Contacts of the strand formed by residues 395 - 399 (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 LYS 395 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    388A  MET*     3.2     9.2    -      -       -      +
    389A  TYR*     3.1    59.6    +      -       +      +
    390A  ASP*     2.9    17.8    +      -       +      +
    393A  LYS*     3.9    25.8    -      -       +      +
    394A  GLY*     1.3    75.1    -      -       -      +
    396A  ILE*     1.3    60.2    +      -       -      +
    416A  ILE*     4.0     8.8    -      -       +      +
    417A  ILE      3.5     1.6    -      -       -      -
    418A  THR*     2.9    37.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 396 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  PHE*     3.7    45.8    -      -       +      -
    346A  PHE*     4.0    13.2    -      -       +      -
    348A  ALA*     4.7     0.4    -      -       +      -
    387A  VAL      3.3     6.5    -      -       -      +
    388A  MET*     4.0    17.5    -      -       +      -
    389A  TYR*     4.0     3.1    -      -       -      -
    394A  GLY      4.2     2.9    -      -       -      +
    395A  LYS*     1.3    78.8    -      -       -      +
    397A  LEU*     1.3    63.0    +      -       -      +
    398A  THR*     3.8    22.6    +      -       +      -
    415A  HIS      3.6     0.9    -      -       -      +
    416A  ILE*     3.3     4.5    -      -       -      +
    417A  ILE*     2.8    45.0    +      -       +      +
    419A  LEU*     3.9    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 397 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386A  ALA*     3.3     1.9    -      -       -      -
    387A  VAL*     2.8    33.9    +      -       +      +
    389A  TYR*     3.8    19.6    -      -       +      -
    396A  ILE*     1.3    72.4    -      -       -      +
    398A  THR*     1.3    63.4    +      -       -      +
    399A  PHE*     3.6    27.9    -      -       +      -
    415A  HIS      3.3    14.1    -      -       -      +
    416A  ILE*     4.4     3.6    -      -       +      +
    431A  ALA*     3.7    24.2    -      -       +      -
    452A  THR*     3.9    16.6    -      -       +      +
    454A  ILE*     4.6     2.9    -      -       +      -
    476A  TYR*     3.7    45.3    -      -       +      -
    483A  PHE*     4.5     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 398 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336A  TRP*     3.5    36.1    -      -       +      -
    348A  ALA*     4.5     0.4    -      -       +      -
    371A  ARG*     3.7     3.3    -      -       -      -
    385A  ASN      3.2     5.8    -      -       -      -
    386A  ALA*     3.9     2.9    -      -       +      -
    396A  ILE*     3.8    13.0    -      -       +      -
    397A  LEU*     1.3    77.2    -      -       -      +
    399A  PHE*     1.3    65.1    +      -       -      +
    414A  ALA*     3.0     5.4    -      -       -      +
    415A  HIS*     2.9    43.0    +      -       -      +
    417A  ILE*     3.8    23.3    -      -       +      -
   1641A  ACT      2.8    21.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 399 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  GLY*     3.3     0.2    -      -       -      -
    385A  ASN*     2.9    52.1    +      -       +      -
    387A  VAL*     4.2     7.9    -      -       +      -
    397A  LEU*     3.6    43.5    -      -       +      -
    398A  THR*     1.3    81.2    -      -       -      +
    400A  GLY*     1.3    62.0    +      -       -      +
    413A  ASN      3.2    10.3    -      -       -      +
    414A  ALA*     3.8    10.1    -      -       +      -
    435A  LEU*     3.9    13.9    -      -       +      -
    442A  HIS*     3.1    20.7    +      +       -      -
    444A  SER*     3.3    27.4    -      -       -      -
    452A  THR*     4.1     2.2    -      -       +      -
    454A  ILE*     3.5    37.7    -      -       +      -
    483A  PHE*     5.4     0.7    -      -       +      -
   1641A  ACT      3.6     5.3    -      -       -      +
----------------------------------------------------------
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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