Contacts of the strand formed by residues 285 - 293 (chain B) in PDB entry 3VAG


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 LEU 285 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276B  LYS*     4.0    21.5    -      -       +      -
    279B  LEU*     4.2    16.6    -      -       +      -
    280B  THR*     4.0    26.7    -      -       +      +
    283B  GLY      4.6     0.4    -      -       -      +
    284B  PRO*     1.3    75.0    -      -       -      +
    286B  LYS*     1.3    57.9    +      -       -      +
    287B  ALA      4.1     6.3    -      -       -      +
    288B  PHE*     4.2    13.7    -      -       +      -
    305B  CYS*     4.0    20.9    -      -       +      -
    306B  GLU      3.6    12.1    -      -       -      +
    307B  TYR*     3.7    31.4    -      -       +      -
    308B  VAL*     3.5     9.5    -      -       -      +
    401B  DIO      3.4    28.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 286 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  GLY*     4.4    20.9    -      -       -      +
    144B  PRO*     4.1    15.2    -      -       +      +
    233B  GLN*     4.0     6.5    +      -       -      -
    285B  LEU*     1.3    71.8    -      -       -      +
    287B  ALA*     1.3    62.3    +      -       +      +
    306B  GLU*     2.8    48.0    +      -       +      +
    307B  TYR      3.2    19.5    +      -       -      +
    308B  VAL*     3.6    30.0    +      -       +      +
    310B  ILE*     3.9    14.3    -      -       -      +
    401B  DIO      3.2    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 287 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  GLY*     5.4    10.3    -      -       -      -
    285B  LEU*     3.6     4.1    -      -       -      +
    286B  LYS*     1.3    82.1    -      -       +      +
    288B  PHE*     1.3    63.6    +      -       -      +
    305B  CYS*     3.3     6.2    -      -       -      +
    306B  GLU*     3.0    41.9    +      -       +      +
    401B  DIO      3.6     6.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 288 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272B  ASP*     3.8    23.1    -      -       -      -
    275B  VAL*     3.8    29.8    -      -       +      -
    276B  LYS*     3.5    28.3    -      -       +      -
    279B  LEU*     3.7    32.5    -      -       +      -
    285B  LEU*     4.2     5.4    -      -       +      -
    287B  ALA*     1.3    77.0    -      -       -      +
    289B  ASN*     1.3    64.8    +      -       -      +
    290B  LEU*     3.7    27.6    -      -       +      -
    303B  ALA*     4.1    11.7    -      -       +      -
    304B  PHE      3.5    14.8    -      -       -      -
    305B  CYS*     4.0     2.2    -      -       +      -
    401B  DIO      3.7    26.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 289 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194A  ASP*     3.9    21.6    +      -       +      +
    195A  LYS*     3.9    15.2    -      -       +      +
    260B  LYS*     5.3     1.7    -      -       -      -
    272B  ASP*     5.1     1.1    -      -       -      -
    288B  PHE*     1.3    84.9    -      -       -      +
    290B  LEU*     1.3    62.1    +      -       -      +
    291B  VAL*     4.1    11.1    -      -       -      +
    303B  ALA*     3.3     4.5    -      -       -      +
    304B  PHE*     3.0    53.9    +      -       -      +
      4P    U      3.0    25.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 290 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  LEU*     4.0    23.8    -      -       +      -
    270B  LEU      3.7    22.4    -      -       -      +
    271B  ASN*     3.9    20.6    -      -       -      +
    272B  ASP*     3.9    17.9    +      -       -      +
    275B  VAL*     4.5     5.2    -      -       +      -
    288B  PHE*     3.7    12.4    -      -       +      -
    289B  ASN*     1.3    76.0    +      -       -      +
    291B  VAL*     1.3    64.0    +      -       -      +
    292B  LYS*     3.1    27.6    +      -       +      +
    299B  SER*     3.7    22.0    -      -       -      +
    302B  TYR      3.5    18.8    -      -       -      +
    303B  ALA*     4.1     2.9    -      -       +      -
    403B  DIO      4.3    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 291 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  LYS*     4.6     6.7    -      -       -      +
    289B  ASN*     4.1     5.8    -      -       -      +
    290B  LEU*     1.3    71.5    -      -       -      +
    292B  LYS*     1.3    68.8    +      -       -      +
    299B  SER*     3.6     5.0    +      -       -      -
    300B  LYS*     2.9    47.0    +      -       +      +
    302B  TYR*     3.1    49.9    +      -       +      +
    304B  PHE*     3.9     7.9    -      -       +      -
      4P    U      3.8    42.6    -      -       -      +
      5P    U      4.3     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 292 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  LYS*     4.3     7.1    +      -       -      +
    272B  ASP*     2.9    32.9    +      -       -      -
    290B  LEU*     3.1    23.1    +      -       +      +
    291B  VAL*     1.3    79.8    -      -       -      +
    293B  ASP*     1.3    65.1    +      -       -      +
    294B  SER*     3.5     3.5    +      -       -      -
    297B  GLY*     3.8    22.4    -      -       -      +
    298B  LEU      3.3     9.6    -      -       -      +
    299B  SER*     4.1    11.4    -      -       -      +
    300B  LYS*     3.9     6.6    -      -       -      +
    403B  DIO      3.8    17.7    -      -       -      -
      5P    U      3.9    15.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 293 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292B  LYS*     1.3    69.4    -      -       -      +
    294B  SER*     1.3    63.7    +      -       -      +
    295B  ALA*     3.2    15.8    +      -       -      +
    296B  THR*     3.5    28.3    +      -       -      +
    297B  GLY*     2.7    35.0    +      -       -      -
    298B  LEU*     2.8    17.5    +      -       +      +
    300B  LYS*     3.7    24.2    +      -       +      +
----------------------------------------------------------
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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