Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 2VZ3


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 ALA 353 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  PRO*     3.7    19.5    -      -       +      +
    347A  GLN*     3.5     6.1    +      -       -      -
    351A  SER*     2.7    31.3    +      -       -      +
    352A  THR*     1.3    79.7    -      -       -      +
    354A  MET*     1.3    59.4    +      -       -      +
    355A  ASN*     3.5     7.2    +      -       -      +
    367A  SER*     6.6     0.4    -      -       -      -
    369A  GLY      3.9     5.8    -      -       -      +
    370A  LYS*     4.5     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    346A  PHE*     3.9    13.5    -      -       +      -
    347A  GLN*     3.3    11.0    -      -       -      +
    348A  ALA      3.5    18.4    -      -       -      +
    352A  THR      4.0     2.0    -      -       -      +
    353A  ALA*     1.3    73.8    -      -       -      +
    355A  ASN*     1.3    70.8    +      -       -      +
    367A  SER*     3.8     1.6    -      -       -      -
    368A  ALA*     2.9    41.8    +      -       +      +
    369A  GLY      2.8    17.5    +      -       -      +
    370A  LYS      4.0     3.6    -      -       -      +
    371A  ARG*     3.9    24.2    -      -       +      +
    417A  ILE*     3.7    30.3    -      -       -      -
    426A  PRO*     3.9    12.3    -      -       +      +
    428A  THR*     3.7    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  PRO*     3.2    46.7    +      -       -      +
    320A  MET*     3.9     1.0    -      -       -      +
    346A  PHE*     3.7     3.5    -      -       -      -
    347A  GLN*     2.8    62.7    +      -       -      +
    353A  ALA*     3.5     8.3    +      -       -      +
    354A  MET*     1.3    84.7    +      -       -      +
    356A  TRP*     1.3    62.4    +      -       -      +
    357A  TYR*     4.0     7.8    +      -       +      -
    365A  VAL*     4.0    15.7    -      -       +      +
    366A  LYS      3.5     5.0    -      -       -      +
    367A  SER*     3.6    18.7    +      -       -      -
    368A  ALA*     3.9     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 356 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340A  TRP*     3.5    35.7    -      +       -      -
    344A  SER*     3.8    13.2    -      -       -      -
    345A  VAL      3.9     2.7    -      -       -      -
    346A  PHE*     3.7    42.2    -      +       +      -
    355A  ASN*     1.3    72.1    -      -       -      +
    357A  TYR*     1.3    61.3    +      -       -      +
    358A  TYR*     3.6    22.2    -      -       +      +
    365A  VAL*     3.2     8.5    -      -       -      +
    366A  LYS*     2.8    39.6    +      -       +      +
    367A  SER      4.6     1.6    -      -       -      -
    368A  ALA*     3.6    23.3    -      -       +      +
    419A  LEU*     4.1    15.0    -      -       +      -
    420A  GLY      4.3     3.8    -      -       -      -
    421A  GLU      3.7    13.7    -      -       -      -
    422A  PRO*     3.8    15.0    -      -       +      -
    423A  GLY*     3.2    26.7    -      -       -      +
    424A  THR*     2.8    24.8    +      -       -      -
    426A  PRO*     4.9     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 357 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  PHE*     3.9    30.3    -      +       +      -
    286A  ILE*     3.5    17.6    -      -       +      +
    315A  ALA*     3.9    15.5    -      -       +      -
    316A  LYS      2.8    29.5    +      -       -      -
    317A  VAL*     3.8     0.2    -      -       -      -
    320A  MET*     3.3    34.2    +      -       -      +
    337A  LEU*     5.1     2.9    -      -       +      -
    343A  GLY      4.5     0.2    -      -       -      +
    344A  SER*     3.3     8.5    -      -       -      -
    345A  VAL*     2.9    42.1    +      -       +      +
    347A  GLN*     3.9    29.6    -      -       +      -
    355A  ASN*     4.0     9.5    -      -       +      +
    356A  TRP*     1.3    75.1    -      -       -      +
    358A  TYR*     1.3    61.8    +      -       -      +
    359A  THR*     5.2     0.9    -      -       -      -
    364A  ASP      3.5    11.7    -      -       -      -
    365A  VAL*     3.4    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  PHE*     5.1     0.2    -      -       -      -
    312A  LEU*     4.5     0.2    -      -       -      +
    315A  ALA*     4.3     5.4    -      -       -      +
    342A  LYS      6.0     1.6    -      -       -      -
    344A  SER*     4.7     9.9    -      -       -      +
    356A  TRP*     3.6    24.2    -      -       +      +
    357A  TYR*     1.3    78.5    -      -       -      +
    359A  THR*     1.3    64.4    +      -       -      +
    360A  SER*     3.6    10.3    -      -       -      +
    363A  GLY*     3.3     5.8    -      -       -      -
    364A  ASP*     2.9    54.2    +      -       +      +
    365A  VAL      4.5     0.4    -      -       -      -
    366A  LYS*     3.6    24.0    -      -       +      +
    422A  PRO*     4.2    19.7    -      -       +      -
    423A  GLY*     2.8    34.2    +      -       -      -
----------------------------------------------------------
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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