Contacts of the strand formed by residues 274 - 277 (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 SER 274 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  GLY*     4.9     0.7    -      -       -      -
    272A  TYR      3.8     0.6    +      -       -      -
    273A  GLN*     1.3    74.6    -      -       -      +
    275A  SER*     1.3    56.9    +      -       -      +
    285A  THR*     2.8    21.6    +      -       -      -
    286A  ILE      3.7     6.6    +      -       -      +
    332A  ASP      5.6     0.2    +      -       -      -
    334A  HIS*     3.3    10.5    -      -       -      +
    335A  ALA*     2.7    43.0    +      -       -      +
    337A  LEU*     3.4    23.7    -      -       -      +
    583A  VAL*     3.5    23.2    -      -       -      +
    585A  THR*     4.5     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  GLY*     3.8     8.7    -      -       -      -
    231A  ILE      3.3    24.5    +      -       -      +
    232A  SER*     2.7    21.5    +      -       -      -
    240A  VAL*     4.7     1.3    +      -       -      -
    242A  THR*     4.7     4.7    -      -       -      -
    273A  GLN      4.2     0.6    +      -       -      -
    274A  SER*     1.3    73.8    -      -       -      +
    276A  ALA*     1.3    55.8    +      -       -      +
    283A  VAL*     3.7    11.8    -      -       -      +
    284A  PHE      3.1    12.3    -      -       -      -
    285A  THR*     3.8    11.0    -      -       -      -
    309A  TRP*     5.5     1.1    -      -       -      -
    337A  LEU*     4.3     2.0    -      -       -      -
    583A  VAL*     5.5     0.6    -      -       -      +
    585A  THR*     2.5    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  SER*     3.5     4.0    -      -       -      -
    275A  SER*     1.3    76.4    -      -       -      +
    277A  THR*     1.3    63.7    +      -       -      +
    278A  MET*     3.6     4.5    +      -       -      +
    283A  VAL*     4.2     0.9    -      -       -      -
    284A  PHE*     2.8    32.5    +      -       -      +
    337A  LEU*     3.7    28.9    -      -       +      -
    339A  GLY      4.1    13.5    -      -       -      +
    345A  VAL*     4.0    15.9    -      -       +      -
    585A  THR*     3.8     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 277 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  SER*     3.4    14.6    +      -       -      -
    233A  MET      2.6    33.5    +      -       -      +
    234A  ASP*     4.2     2.0    -      -       -      -
    276A  ALA*     1.3    74.8    -      -       -      +
    278A  MET*     1.3    71.7    +      -       -      +
    281A  GLY*     4.1    14.4    -      -       -      +
    282A  ARG      3.3    11.9    -      -       -      +
    283A  VAL*     4.1     3.4    -      -       -      +
    339A  GLY*     3.3    20.1    +      -       -      -
    575A  ARG*     3.7    15.3    -      -       -      +
    585A  THR*     4.9     3.4    +      -       -      -
    586A  ASP*     3.5     6.5    +      -       -      -
    614A  LEU*     3.5    17.3    -      -       +      +
    615A  PRO      4.3     5.6    -      -       -      +
----------------------------------------------------------
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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