Contacts of the strand formed by residues 20 - 30 (chain B) in PDB entry 2VAA


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 PRO 20 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  HIS*     4.6     6.4    -      -       -      -
     18B  GLY      3.6     7.0    -      -       -      +
     19B  LYS*     1.3    93.8    -      -       +      +
     21B  ASN*     1.3    61.0    +      -       -      +
     69B  GLU*     6.5     0.7    -      -       +      -
     70B  PHE      3.6     0.9    -      -       -      +
     71B  THR*     3.4    21.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  SER*     3.7    12.6    +      -       -      -
     12B  ARG      3.2     4.7    +      -       -      -
     13B  HIS*     3.0    64.9    +      -       -      +
     14B  PRO      4.1     5.7    +      -       -      -
     15B  PRO*     4.1     8.9    -      -       -      +
     16B  GLU      5.2     1.0    -      -       -      +
     19B  LYS      4.2     4.7    +      -       -      +
     20B  PRO*     1.3    75.5    +      -       -      +
     22B  ILE*     1.3    79.9    +      -       -      +
     69B  GLU*     3.3     8.5    -      -       -      +
     70B  PHE*     2.6    42.8    +      -       +      +
     72B  PRO*     4.3     3.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  ALA      3.9     4.0    -      -       -      +
    237A  GLY*     4.1     9.9    -      -       -      +
    238A  ASP*     4.0    27.4    -      -       +      -
     11B  SER*     3.1     7.1    -      -       -      -
     12B  ARG*     2.9    39.3    +      -       +      -
     13B  HIS*     5.9     1.1    -      -       -      +
     21B  ASN*     1.3    90.4    +      -       -      +
     23B  LEU*     1.3    69.6    +      -       -      +
     24B  ASN*     3.9    17.7    +      -       -      +
     67B  HIS*     4.0    14.1    -      -       +      +
     68B  THR      3.4    12.6    -      -       -      +
     69B  GLU*     4.5    14.1    -      -       +      -
     70B  PHE*     3.5     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  VAL*     4.0    12.6    -      -       +      -
     10B  TYR      3.7    17.3    -      -       -      +
     11B  SER      4.5     0.2    -      -       -      +
     22B  ILE*     1.3    73.4    -      -       -      +
     24B  ASN*     1.3    62.6    +      -       -      +
     39B  MET*     3.5    25.9    -      -       +      +
     46B  ILE*     5.2     1.6    -      -       +      -
     67B  HIS*     3.2     6.6    -      -       -      +
     68B  THR*     2.8    38.4    +      -       +      +
     70B  PHE*     3.5    20.9    -      -       +      -
     78B  TYR*     3.4    42.8    -      -       +      -
     79B  ALA      5.1     2.7    -      -       -      +
     95B  TRP*     3.9    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  ALA*     2.9    42.1    +      -       -      +
    237A  GLY*     3.4     1.9    +      -       -      -
      8B  GLN      4.2     0.4    -      -       -      -
      9B  VAL*     3.2    10.6    -      -       -      +
     10B  TYR*     2.7    68.4    +      -       +      +
     12B  ARG      4.0     5.3    -      -       -      +
     22B  ILE*     3.9     9.5    +      -       -      +
     23B  LEU*     1.3    77.3    -      -       -      +
     25B  CYS*     1.3    60.4    +      -       -      +
     26B  TYR      4.0     0.4    -      -       -      -
     39B  MET*     4.0     2.5    -      -       -      -
     65B  LEU*     3.8    10.1    -      -       +      +
     66B  ALA      3.4     2.7    -      -       -      -
     67B  HIS*     3.2    21.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ILE*     3.7    20.4    -      -       -      -
      8B  GLN      3.2     4.5    -      -       -      -
      9B  VAL*     4.5     0.7    -      -       +      +
     24B  ASN*     1.3    73.6    -      -       -      +
     26B  TYR*     1.3    58.6    +      -       -      +
     27B  VAL*     3.7    14.1    +      -       -      +
     37B  ILE*     4.3     0.9    -      -       -      -
     39B  MET*     3.9     9.9    -      -       +      -
     64B  ILE      3.9     0.2    -      -       -      +
     65B  LEU*     3.7     1.5    -      -       -      -
     66B  ALA*     2.7    43.0    +      -       +      +
     80B  CYS*     2.0    53.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  GLU*     5.6     3.1    -      -       +      -
    233A  THR      4.6     5.4    +      -       -      -
    234A  ARG*     3.6    29.6    -      -       +      -
    235A  PRO*     3.6    24.3    -      -       +      +
      6B  GLN      3.4     4.2    -      -       -      +
      7B  ILE*     3.6     0.5    -      -       -      -
      8B  GLN*     2.9    45.3    +      -       +      +
     10B  TYR*     3.6    23.3    -      -       +      +
     24B  ASN      4.0     0.4    -      -       -      -
     25B  CYS*     1.3    71.9    -      -       -      +
     27B  VAL*     1.3    62.1    +      -       -      +
     28B  THR*     3.3    28.1    +      -       +      +
     53B  ASP*     4.5     7.2    +      -       -      +
     55B  SER*     4.7     4.3    +      -       -      -
     63B  TYR*     3.4    22.7    -      +       +      +
     64B  ILE      3.3    28.9    -      -       -      -
     65B  LEU*     3.9    13.0    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
      5B  PRO*     3.7    19.7    -      -       +      -
      6B  GLN      3.4     4.5    -      -       -      +
      7B  ILE*     4.3     8.5    -      -       +      -
     25B  CYS*     3.8    23.8    -      -       -      +
     26B  TYR*     1.3    74.5    -      -       -      +
     28B  THR*     1.3    59.7    +      -       -      +
     30B  PHE*     3.3    10.5    -      -       +      -
     35B  ILE*     3.6    29.8    -      -       +      -
     37B  ILE*     3.7    20.0    -      -       +      -
     64B  ILE*     2.9    40.7    +      -       +      +
     82B  VAL*     4.0    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 28 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  GLU*     4.8     1.3    +      -       -      +
      5B  PRO*     3.4     3.1    -      -       -      +
      6B  GLN*     2.8    52.1    +      -       -      +
      8B  GLN*     3.7    11.8    +      -       -      +
     26B  TYR*     3.3    37.2    -      -       +      -
     27B  VAL*     1.3    80.1    -      -       -      +
     29B  GLN*     1.3    73.7    +      -       -      +
     30B  PHE*     3.5     1.8    -      -       -      -
     62B  PHE      3.4     5.4    -      -       -      -
     63B  TYR*     3.4    30.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  GLU*     2.7    34.1    +      -       -      -
      3B  LYS*     3.5    12.7    -      -       +      +
      4B  THR      3.3    15.3    -      -       -      +
      6B  GLN*     3.3    21.7    -      -       +      +
     28B  THR*     1.3    79.2    +      -       -      +
     30B  PHE*     1.3    57.0    +      -       -      +
     57B  SER*     5.1     0.2    -      -       -      +
     59B  ASP*     5.6     2.7    -      -       -      +
     61B  SER*     3.3    23.7    -      -       -      +
     62B  PHE      2.8     9.8    +      -       -      -
     63B  TYR*     2.9    21.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3B  LYS*     3.4    14.1    -      -       -      +
      5B  PRO*     3.7    17.7    -      -       +      -
     27B  VAL*     3.3    39.9    -      -       +      -
     28B  THR      4.0     3.6    -      -       -      -
     29B  GLN*     1.3    77.6    -      -       -      +
     31B  HIS*     1.3    64.5    +      -       -      +
     32B  PRO      3.5    13.2    -      -       -      -
     33B  PRO*     3.8    24.9    -      -       +      -
     35B  ILE*     4.0    19.5    -      -       +      -
     61B  SER*     3.6     1.8    -      -       -      -
     62B  PHE*     2.9    59.9    +      +       +      -
     64B  ILE*     3.9    21.3    -      -       +      -
     84B  HIS*     4.0     8.1    -      -       -      +
----------------------------------------------------------
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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