Contacts of the strand formed by residues 142 - 147 (chain A) in PDB entry 1QIB


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 ILE 142 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  TRP*     4.8     3.6    -      -       +      -
     97A  ILE*     4.1    21.3    -      -       +      -
     98A  THR      3.1    11.5    +      -       -      +
     99A  TYR*     3.3     8.1    -      -       +      +
    100A  ARG      3.1    24.9    +      -       -      +
    121A  PHE*     4.4    22.7    -      -       +      -
    132A  PHE*     5.4     0.2    -      -       +      -
    140A  ALA*     4.1     0.8    -      -       -      +
    141A  ASP*     1.3    82.2    -      -       +      +
    143A  MET*     1.3    62.4    -      -       -      +
    144A  ILE*     3.6    23.7    +      -       +      +
    176A  GLY*     3.2    27.4    -      -       -      +
    177A  ASP*     4.4     0.4    -      -       -      -
    178A  SER*     4.1     6.3    -      -       -      +
    203A  PHE*     4.9     1.6    -      -       +      -
    206A  ALA*     4.1    19.5    -      -       +      +
    207A  MET*     4.5    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 143 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  ARG*     3.8    11.4    -      -       -      +
    102A  ILE*     3.7    39.7    -      -       +      -
    138A  GLY      4.8     2.5    -      -       -      +
    139A  GLU*     4.0    25.8    -      -       +      +
    140A  ALA*     3.4    40.6    -      -       -      +
    142A  ILE*     1.3    71.6    -      -       -      +
    144A  ILE*     1.3    61.3    +      -       -      +
    145A  ASN*     5.4     0.7    -      -       +      -
    177A  ASP*     3.5    31.6    +      -       -      +
    178A  SER      3.2    23.2    +      -       -      +
    179A  HIS*     4.5     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 144 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  TYR*     4.8     7.0    -      -       +      -
    100A  ARG      3.0    20.8    +      -       -      +
    101A  ILE*     4.0    16.6    -      -       +      -
    102A  ILE*     3.2    26.6    +      -       -      +
    103A  GLY      3.6     3.6    +      -       -      -
    117A  PHE*     3.6    38.1    -      -       +      -
    121A  PHE*     5.0     3.6    -      -       +      -
    142A  ILE*     3.6    30.1    -      -       +      +
    143A  MET*     1.3    72.8    -      -       -      +
    145A  ASN*     1.3    67.5    +      -       -      +
    146A  PHE*     5.2     1.8    -      -       +      -
    178A  SER*     3.6     6.5    -      -       -      -
    180A  PHE*     4.1    10.5    -      -       +      -
    203A  PHE*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 145 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  ILE*     3.4    21.4    +      -       -      +
    103A  GLY*     3.4    18.4    -      -       -      -
    143A  MET*     5.2     0.7    -      -       +      +
    144A  ILE*     1.3    76.5    -      -       -      +
    146A  PHE*     1.3    81.3    +      -       -      +
    178A  SER      3.1     7.7    +      -       -      -
    179A  HIS*     3.4    23.9    +      -       +      +
    180A  PHE*     2.8    36.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  GLY      3.4    24.9    -      -       -      -
    104A  TYR*     3.7    15.0    -      -       -      +
    105A  THR*     3.8    35.9    -      -       +      -
    113A  VAL*     4.9     2.2    -      -       +      -
    117A  PHE*     4.0    31.9    -      +       -      -
    144A  ILE*     5.2     0.9    -      -       +      -
    145A  ASN*     1.3    93.4    +      -       -      +
    147A  GLY*     1.3    58.5    +      -       -      +
    151A  HIS*     5.6     3.4    -      -       -      +
    157A  PHE*     5.6     0.2    -      -       -      -
    179A  HIS*     5.8     0.7    -      -       -      -
    180A  PHE*     3.1    34.3    -      +       +      +
    182A  ASP*     3.7    24.2    -      -       -      +
    186A  TRP*     4.0    15.9    -      +       -      -
    195A  LEU*     4.5     9.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  PHE*     1.3    75.9    -      -       -      +
    148A  ARG*     1.3    60.8    +      -       -      -
    151A  HIS*     4.5    15.7    -      -       -      -
    157A  PHE*     3.5    11.3    -      -       -      -
    180A  PHE      2.9     7.5    +      -       -      -
    181A  ASP*     3.2     9.5    -      -       -      +
    182A  ASP*     2.8    28.3    +      -       -      +
----------------------------------------------------------
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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