Contacts of the strand formed by residues 295 - 300 (chain A) 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 ASP 295 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  PHE*     3.4     3.3    -      -       -      +
    277A  LEU*     2.8    44.2    +      -       +      +
    291A  MET*     3.7    10.4    -      -       -      +
    292A  GLN*     2.9    40.9    +      -       -      +
    294A  GLY*     1.3    77.9    -      -       -      +
    296A  ARG*     1.3    59.2    +      -       -      +
    328A  VAL*     3.5    28.8    -      -       +      +
    329A  VAL      3.6     3.4    -      -       -      -
    330A  ASP*     2.5    35.6    -      -       -      +
    331A  PRO*     3.3     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 296 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  GLY*     4.2    15.2    -      -       -      -
    275A  GLN      3.8    11.4    -      -       -      +
    276A  PHE*     3.7    39.9    -      -       +      -
    294A  GLY      3.5     1.8    +      -       -      +
    295A  ASP*     1.3    73.7    -      -       -      +
    297A  LEU*     1.3    65.6    +      -       -      +
    298A  VAL*     3.5    24.5    +      -       +      +
    306A  GLU*     5.9     2.0    -      -       -      -
    328A  VAL*     3.2     7.2    -      -       -      -
    329A  VAL*     2.9    47.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 297 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261A  PHE*     5.5     2.0    -      -       +      -
    263A  LEU*     4.0    13.0    -      -       +      -
    275A  GLN*     3.0    27.1    +      -       +      +
    277A  LEU*     4.0    13.7    -      -       +      +
    295A  ASP      3.8     2.0    +      -       -      -
    296A  ARG*     1.3    71.9    -      -       -      +
    298A  VAL*     1.3    60.1    +      -       -      +
    299A  ALA      3.6    20.6    -      -       -      +
    300A  VAL*     3.9    10.5    -      -       +      -
    305A  VAL*     3.4    21.0    -      -       +      +
    306A  GLU*     5.4     0.9    -      -       -      +
    313A  THR*     3.6    30.3    -      -       +      -
    317A  ILE*     4.0    13.7    -      -       +      -
    326A  LEU*     4.0    25.1    -      -       +      -
    327A  THR      3.7     8.7    -      -       -      +
    328A  VAL*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 298 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247A  PRO*     4.7     5.4    -      -       +      -
    296A  ARG*     3.5    30.3    +      -       +      +
    297A  LEU*     1.3    72.1    -      -       -      +
    299A  ALA*     1.3    62.7    +      -       +      +
    304A  SER*     3.4     9.2    +      -       -      -
    305A  VAL*     2.9    23.5    +      -       -      -
    306A  GLU*     3.5    32.9    +      -       +      +
    327A  THR*     2.8    38.9    +      -       +      +
    328A  VAL*     4.4     2.5    -      -       -      +
    329A  VAL*     4.0    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 299 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  LEU*     3.6     6.4    -      -       -      +
    298A  VAL*     1.3    81.8    -      -       +      +
    300A  VAL*     1.3    62.4    +      -       -      +
    302A  GLY*     4.4     8.1    -      -       -      +
    303A  GLU      3.2    23.6    -      -       -      +
    304A  SER*     4.2     2.0    -      -       -      -
    305A  VAL*     3.7     2.6    -      -       -      +
    326A  LEU*     3.6     3.5    -      -       -      -
    327A  THR*     2.8    48.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  LEU*     3.9    15.9    -      -       +      -
    299A  ALA*     1.3    77.0    -      -       -      +
    301A  ALA*     1.3    77.5    +      -       +      +
    302A  GLY      3.0     1.6    -      -       -      -
    303A  GLU*     2.9    23.4    +      -       -      +
    305A  VAL*     3.9    22.1    -      -       +      +
    313A  THR*     4.6     4.0    -      -       +      +
    316A  ARG*     3.5    37.3    +      -       +      +
    317A  ILE*     3.8    26.5    -      -       +      +
    324A  VAL*     4.0    14.4    -      -       +      -
    325A  SER      3.5     3.6    -      -       -      -
    326A  LEU*     4.0     3.4    -      -       +      -
----------------------------------------------------------
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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