Contacts of the strand formed by residues 296 - 300 (chain D) 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 ARG 296 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274D  GLY*     5.0     6.3    -      -       -      -
    275D  GLN      3.7    14.4    -      -       -      +
    276D  PHE*     3.8    32.5    -      -       +      -
    294D  GLY      3.6     1.2    +      -       -      -
    295D  ASP*     1.3    72.1    -      -       -      +
    297D  LEU*     1.3    70.0    +      -       -      +
    298D  VAL*     3.5    17.2    +      -       +      +
    306D  GLU*     3.0    25.7    +      -       -      +
    328D  VAL*     3.2     7.1    -      -       -      -
    329D  VAL*     2.9    52.0    +      -       +      +
    266F  GLU*     5.0     1.8    -      -       -      +
    267F  LYS*     3.8     7.5    +      -       -      +
    268F  GLY      3.3    30.9    +      -       -      -
    269F  LEU*     3.7    14.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 297 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261D  PHE*     5.6     0.2    -      -       +      -
    263D  LEU*     4.1    15.9    -      -       +      -
    275D  GLN*     2.9    24.5    +      -       +      +
    276D  PHE*     4.8     0.2    -      -       -      +
    277D  LEU*     4.7     8.4    -      -       +      +
    295D  ASP      4.1     1.4    +      -       -      -
    296D  ARG*     1.3    76.8    -      -       -      +
    298D  VAL*     1.3    61.7    +      -       -      +
    299D  ALA      3.4    20.9    -      -       -      +
    300D  VAL*     3.9    11.2    -      -       +      -
    305D  VAL*     4.0    14.1    -      -       +      +
    306D  GLU*     4.6     5.4    -      -       -      +
    313D  THR*     3.5    32.3    -      -       +      -
    317D  ILE*     4.0    13.0    -      -       +      -
    326D  LEU*     4.0    23.6    -      -       +      -
    327D  THR      3.5     9.9    -      -       -      +
    328D  VAL*     4.1     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 298 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247D  PRO*     4.9     3.4    -      -       +      -
    296D  ARG*     3.7    24.0    -      -       -      +
    297D  LEU*     1.3    78.0    -      -       -      +
    299D  ALA*     1.3    63.5    +      -       +      +
    304D  SER*     3.5     6.4    +      -       -      -
    305D  VAL*     2.9    23.1    +      -       -      -
    306D  GLU*     3.6    29.7    +      -       +      +
    327D  THR*     2.8    42.2    +      -       +      +
    328D  VAL      4.2     1.3    -      -       -      +
    329D  VAL*     3.7    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 299 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297D  LEU*     3.4    12.5    -      -       -      +
    298D  VAL*     1.3    82.1    -      -       +      +
    300D  VAL*     1.3    64.2    +      -       -      +
    302D  GLY*     4.4    11.7    -      -       -      +
    303D  GLU      3.2    19.5    -      -       -      +
    304D  SER*     4.1     2.5    -      -       -      +
    305D  VAL*     3.7     4.4    -      -       -      +
    326D  LEU*     3.6     0.9    -      -       -      -
    327D  THR*     3.1    45.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 300 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297D  LEU*     3.9    16.8    -      -       +      -
    299D  ALA*     1.3    77.5    -      -       -      +
    301D  ALA*     1.3    80.1    +      -       +      +
    302D  GLY      3.1     0.4    -      -       -      -
    303D  GLU*     2.9    24.6    +      -       -      +
    305D  VAL*     3.9    20.5    -      -       +      +
    313D  THR*     4.6     3.1    -      -       +      -
    316D  ARG*     4.0    33.4    +      -       +      +
    317D  ILE*     3.9    10.1    -      -       +      +
    320D  GLN*     4.3     0.9    -      -       +      -
    324D  VAL*     4.0    20.0    -      -       +      -
    325D  SER      3.5     2.9    -      -       -      -
    326D  LEU*     3.9    13.5    -      -       +      -
----------------------------------------------------------
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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