Contacts of the strand formed by residues 420 - 426 (chain A) in PDB entry 1D0N


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 LYS 420 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418A  GLY      3.5     6.7    +      -       -      +
    419A  GLN*     1.3    75.8    -      -       -      +
    421A  GLN*     1.3    66.7    +      -       -      +
    422A  ILE*     4.4     8.1    -      -       +      -
    438A  TYR*     3.8    35.6    +      -       +      +
    449A  ILE*     4.6     4.3    -      -       +      -
    450A  LEU      3.1    12.1    -      -       -      +
    451A  TYR*     3.9    14.6    -      -       +      -
    452A  ASN*     5.2     0.4    -      -       -      +
    511A  LEU*     2.8    45.6    +      -       +      +
    512A  PHE*     3.8    24.1    -      -       +      +
    513A  GLY      5.6     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  LYS*     1.3    78.3    -      -       -      +
    422A  ILE*     1.3    65.5    +      -       -      +
    423A  TRP*     3.2    39.8    -      -       +      -
    438A  TYR*     4.0     4.9    -      -       -      +
    448A  ILE      4.0     0.5    -      -       -      +
    449A  ILE*     3.4     6.1    -      -       -      +
    450A  LEU*     3.0    47.5    +      -       +      +
    452A  ASN*     5.9     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 422 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    420A  LYS*     4.4     6.1    -      -       +      -
    421A  GLN*     1.3    79.2    -      -       -      +
    423A  TRP*     1.3    68.7    +      -       -      +
    432A  PRO*     3.8     4.2    -      -       -      +
    433A  VAL*     2.9    43.0    +      -       +      +
    438A  TYR*     3.3    53.6    +      -       +      -
    441A  PHE*     4.4    19.1    -      -       +      -
    447A  TYR*     4.5     2.7    -      -       +      -
    448A  ILE      3.8     1.6    -      -       -      -
    449A  ILE*     3.9    27.1    -      -       +      -
    512A  PHE*     4.0    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 423 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421A  GLN*     3.2    42.8    -      -       +      -
    422A  ILE*     1.3    76.0    -      -       -      +
    424A  ARG*     1.3    60.2    +      -       -      +
    430A  LYS*     3.7    45.7    +      -       +      +
    431A  VAL      3.4     2.7    -      -       -      +
    432A  PRO*     3.5    34.4    -      -       +      +
    433A  VAL*     3.7     4.7    -      -       -      -
    447A  TYR*     3.1    10.0    -      -       -      +
    448A  ILE*     3.0    65.5    +      -       +      -
    450A  LEU*     3.9    31.4    -      -       +      -
    486A  LEU*     4.1    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 424 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423A  TRP*     1.3    75.0    -      -       -      +
    425A  VAL*     1.3    70.3    +      -       -      +
    426A  GLU*     2.7    33.4    +      -       -      -
    429A  ASN      3.6     0.3    -      -       -      +
    430A  LYS*     3.7     1.6    -      -       -      -
    431A  VAL*     2.8    50.5    +      -       +      +
    432A  PRO      4.5     3.6    +      -       -      -
    433A  VAL*     3.7    27.0    -      -       +      +
    434A  ASP      5.4     0.4    -      -       -      +
    445A  ASP*     3.5    39.9    -      -       +      -
    446A  SER      3.9     3.6    -      -       -      -
    447A  TYR*     3.9     7.1    -      -       +      -
    525A  SER*     3.6    22.3    +      -       -      -
    526A  ARG*     3.4    25.9    -      -       -      +
    527A  GLU      4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 425 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    424A  ARG*     1.3    77.0    -      -       -      +
    426A  GLU*     1.3    64.1    +      -       -      +
    427A  GLY      4.0    17.5    -      -       -      +
    429A  ASN      3.6     8.5    -      -       -      +
    430A  LYS*     5.5     1.3    -      -       -      -
    445A  ASP*     5.1     1.2    -      -       -      +
    446A  SER*     3.1    23.2    +      -       -      +
    448A  ILE*     4.5    16.4    -      -       +      -
    475A  GLU*     3.5    38.2    -      -       +      +
    478A  ALA*     4.1     4.0    -      -       +      -
    479A  SER*     3.7    26.7    -      -       -      -
    482A  LEU*     4.1    20.0    -      -       +      -
    526A  ARG*     4.0     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    424A  ARG*     2.7    42.4    +      -       +      +
    425A  VAL*     1.3    76.3    -      -       -      +
    427A  GLY*     1.3    59.5    +      -       -      +
    428A  SER      2.9     9.9    +      -       -      -
    429A  ASN*     3.1    24.3    +      -       -      +
    431A  VAL*     3.8    29.0    -      -       +      +
    475A  GLU*     3.7     4.0    -      -       -      -
    526A  ARG*     3.1    27.9    -      -       +      +
    527A  GLU*     4.3     3.7    +      -       -      +
----------------------------------------------------------
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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