Contacts of the strand formed by residues 25 - 30 (chain B) in PDB entry 2E3V


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 ALA 25 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  VAL*     4.2     9.6    -      -       +      -
     19B  GLU      3.4     9.4    -      -       -      +
     20B  PRO*     4.1     5.2    -      -       +      -
     21B  TYR*     4.6     0.2    -      -       -      -
     24B  THR*     1.3    76.6    -      -       -      +
     26B  GLN*     1.3    63.5    +      -       -      +
     27B  VAL*     3.7     1.9    +      -       +      -
     71B  VAL      3.8     0.2    -      -       -      +
     72B  THR*     3.4     3.4    -      -       -      -
     73B  ILE*     2.8    40.4    +      -       +      +
     76B  LEU*     4.0     2.9    -      -       +      -
    103B  PHE*     3.7    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  GLN      3.7     1.7    -      -       -      +
     18B  VAL*     3.2     3.8    -      -       -      -
     19B  GLU*     2.8    49.7    +      -       +      +
     21B  TYR*     3.2    35.7    +      -       +      -
     24B  THR*     5.8     0.2    -      -       -      +
     25B  ALA*     1.3    71.7    -      -       -      +
     27B  VAL*     1.3    61.6    +      -       -      +
     28B  GLN*     3.9     0.4    -      -       -      -
     70B  ILE*     3.7    24.5    -      -       +      +
     71B  VAL      3.7     4.3    -      -       -      -
     72B  THR*     3.7    21.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ILE*     3.9    40.2    -      -       +      -
     17B  GLN      3.6     2.7    -      -       -      -
     18B  VAL*     4.2    17.5    -      -       +      +
     25B  ALA*     4.3     3.1    -      -       +      +
     26B  GLN*     1.3    74.4    -      -       -      +
     28B  GLN*     1.3    62.7    +      -       -      +
     29B  PHE*     3.9     3.1    -      -       -      -
     69B  GLY      3.8     0.5    -      -       -      +
     70B  ILE*     3.4     4.7    -      -       -      +
     71B  VAL*     2.8    43.1    +      -       +      +
     73B  ILE*     3.9    26.7    -      -       +      -
     84B  VAL*     4.3    13.2    -      -       +      -
     86B  LEU*     4.1    16.8    -      -       +      -
    103B  PHE*     5.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  ILE*     3.7     4.2    -      -       -      +
     16B  ASP*     2.8    24.6    +      -       -      -
     17B  GLN*     2.7    47.6    +      -       +      +
     19B  GLU*     5.9     1.6    -      -       -      +
     26B  GLN*     3.9     1.0    +      -       +      -
     27B  VAL*     1.3    72.5    -      -       -      +
     29B  PHE*     1.3    60.8    +      -       -      +
     68B  GLU*     3.1    20.3    -      -       -      +
     69B  GLY      3.2     3.1    -      -       -      +
     70B  ILE*     4.1    19.0    -      -       +      +
     44C  LYS*     4.7     0.8    -      -       -      +
     57C  SER*     2.9    43.7    +      -       -      +
     58C  LYS*     3.9     1.6    -      -       -      -
     59C  TRP*     3.5    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  PRO*     3.8    14.6    -      -       +      -
     14B  SER      3.0    17.9    -      -       -      +
     15B  ILE*     4.2     0.7    -      -       -      -
     16B  ASP*     3.6     5.4    -      -       -      -
     27B  VAL      3.9     7.4    -      -       -      -
     28B  GLN*     1.3    75.1    -      -       -      +
     30B  ASP*     1.3    69.5    +      -       -      +
     31B  GLU*     4.2     3.4    -      -       +      -
     43B  TYR*     3.4    53.6    -      +       -      -
     65B  ALA*     4.2     4.3    -      -       +      -
     66B  SER*     6.1     0.2    -      -       -      -
     69B  GLY*     2.8    49.2    +      -       -      +
     70B  ILE      3.7     4.3    -      -       -      -
     71B  VAL*     3.9    20.9    -      -       +      -
     86B  LEU*     3.6    30.5    -      -       +      -
     58C  LYS*     5.2     0.9    -      -       -      +
     59C  TRP*     4.0    12.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  PRO*     3.4     6.1    -      -       -      +
     14B  SER*     2.9    38.6    +      -       -      -
     16B  ASP*     2.5    26.7    +      -       -      +
     29B  PHE*     1.3    75.8    -      -       -      +
     31B  GLU*     1.3    64.3    +      -       -      +
     32B  PRO*     4.9     2.1    -      -       -      +
     42C  LYS*     2.8    28.0    +      -       -      +
     58C  LYS*     6.2     1.3    -      -       -      +
     59C  TRP      3.4    20.4    -      -       -      +
     60C  TYR*     4.0     0.7    -      -       -      -
     61C  ASP*     3.3    35.4    -      -       -      +
----------------------------------------------------------
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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