Contacts of the strand formed by residues 105 - 110 (chain A) in PDB entry 1DTQ


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 SER 105 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  LYS*     4.0     0.4    -      -       -      +
    104A  LYS*     1.3    80.9    -      -       -      +
    106A  VAL*     1.3    67.5    +      -       -      +
    107A  THR*     6.1     0.2    -      -       -      -
    190A  GLY*     3.2     0.7    -      -       -      -
    191A  SER      2.8    28.5    +      -       -      -
    193A  LEU      3.3    18.0    +      -       -      -
    195A  ILE*     4.7    10.0    +      -       -      -
    198A  HIS*     3.2    39.1    +      -       -      +
    236A  PRO*     5.2     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103A  LYS*     3.9    13.9    -      -       +      +
    105A  SER*     1.3    84.7    -      -       -      +
    107A  THR*     1.3    78.5    +      -       -      +
    188A  TYR*     5.3     2.0    -      -       +      -
    189A  VAL      3.1    11.4    -      -       -      +
    190A  GLY*     3.6    12.6    -      -       -      -
    198A  HIS*     4.1     0.9    -      -       -      -
    224A  GLU*     4.1     0.2    -      -       -      +
    225A  PRO*     3.3    23.4    -      -       +      +
    227A  PHE*     3.3    25.6    -      -       +      -
    236A  PRO*     5.0     7.2    -      -       +      +
    999A  FPT      3.8    46.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105A  SER*     6.1     0.2    -      -       -      -
    106A  VAL*     1.3    86.0    -      -       -      +
    108A  VAL*     1.3    60.3    +      -       -      +
    109A  LEU*     4.0     4.2    -      -       -      +
    187A  LEU      3.6     1.4    -      -       -      +
    189A  VAL*     2.9    29.0    +      -       -      +
    198A  HIS*     3.3    13.7    +      -       +      +
    202A  ILE*     2.8    35.7    -      -       +      +
    219A  LYS*     5.3     7.6    -      -       -      -
    222A  GLN*     4.2    18.4    -      -       -      +
    223A  LYS      3.8     8.1    -      -       -      +
    224A  GLU*     4.3    18.8    -      -       +      +
    227A  PHE*     4.0     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  THR*     1.3    72.8    -      -       -      +
    109A  LEU*     1.3    71.5    +      -       -      +
    110A  ASP*     4.3     3.5    +      -       -      +
    186A  ASP*     3.8    19.3    -      -       +      +
    187A  LEU      2.9    11.2    -      -       -      +
    188A  TYR*     3.7    42.8    -      -       +      -
    217A  PRO*     4.8     0.7    -      -       -      +
    222A  GLN*     4.7     2.9    +      -       -      +
    223A  LYS*     3.3    43.3    +      -       +      +
    227A  PHE*     3.4    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  THR*     4.0    12.6    -      -       -      +
    108A  VAL*     1.3    91.3    -      -       -      +
    110A  ASP*     1.3    62.7    +      -       -      +
    111A  VAL*     3.7     2.2    +      -       +      +
    186A  ASP*     3.0     7.3    -      -       -      -
    187A  LEU*     2.6    48.8    +      -       +      +
    189A  VAL*     5.2     2.5    -      -       +      -
    202A  ILE*     4.6    11.0    -      -       +      +
    205A  LEU*     4.2    24.5    -      -       +      -
    206A  ARG*     4.0    15.5    -      -       +      -
    209A  LEU*     4.6     2.5    -      -       +      -
    216A  THR*     3.8    31.0    -      -       +      -
    217A  PRO*     4.0     9.9    -      -       +      -
    222A  GLN*     4.3    21.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  VAL      4.3     3.8    -      -       -      +
    109A  LEU*     1.3    75.2    -      -       -      +
    111A  VAL*     1.3    64.7    +      -       -      +
    112A  GLY      3.6     1.9    +      -       -      -
    185A  ASP      3.3     7.9    -      -       -      +
    186A  ASP*     3.3    16.2    -      -       -      +
    215A  THR      3.6     2.8    -      -       -      +
    216A  THR*     3.7     0.3    -      -       -      -
    217A  PRO*     2.9    39.5    -      -       +      +
    222A  GLN      5.8     0.9    -      -       -      -
    223A  LYS*     3.9    24.7    +      -       -      +
----------------------------------------------------------
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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