    -      -       -      +
    113A  ARG*     2.9    41.5    +      -       +      +
    115A  TYR*     4.4     9.7    +      -       +      -
    121A  ALA*     1.3    74.1    -      -       -      +
    123A  VAL*     1.3    73.1    +      -       -      +
    124A  ALA*     3.4     9.3    +      -       +      +
    158A  LEU*     3.2    14.6    -      -       +      +
    159A  THR*     4.7     1.6    -      -       -      -
    160A  TYR*     4.3    17.0    +      -       +      +
    189A  ILE*     3.7    45.0    -      -       +      +
    190A  LYS      4.8     1.6    +      -       -      -
    192A  TYR*     5.8     1.7    -      -       -      -
    197A  LEU*     6.1     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  ILE*     4.0    13.5    -      -       +      -
    111A  CYS      3.8     2.9    -      -       -      -
    112A  PHE*     4.3     1.1    -      -       -      -
    122A  GLU*     1.3    75.3    -      -       -      +
    124A  ALA*     1.3    61.5    +      -       -      +
    125A  PHE      4.0    18.6    -      -       -      +
    126A  LEU*     4.2    18.4    -      -       +      -
    142A  MET*     5.4     3.4    -      -       +      -
    145A  PHE*     3.9    28.9    -      -       +      -
    157A  LEU*     4.9     7.2    -      -       +      -
    158A  LEU      2.8    12.0    +      -       -      +
    159A  THR*     2.8    42.1    +      -       -      +
    160A  TYR      4.7     0.9    +      -       -      -
    169A  PHE*     4.7     4.3    -      -       +      -
    174A  PHE*     4.8    15.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  MET*     5.2     1.9    -      -       -      +
     88A  LEU*     4.3     8.1    -      -       +      -
     94A  HIS*     4.1    26.5    -      -       +      +
    111A  CYS      2.8    15.4    +      -       -      +
    122A  GLU*     3.4    16.1    +      -       -      +
    123A  VAL*     1.3    75.5    -      -       -      +
    125A  PHE*     1.3    87.7    +      -       +      +
    159A  THR*     5.1     0.7    +      -       -      -
    160A  TYR      5.7     1.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  PHE*     3.7    35.9    -      +       +      -
     77A  LEU*     3.8    20.0    -      -       +      -
     80A  MET*     3.8    32.8    -      -       +      -
     84A  TYR*     4.3     6.7    -      +       -      -
     85A  ILE*     3.9    31.0    -      -       +      -
     88A  LEU*     3.6    43.7    -      -       +      -
     89A  VAL*     4.5     1.1    -      -       +      -
    110A  ILE*     3.3     4.9    -      -       -      +
    111A  CYS*     2.7    48.3    +      -       +      +
    123A  VAL*     4.0     3.5    -      -       -      +
    124A  ALA*     1.3    93.5    -      -       +      +
    126A  LEU*     1.3    61.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  PHE*     3.8     1.8    -      -       -      -
     77A  LEU*     4.7     4.2    -      -       -      +
    109A  GLY      3.4     6.1    -      -       -      +
    110A  ILE*     3.6    26.2    -      -       +      -
    123A  VAL*     4.2    10.5    -      -       +      +
    125A  PHE*     1.3    76.8    -      -       -      +
    127A  ALA*     1.3    70.6    -      -       -      +
    128A  VAL*     5.6     1.6    -      -       +      -
    138A  GLY*     6.1     0.2    -      -       -      -
    141A  LEU*     4.6     5.4    -      -       +      -
    142A  MET*     3.5    32.1    -      -       +      -
    168A  TYR*     3.5    32.1    -      -       +      +
    169A  PHE*     3.9    13.7    -      -       +      -
    401A  EPE      3.2    45.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  ILE*     4.3     7.3    -      -       +      +
     73A  PHE*     3.8    17.8    -      -       +      -
     76A  GLN*     3.7    31.2    -      -       +      +
     77A  LEU*     5.5     1.3    -      -       +      -
    108A  GLY*     3.1     3.0    -      -       -      -
    109A  GLY      2.9    33.5    +      -       -      +
    126A  LEU*     1.3    84.5    -      -       -      +
    128A  VAL*     1.3    66.2    +      -       -      +
    141A  LEU*     4.7     1.0    -      -       -      +
    401A  EPE      4.6     7.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  ILE*     4.4     0.9    -      -       -      -
     76A  GLN*     3.5    11.2    -      -       -      +
     99A  ILE*     4.4    12.6    -      -       +      -
    107A  ILE      3.5    13.0    -      -       -      +
    126A  LEU*     5.6     1.3    -      -       +      -
    127A  ALA*     1.3    79.6    -      -       -      +
    129A  THR*     1.3    73.9    +      -       -      +
    130A  ALA      3.4     0.5    +      -       -      -
    132A  GLU*     3.6    28.9    -      -       +      +
    133A  GLN*     3.1    19.6    -      -       +      +
    137A  TYR*     4.6     8.1    -      -       +      -
    138A  GLY*     4.1    19.3    -      -       -      +
    141A  LEU*     5.2     3.1    -      -       +      -
    401A  EPE      3.4    34.8    -      -       +      +
----------------------------------------------------------
 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