Contacts of the strand formed by residues 462 - 470 (chain B) 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 ASP 462 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    458B  LEU*     3.5     8.2    -      -       -      -
    459B  SER*     2.9    30.5    +      -       -      +
    460B  ASN      4.3     6.8    -      -       -      +
    461B  HIS*     1.4    81.4    -      -       -      +
    463B  TYR*     1.3    66.0    +      -       -      +
    464B  LYS*     3.5    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 463 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438B  CYS*     3.8    30.7    -      -       +      -
    456B  THR*     4.0    18.8    -      -       +      -
    457B  TYR      3.4     2.5    -      -       -      -
    458B  LEU*     3.7    23.3    -      -       +      +
    462B  ASP*     1.3    73.9    -      -       -      +
    464B  LYS*     1.3    63.7    +      -       -      +
    465B  HIS*     4.1    16.8    +      +       +      +
----------------------------------------------------------
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Residues in contact with LYS 464 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    456B  THR*     3.2     5.7    -      -       -      +
    457B  TYR*     2.8    58.7    +      -       +      +
    459B  SER*     3.6    37.1    +      -       -      +
    462B  ASP*     4.0    24.0    +      -       -      +
    463B  TYR*     1.3    78.1    -      -       -      +
    465B  HIS*     1.3    69.3    +      -       -      +
    466B  LEU*     5.7     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 465 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393A  ARG*     4.6    12.4    +      -       -      -
    395A  ARG*     5.2     5.9    +      -       -      -
    454B  LYS*     3.2    24.5    +      -       +      +
    455B  LEU      3.3     4.9    -      -       -      +
    456B  THR*     2.9    38.2    +      -       +      -
    463B  TYR*     4.1    19.4    +      +       +      +
    464B  LYS*     1.3    78.4    +      -       -      +
    466B  LEU*     1.3    70.1    +      -       -      +
    467B  TYR*     3.8    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 466 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390B  MET*     3.3    27.4    -      -       +      -
    411B  ILE*     3.4    32.1    -      -       +      -
    430B  ILE*     4.8     6.7    -      -       +      -
    432B  ILE*     4.2     7.6    -      -       +      -
    453B  PHE      3.8     0.3    -      -       -      +
    454B  LYS*     3.3     3.8    -      -       -      -
    455B  LEU*     2.7    40.4    +      -       +      +
    457B  TYR*     3.6    32.8    -      -       +      +
    464B  LYS*     5.9     0.9    -      -       +      -
    465B  HIS*     1.3    82.2    -      -       -      +
    467B  TYR*     1.3    63.6    +      -       -      +
    468B  PHE*     3.5    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 467 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393A  ARG*     3.2    34.9    +      -       +      +
    395A  ARG*     3.5    38.6    -      -       +      -
    396A  PHE*     3.9    32.1    -      +       -      -
    390B  MET*     3.6     5.1    -      -       -      +
    391B  ILE*     2.9    48.1    +      -       +      +
    443B  ALA*     5.4     0.9    -      -       +      -
    452B  ILE*     4.6     3.6    -      -       +      -
    453B  PHE      3.3     7.2    -      -       -      +
    454B  LYS*     3.2    44.5    +      -       +      -
    465B  HIS*     3.8    26.2    -      -       +      +
    466B  LEU*     1.3    78.1    -      -       -      +
    468B  PHE*     1.3    69.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 468 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388B  VAL*     3.7    20.4    -      -       +      -
    389B  SER      3.1     8.3    -      -       -      +
    390B  MET*     3.7    36.8    -      -       +      -
    391B  ILE*     4.1     4.3    -      -       -      -
    400B  VAL*     4.2    10.1    -      -       +      -
    402B  LEU*     4.5     8.7    -      -       +      -
    411B  ILE*     3.8    26.7    -      -       +      -
    452B  ILE*     3.3     4.3    -      -       -      +
    453B  PHE*     3.1    69.8    +      +       +      -
    455B  LEU*     4.3    15.7    -      -       +      -
    466B  LEU*     3.5    34.8    -      -       +      -
    467B  TYR*     1.3    76.3    -      -       -      +
    469B  GLU*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 469 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388B  VAL*     3.7     2.6    -      -       -      +
    389B  SER*     2.7    55.5    +      -       -      +
    391B  ILE*     3.8    21.4    -      -       +      +
    397B  THR*     3.8    14.9    +      -       -      +
    450B  HIS*     2.9    30.9    +      -       +      +
    451B  ALA      3.1    15.3    -      -       -      +
    452B  ILE*     3.7     9.5    -      -       +      +
    453B  PHE*     5.6     0.2    -      -       -      -
    468B  PHE*     1.3    76.8    -      -       -      +
    470B  SER*     1.3    64.5    +      -       -      +
    475B  VAL*     4.7     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 470 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387B  LYS      3.9    10.4    +      -       -      -
    388B  VAL*     3.8    18.3    -      -       -      +
    449B  SER      4.1     4.0    -      -       -      -
    450B  HIS*     3.6     2.8    -      -       -      -
    451B  ALA      2.9    27.4    +      -       -      +
    469B  GLU*     1.3    77.8    -      -       -      +
    471B  ASP*     1.3    84.6    +      -       -      +
    474B  THR*     3.5    13.0    +      -       -      +
    475B  VAL*     3.9     9.8    -      -       -      +
----------------------------------------------------------
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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