Contacts of the strand formed by residues 630 - 639 (chain A) in PDB entry 1DQ8


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 ARG 630 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    619A  LYS*     3.9     5.2    -      -       -      +
    623A  ASP*     3.4     9.2    -      -       -      +
    627A  ARG*     3.3    24.8    +      -       -      +
    628A  PHE*     3.2    24.1    +      -       -      +
    629A  ALA*     1.3    78.3    -      -       -      +
    631A  LEU*     1.3    66.6    +      -       -      +
    632A  GLN*     3.0     9.9    +      -       -      +
    649A  SER*     3.3    19.0    +      -       -      -
    650A  ARG*     3.8    19.5    +      -       +      +
    831A  PRO*     6.2     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 631 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    615A  PHE*     3.8    22.1    -      -       +      -
    618A  ILE*     3.9    20.6    -      -       +      -
    619A  LYS*     3.0    53.6    +      -       +      +
    622A  PHE*     4.0    19.7    -      -       +      -
    623A  ASP*     2.8    17.8    +      -       -      +
    629A  ALA      4.0     0.2    -      -       -      -
    630A  ARG*     1.3    66.9    -      -       -      +
    632A  GLN*     1.3    61.3    +      -       -      +
    633A  LYS      3.8    12.8    -      -       -      +
    634A  LEU*     4.1     4.9    -      -       +      -
    647A  PHE*     3.9    19.3    -      -       +      -
    648A  GLN      3.6    25.6    -      -       -      +
    649A  SER*     3.8     3.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 632 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  ASP      2.8    30.3    +      -       -      +
    587A  GLY*     3.6     1.4    -      -       -      -
    615A  PHE*     3.9     5.6    -      -       -      -
    630A  ARG      3.0    10.4    +      -       -      +
    631A  LEU*     1.3    74.1    -      -       -      +
    633A  LYS*     1.3    78.1    +      -       +      +
    648A  GLN*     2.8    32.9    +      -       +      +
    649A  SER*     3.3     7.6    -      -       -      -
    650A  ARG*     3.0    43.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 633 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    615A  PHE*     4.1    32.8    -      -       +      -
    631A  LEU*     3.6     2.7    -      -       -      +
    632A  GLN*     1.3    94.4    +      -       +      +
    634A  LEU*     1.3    81.7    +      -       -      +
    646A  ARG      3.8     0.9    -      -       -      +
    648A  GLN*     3.3    34.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 634 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    609A  LEU*     3.9    42.8    -      -       +      +
    615A  PHE*     4.1    21.5    -      -       +      -
    618A  ILE*     4.7     8.3    -      -       +      -
    631A  LEU*     4.1    11.2    -      -       +      -
    633A  LYS*     1.3    97.9    -      -       -      +
    635A  HIS*     1.3    61.6    +      -       -      +
    636A  THR*     4.1     6.3    +      -       +      +
    645A  ILE*     4.0    16.6    -      -       +      -
    646A  ARG      3.5     6.5    -      -       -      +
    647A  PHE*     3.8    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 635 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    634A  LEU*     1.3    75.4    -      -       -      +
    636A  THR*     1.3    72.4    +      -       -      +
    645A  ILE*     3.8     0.3    -      -       -      -
    646A  ARG*     2.9    48.3    +      -       +      +
    687A  TYR*     2.9    34.1    +      -       -      -
    696A  ILE*     4.3     2.0    -      -       -      +
    700A  GLU*     3.2    19.6    +      -       +      +
    699D  ILE*     3.1    26.0    +      -       +      -
    700D  GLU*     2.8    30.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 636 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    606A  LYS*     2.8    49.4    +      -       +      +
    609A  LEU*     4.2    24.2    -      -       +      -
    610A  GLU*     3.5     7.6    +      -       +      +
    634A  LEU*     4.1     7.1    -      -       +      -
    635A  HIS*     1.3    95.8    +      -       -      +
    637A  SER*     1.3    62.6    +      -       -      +
    643A  LEU*     3.9    11.2    -      -       +      -
    644A  TYR      3.3     6.3    -      -       -      +
    645A  ILE*     4.1    22.4    -      -       +      -
    699D  ILE      5.3     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 637 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    606A  LYS*     5.3     1.1    -      -       -      +
    635A  HIS*     5.0     0.7    -      -       -      -
    636A  THR*     1.3    73.7    -      -       -      +
    638A  ILE*     1.3    63.4    +      -       -      +
    643A  LEU*     3.6     2.5    -      -       -      +
    644A  TYR*     2.7    43.5    +      -       -      +
    687A  TYR*     3.1    34.9    -      -       -      -
    742B  MET*     3.4    28.9    +      -       -      +
    698D  TRP      5.6     1.6    +      -       -      -
    699D  ILE*     5.4     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 638 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    602A  SER*     3.3    48.9    -      -       -      +
    603A  ALA*     3.7     4.0    -      -       -      +
    606A  LYS*     3.9    25.7    -      -       +      +
    637A  SER*     1.3    74.8    +      -       -      +
    639A  ALA*     1.3    61.8    +      -       -      +
    640A  GLY      3.4    19.3    -      -       -      +
    642A  ASN      3.6     5.6    -      -       -      +
    643A  LEU*     4.1     8.3    -      -       +      -
    742B  MET*     3.5    15.8    -      -       -      +
    584D  LEU*     3.8    26.6    -      -       +      +
    707D  VAL*     4.2     9.9    -      -       +      -
    796D  THR*     3.3    20.8    -      -       +      +
    798D  PRO*     6.0     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 639 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    637A  SER      4.3     0.2    +      -       -      -
    638A  ILE*     1.3    74.3    -      -       -      +
    640A  GLY*     1.3    64.6    +      -       -      +
    641A  ARG      3.1     1.0    +      -       -      -
    642A  ASN*     3.0    25.7    +      -       +      +
    644A  TYR*     4.0    13.2    -      -       +      -
    738B  VAL*     3.9    27.8    -      -       +      -
    742B  MET*     4.1    12.3    -      -       -      -
    778D  ILE*     4.5     4.0    -      -       +      -
    780D  LEU*     3.7    19.3    -      -       +      +
    796D  THR*     3.6     7.9    -      -       -      -
----------------------------------------------------------
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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