Contacts of the strand formed by residues 106 - 111 (chain A) in PDB entry 1Q62


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 LEU 106 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  LYS*     4.7     7.6    -      -       +      +
     95A  LEU*     4.0    33.4    +      -       +      +
     96A  GLN*     3.9    32.4    -      -       +      +
    104A  VAL      3.6     3.8    +      -       -      -
    105A  LYS*     1.3    73.5    -      -       -      +
    107A  GLU*     1.3    62.6    +      -       -      +
    108A  PHE      3.4    22.0    -      -       -      +
    109A  SER*     4.2    19.1    -      -       -      +
    118A  MET*     3.6    25.6    -      -       +      -
    119A  VAL      3.4     8.3    -      -       -      +
    120A  MET*     3.8    11.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  THR*     4.3     3.6    +      -       -      +
     69A  TYR*     3.7    34.3    +      -       +      -
    105A  LYS*     4.2    35.5    +      -       -      +
    106A  LEU*     1.3    77.6    -      -       -      +
    108A  PHE*     1.3    95.2    +      -       +      +
    119A  VAL      2.8    12.1    +      -       -      +
    121A  GLU*     4.5     6.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  THR*     3.3    32.5    -      -       -      +
     38A  ALA*     3.8    18.8    -      -       +      -
     42A  GLN*     6.0     0.2    -      -       -      -
     43A  PHE*     3.8    13.5    -      +       -      -
     62A  HIS*     4.1    22.9    -      +       -      -
     69A  TYR*     3.8    27.1    -      +       -      -
    106A  LEU*     3.4    11.5    -      -       -      +
    107A  GLU*     1.3   104.6    -      -       +      +
    109A  SER*     1.3    59.3    +      -       -      +
    110A  PHE*     4.7     0.2    -      -       +      -
    119A  VAL*     2.8    50.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  ALA      4.4     4.7    +      -       -      -
     35A  GLN*     4.7     2.3    -      -       -      -
     36A  ASN      3.4     4.3    +      -       -      -
     37A  THR*     3.3    23.0    +      -       -      +
     92A  LYS*     3.4    28.5    -      -       -      -
    106A  LEU*     4.2    15.4    -      -       -      +
    108A  PHE*     1.3    75.8    -      -       -      +
    110A  PHE*     1.3    69.8    +      -       -      +
    117A  TYR      3.2    14.4    -      -       -      -
    118A  MET*     4.4     2.5    -      -       -      -
    350A  PHE*     4.2    11.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  ASN*     3.9    18.2    -      -       -      +
     38A  ALA*     3.2    48.5    -      -       +      +
     39A  HIS*     3.8    14.6    -      +       -      -
     40A  LEU*     3.6    19.3    -      -       +      -
     43A  PHE*     3.9     8.1    -      +       -      -
     71A  MET*     3.7    17.9    -      -       +      -
    109A  SER*     1.3    79.6    -      -       -      +
    111A  LYS*     1.3    65.6    +      -       -      +
    112A  ASP*     5.9     0.7    -      -       +      -
    117A  TYR*     2.7    72.2    +      +       +      +
    119A  VAL*     4.0    12.1    -      -       +      -
    350A  PHE*     3.6     8.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  GLN*     4.8     1.7    -      -       -      +
     36A  ASN*     5.3     6.2    +      -       +      +
     76A  LYS*     5.0     6.7    -      -       -      +
    110A  PHE*     1.3    84.0    -      -       -      +
    112A  ASP*     1.3    66.4    +      -       -      +
    115A  ASN      3.2    13.5    -      -       -      +
    116A  LEU*     3.8    15.7    -      -       +      -
    117A  TYR*     4.2     3.6    -      -       -      -
    344A  GLY      5.2     0.8    +      -       -      -
    347A  PHE*     2.8    31.9    +      -       +      +
    348A  SER*     3.0    24.7    +      -       -      +
    350A  PHE*     3.2    24.9    +      -       +      +
----------------------------------------------------------
 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