Contacts of the strand formed by residues 66 - 73 (chain A) in PDB entry 1Q9S


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 HIS 66 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  TRP*     3.4    10.8    -      -       -      -
     58A  ALA*     2.8    32.1    +      -       -      +
     59A  SER*     5.8     0.2    -      -       -      -
     64A  ASP*     3.6    41.3    +      -       +      +
     65A  VAL*     1.3    74.6    +      -       -      +
     67A  LYS*     1.3    64.9    +      -       -      +
     89A  ILE*     3.6    22.9    -      -       +      -
     90A  MET      4.4     3.5    +      -       -      +
     91A  HIS*     3.1    54.8    +      +       +      +
     93A  PHE*     4.6     7.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with LYS 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  GLY      3.6     5.8    -      -       -      -
     57A  TRP*     3.5    20.1    -      -       +      -
     66A  HIS*     1.3    80.4    -      -       -      +
     68A  MET*     1.3    62.3    +      -       -      +
     89A  ILE*     3.3     3.8    -      -       -      +
     90A  MET*     2.9    39.6    +      -       +      +
    134A  LYS*     2.7    49.5    +      -       +      +
    137A  LEU*     3.4    31.4    -      -       +      -
    138A  GLU*     3.5    27.4    +      -       -      -
    143A  LEU*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  TYR*     3.3     5.2    -      -       -      +
     56A  GLY*     2.8    46.1    +      -       -      +
     57A  TRP      3.4    28.7    -      -       -      +
     58A  ALA*     3.7     9.0    -      -       +      -
     67A  LYS*     1.3    78.2    -      -       -      +
     69A  VAL*     1.3    80.5    +      -       -      +
     70A  VAL*     4.0    18.6    -      -       +      -
     87A  THR*     3.7    12.6    -      -       +      -
     88A  HIS      3.2    15.5    -      -       -      +
     89A  ILE*     3.8     4.5    -      -       -      -
     90A  MET*     3.5     9.0    -      -       -      +
    104A  VAL*     3.7    24.7    -      -       +      -
    105A  ALA      3.7    16.8    -      -       -      +
    106A  ILE*     4.7     1.1    -      -       -      -
    137A  LEU*     4.2     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  TYR      3.2    13.5    -      -       -      +
     55A  TYR*     4.3     1.1    -      -       +      -
     68A  MET*     1.3    75.2    -      -       -      +
     70A  VAL*     1.3    59.2    +      -       -      +
     86A  GLU      4.0     0.2    -      -       -      +
     87A  THR*     3.5     2.1    -      -       -      +
     88A  HIS*     2.7    50.3    +      -       +      +
     90A  MET*     4.1     5.4    -      -       +      -
    110A  LEU*     4.3     4.9    -      -       +      -
    126A  ILE*     5.6     0.2    -      -       +      -
    129A  ASP*     3.9    15.3    -      -       +      +
    130A  ILE*     4.1    15.7    -      -       +      -
    133A  ALA*     3.5    32.3    -      -       +      -
    401A  FMN      3.3    27.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  GLY      3.9     0.9    -      -       -      +
     53A  ILE*     3.6     4.8    -      -       -      +
     54A  TYR*     2.8    55.1    +      -       +      +
     68A  MET*     4.0    20.0    -      -       +      -
     69A  VAL*     1.3    75.7    -      -       -      +
     71A  SER*     1.3    72.7    +      -       -      +
     72A  ILE*     4.2     3.3    +      -       +      -
     85A  MET*     3.9    23.3    -      -       +      -
     86A  GLU      3.1    14.1    -      -       -      +
     87A  THR*     3.5    18.4    -      -       -      +
    106A  ILE*     4.4    12.8    -      -       +      -
    401A  FMN      4.9     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  GLY      3.8     4.0    -      -       -      -
     53A  ILE*     3.7    12.8    -      -       -      -
     70A  VAL*     1.3    74.5    -      -       -      +
     72A  ILE*     1.3    62.0    +      -       -      +
     73A  GLY      4.1     0.7    -      -       -      -
     75A  ASN*     4.4     6.9    +      -       -      -
     84A  SER*     3.5     1.0    +      -       -      +
     85A  MET*     3.3     5.5    -      -       -      -
     86A  GLU*     2.8    51.6    +      -       -      +
    113A  GLU*     5.5     1.3    -      -       -      -
    401A  FMN      3.5    45.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  VAL*     5.4     0.2    -      -       +      -
     45A  LEU*     3.9    30.7    -      -       +      -
     49A  ILE*     4.0    16.6    -      -       +      +
     50A  SER      4.2    11.0    -      -       -      +
     51A  THR*     3.1    10.4    -      -       -      -
     52A  GLY*     2.8    42.4    +      -       -      +
     54A  TYR*     4.3     9.9    -      -       +      -
     70A  VAL*     4.4     4.7    -      -       +      -
     71A  SER*     1.3    77.4    -      -       -      +
     73A  GLY*     1.3    60.2    +      -       -      +
     83A  LYS*     4.3    15.5    -      -       +      +
     84A  SER      3.3     6.5    -      -       -      +
     85A  MET*     4.1    17.9    -      -       +      -
    106A  ILE*     4.0    26.7    -      -       +      -
    113A  GLU*     4.3     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  THR*     4.3     1.8    -      -       -      -
     71A  SER      4.1     0.8    -      -       -      -
     72A  ILE*     1.3    76.8    -      -       -      +
     74A  TRP*     1.3    68.1    +      -       -      -
     75A  ASN*     3.6     1.9    -      -       -      +
     82A  LYS      4.2     0.2    -      -       -      +
     83A  LYS*     3.3    13.3    -      -       -      +
     84A  SER*     2.7    43.8    +      -       -      -
    113A  GLU*     3.2    16.9    +      -       -      -
----------------------------------------------------------
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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