Contacts of the strand formed by residues 408 - 413 (chain A) in PDB entry 3VOQ


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 408 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383A  TYR*     5.8     1.2    -      -       +      -
    403A  GLY      3.8     1.4    -      -       -      +
    404A  ILE*     3.7     2.3    -      -       -      -
    405A  SER*     3.0    31.0    +      -       -      +
    407A  ASP*     1.3    92.6    -      -       +      +
    409A  VAL*     1.4    63.2    +      -       -      +
    410A  GLU*     3.6    32.5    -      -       +      +
    431A  SER*     3.6    16.9    +      -       -      +
    432A  ILE      3.2    17.7    -      -       -      +
    433A  ASP*     4.3     2.9    -      -       -      +
    434A  SER*     3.7     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 409 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  LEU*     3.6    28.3    -      -       +      -
    403A  GLY      3.4     4.5    -      -       -      +
    404A  ILE*     4.2    25.1    -      -       +      -
    405A  SER      5.2     1.1    -      -       -      +
    408A  LYS*     1.4    77.0    -      -       -      +
    410A  GLU*     1.3    61.0    +      -       -      +
    411A  ILE*     4.1     7.6    -      -       +      +
    430A  ILE      3.9     0.3    -      -       -      +
    431A  SER*     3.6     1.6    -      -       -      -
    432A  ILE*     2.8    44.4    +      -       +      +
    437A  LEU*     3.8    36.3    -      -       +      -
    455A  LEU*     4.1    19.3    -      -       +      -
    482A  VAL*     5.1     4.3    -      -       +      -
    485A  ILE*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383A  TYR*     4.0    23.9    +      -       -      -
    401A  GLN      3.4     1.4    -      -       -      +
    402A  LEU*     3.3     7.1    -      -       -      +
    403A  GLY*     2.8    38.7    +      -       -      +
    408A  LYS*     3.6    26.2    -      -       +      +
    409A  VAL*     1.3    75.6    -      -       -      +
    411A  ILE*     1.3    61.3    +      -       -      +
    412A  ASP*     3.9    15.7    -      -       -      +
    430A  ILE      3.3     7.4    -      -       -      +
    431A  SER*     3.9    17.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390A  MET*     4.1    16.2    -      -       -      -
    400A  VAL*     3.7    34.5    -      -       +      -
    401A  GLN      3.4     2.9    -      -       -      -
    402A  LEU*     3.8    14.1    -      -       +      -
    409A  VAL*     4.1    17.5    -      -       +      -
    410A  GLU*     1.3    77.7    -      -       -      +
    412A  ASP*     1.3    65.6    +      -       -      +
    413A  PRO*     4.4     1.1    -      -       +      -
    428A  LYS      4.6     0.5    -      -       -      +
    429A  PRO*     3.3     5.5    -      -       -      +
    430A  ILE*     2.8    65.8    +      -       +      +
    432A  ILE*     4.4     3.8    -      -       +      -
    455A  LEU*     5.2     0.4    -      -       +      -
    466A  LEU*     4.0    18.2    -      -       +      -
    468A  PHE*     3.8    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400A  VAL*     3.2     4.6    -      -       -      -
    401A  GLN*     2.7    56.1    +      -       +      +
    410A  GLU*     3.9    18.9    -      -       -      +
    411A  ILE*     1.3    77.4    -      -       -      +
    413A  PRO*     1.3    70.3    -      -       +      +
    429A  PRO*     3.4    24.2    -      -       -      +
    430A  ILE      5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398A  THR*     6.0     2.2    -      -       -      +
    399A  ASP      3.8     7.6    -      -       -      +
    400A  VAL*     4.2     8.0    -      -       +      -
    411A  ILE*     4.2     5.2    -      -       +      +
    412A  ASP*     1.3    89.3    -      -       +      +
    414A  VAL*     1.3    66.1    +      -       -      +
    424A  TRP*     6.0     3.6    -      -       +      -
    427A  GLN*     3.6    36.8    -      -       +      +
    428A  LYS      4.6     2.5    -      -       -      +
    429A  PRO*     4.2    19.7    -      -       +      -
----------------------------------------------------------
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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