Contacts of the strand formed by residues 203 - 208 (chain A) in PDB entry 1Q6X


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 GLN 203 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  VAL      3.5     1.4    -      -       -      +
    199A  ALA*     3.3     5.9    -      -       -      -
    200A  CYS      2.8    36.8    +      -       -      +
    201A  CYS*     3.4    23.6    +      -       +      +
    202A  ASN*     1.3    86.5    +      -       -      +
    204A  PHE*     1.3    61.2    +      -       -      +
    205A  PHE*     3.7    19.5    -      -       +      -
    232A  ALA*     4.5     5.8    -      -       +      +
    238A  ARG*     3.5    12.8    -      -       +      +
    239A  LEU*     2.9    53.3    +      -       -      +
    240A  PRO      4.8     0.2    +      -       -      -
    374A  ARG*     3.0    33.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  ILE*     3.8    21.1    -      -       +      -
    198A  VAL      3.5     1.6    -      -       -      -
    199A  ALA*     3.8    24.5    -      -       +      -
    202A  ASN      3.7    16.8    -      -       -      -
    203A  GLN*     1.3    72.7    -      -       -      +
    205A  PHE*     1.3    63.6    +      -       -      +
    242A  ILE      4.9     2.9    -      -       -      -
    243A  GLY*     3.9    20.2    -      -       -      -
    273A  ILE*     4.8     4.0    -      -       +      -
    279A  LEU*     4.5     6.5    -      -       +      -
    310A  ALA      4.2     7.6    -      -       -      -
    311A  ASN      5.1     0.2    -      -       -      -
    312A  ARG      3.4    29.6    -      -       -      -
    313A  TRP*     3.7    19.1    -      +       +      -
    374A  ARG*     3.6     6.1    -      -       -      +
    375A  LEU*     2.9    49.7    +      -       +      +
    377A  TRP*     4.4    22.8    -      +       -      +
----------------------------------------------------------
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Residues in contact with PHE 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  ILE*     3.4    10.3    -      -       -      -
    198A  VAL*     2.9    37.0    +      -       -      +
    200A  CYS*     5.2     0.9    -      -       +      -
    203A  GLN*     3.7    24.5    -      -       +      -
    204A  PHE*     1.3    79.1    -      -       -      +
    206A  VAL*     1.3    65.2    +      -       -      +
    207A  LEU      3.6     0.5    +      -       -      -
    228A  ILE*     3.8    40.6    -      -       +      -
    231A  MET*     3.9    27.1    -      -       +      -
    232A  ALA*     3.9    32.5    -      -       +      -
    372A  PRO*     4.1     8.3    -      -       +      -
    373A  ARG      3.3     6.7    -      -       -      +
    374A  ARG*     3.6    43.3    -      -       +      -
    375A  LEU*     4.7     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  HIS*     3.9    11.4    -      -       +      -
    196A  VAL      4.0     3.1    -      -       -      -
    197A  ILE*     4.3     8.3    -      -       +      -
    205A  PHE*     1.3    71.2    -      -       -      +
    207A  LEU*     1.3    60.8    +      -       -      +
    208A  ASP*     3.8    22.2    +      -       -      +
    272A  MET*     3.6    26.9    -      -       +      -
    372A  PRO*     3.4    10.8    -      -       -      +
    373A  ARG*     2.7    63.8    +      -       +      +
    375A  LEU*     3.6    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  ILE*     4.1    16.4    -      -       +      -
    195A  HIS*     3.3     3.6    -      -       -      +
    196A  VAL*     3.0    54.8    +      -       +      +
    198A  VAL*     4.0    20.4    -      -       +      -
    205A  PHE      3.6     0.2    +      -       -      -
    206A  VAL*     1.3    72.7    -      -       -      +
    208A  ASP*     1.3    74.4    +      -       -      +
    209A  VAL*     3.4     2.2    +      -       +      +
    216A  LEU*     4.7     0.2    -      -       +      -
    221A  LEU*     4.2    17.3    -      -       +      -
    224A  GLN*     3.5    36.1    -      -       +      +
    225A  LEU*     4.3    12.3    -      -       +      -
    228A  ILE*     4.7     4.9    -      -       +      -
    372A  PRO*     4.2    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  PRO*     3.9    20.6    -      -       +      +
    194A  GLU      3.5     6.7    -      -       -      +
    195A  HIS*     3.8     6.4    +      -       -      +
    206A  VAL*     3.8    21.2    +      -       -      +
    207A  LEU*     1.3    75.7    -      -       -      +
    209A  VAL*     1.3    61.6    +      -       -      +
    210A  VAL      3.4    13.2    -      -       -      +
    211A  ILE*     4.6    14.4    -      -       +      +
    216A  LEU*     3.2    24.4    -      -       -      +
    224A  GLN*     5.6     1.6    +      -       -      +
    272A  MET*     5.3     1.7    -      -       -      +
    370A  PRO*     6.2     0.2    -      -       -      +
    373A  ARG*     5.7     5.4    -      -       -      +
----------------------------------------------------------
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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