Contacts of the strand formed by residues 336 - 339 (chain C) in PDB entry 2V90


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 GLU 336 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  PRO*     3.7    24.1    -      -       -      +
    283A  GLY*     3.5    14.1    +      -       -      +
    287A  LYS*     4.3    15.3    -      -       +      +
    288A  LYS*     2.9    25.7    +      -       +      -
    333C  ALA*     4.5    14.0    -      -       -      +
    334C  ASP      3.6     0.6    -      -       -      -
    335C  ARG*     1.3    78.9    -      -       -      +
    337C  THR*     1.3    61.7    +      -       -      +
    262E  LEU*     3.5    19.2    -      -       +      +
    263E  LEU      3.1    11.2    -      -       -      +
    264E  ARG*     2.8    47.1    +      -       +      +
    278E  TRP*     5.0     0.5    -      -       -      -
    310E  HIS*     3.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 337 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283A  GLY*     3.6     8.0    -      -       -      +
    288A  LYS*     2.6    25.6    +      -       -      +
    336C  GLU*     1.3    69.3    -      -       -      +
    338C  SER*     1.3    73.7    +      -       -      +
    339C  VAL*     3.7    17.2    +      -       +      +
    262E  LEU*     3.7     4.2    -      -       -      +
    263E  LEU*     2.8    34.1    +      -       -      +
    310E  HIS*     3.0    21.1    +      -       -      -
    311E  GLU*     4.9     1.6    +      -       -      -
    314E  VAL*     4.0    21.4    -      -       +      +
    318E  GLN*     5.5     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 338 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  GLN*     3.1    25.4    +      -       -      -
    282A  PRO      4.1     9.6    -      -       -      -
    283A  GLY*     3.0    12.6    +      -       -      +
    284A  LEU*     3.7    29.4    -      -       -      +
    337C  THR*     1.3    77.5    -      -       -      +
    339C  VAL*     1.3    68.0    +      -       -      +
    261E  PHE      3.5    11.6    +      -       -      -
    262E  LEU*     3.7     7.2    +      -       -      +
    281E  ASP*     4.9     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 339 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  GLN*     4.3    12.6    +      -       -      +
    337C  THR*     3.8    20.6    -      -       +      +
    338C  SER*     1.3    82.3    +      -       -      +
    254E  LYS*     5.7     0.2    -      -       -      +
    257E  GLN      4.6     0.9    -      -       -      +
    258E  GLY*     3.6     9.3    -      -       -      -
    259E  PHE*     2.8    39.7    +      -       +      -
    260E  GLY*     3.0    24.1    +      -       -      -
    261E  PHE*     2.9    60.7    +      -       +      +
    263E  LEU*     5.3     2.0    -      -       +      -
    314E  VAL*     4.5    17.0    -      -       +      -
    317E  ILE*     4.6    16.8    -      -       +      -
    318E  GLN*     5.1     8.7    -      -       +      +
----------------------------------------------------------
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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