Contacts of the strand formed by residues 397 - 401 (chain A) in PDB entry 2VGZ


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 TYR 397 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  TRP*     3.2    53.3    +      +       +      -
    358A  ILE      3.2    16.2    -      -       -      -
    359A  LYS*     3.5    37.6    +      -       +      +
    366A  VAL*     3.3    11.3    -      -       -      +
    383A  PRO      3.5     0.2    -      -       -      -
    384A  GLY      2.7    27.1    +      -       -      -
    388A  TYR*     3.8    22.2    -      -       -      -
    395A  SER*     3.2    12.4    +      -       -      +
    396A  PRO*     1.3    99.0    -      -       +      +
    398A  LEU*     1.3    59.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 398 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LEU      3.9     0.2    -      -       -      +
    357A  TRP*     3.6     7.8    -      -       -      -
    358A  ILE*     2.8    37.8    +      -       +      +
    360A  VAL*     4.1    17.0    -      -       +      -
    366A  VAL*     3.5    28.9    -      -       +      -
    369A  LEU*     6.0     0.7    -      -       +      -
    370A  ILE*     3.6    28.0    -      -       +      -
    381A  MET*     3.6    28.5    -      -       +      -
    382A  LEU      3.2    12.1    -      -       -      +
    383A  PRO*     4.0     3.6    -      -       +      -
    397A  TYR*     1.3    73.9    -      -       -      +
    399A  ARG*     1.3    59.9    +      -       -      +
    400A  ALA      4.1     0.8    +      -       -      -
    417A  LEU*     3.9    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 399 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  TYR*     5.6     2.0    -      -       -      -
    202A  ASN*     3.0    30.0    +      -       -      +
    203A  PRO*     3.6    28.3    -      -       +      +
    355A  PHE*     3.3    41.3    -      -       +      -
    356A  LEU      3.5     3.1    -      -       -      +
    357A  TRP*     3.9    13.9    -      -       +      -
    381A  MET*     4.0     3.7    -      -       -      +
    382A  LEU*     2.7    57.2    +      -       +      +
    387A  PHE*     3.9    13.4    -      -       +      -
    398A  LEU*     1.3    72.3    -      -       -      +
    400A  ALA*     1.3    61.0    +      -       -      +
    401A  SER      5.5     0.4    -      -       -      +
     36B  LEU      3.6     7.1    -      -       -      +
     37B  ALA      2.9    26.7    +      -       -      -
     38B  GLY      3.4    18.4    +      -       -      -
     39B  GLY*     3.7     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 400 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  ILE*     3.9    20.9    -      -       +      -
    355A  PHE*     3.3     5.1    -      -       -      -
    356A  LEU*     2.8    44.1    +      -       +      +
    358A  ILE*     3.9    10.1    -      -       +      -
    381A  MET*     3.5    27.1    -      -       +      -
    398A  LEU      4.1     0.6    -      -       -      -
    399A  ARG*     1.3    72.3    -      -       -      +
    401A  SER*     1.3    61.5    +      -       -      +
    402A  PHE*     3.7     1.0    +      -       -      -
    414A  PHE*     4.5     1.3    -      -       +      -
     36B  LEU*     3.5     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 401 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333A  ILE*     4.2     3.6    -      -       -      +
    354A  MET*     3.4    10.5    +      -       -      +
    355A  PHE*     3.9    11.8    -      -       -      -
    399A  ARG*     4.1     0.6    +      -       -      +
    400A  ALA*     1.3    73.3    -      -       -      +
    402A  PHE*     1.3    60.8    +      -       -      +
    403A  SER*     3.4    22.2    +      -       -      -
    404A  SER      5.3     0.5    +      -       -      -
    405A  ALA*     5.2     0.9    +      -       -      +
     36B  LEU*     2.7    41.8    +      -       -      +
     38B  GLY      3.2    27.2    +      -       -      -
     39B  GLY*     5.1     0.2    -      -       -      -
     40B  LEU      4.8     2.1    +      -       -      -
----------------------------------------------------------
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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