Contacts of the strand formed by residues 32 - 37 (chain C) in PDB entry 1VI9


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 ASN 32 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  MSE      3.2    33.3    -      -       -      +
      3C  LYS      2.8    10.3    +      -       -      +
      4C  ASN*     3.1    29.4    +      -       -      +
      5C  ILE*     2.8    28.1    +      -       -      +
     27C  ARG*     4.9     1.5    +      -       -      -
     31C  ALA*     1.3    74.1    -      -       -      +
     33C  VAL*     1.3    63.1    +      -       -      +
     34C  TRP*     4.5     9.0    -      -       +      +
     16D  HIS*     4.4    14.5    +      -       -      -
    267D  GLN*     4.8     8.5    +      -       -      +
    269D  VAL*     3.5    18.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 33 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  ILE*     3.4     5.2    -      -       +      +
      7C  ALA*     4.0    26.2    -      -       +      -
     19C  ASN*     5.5     0.4    -      -       -      +
     23C  GLU*     4.3    18.4    -      -       +      +
     26C  MSE      3.7    42.6    -      -       +      -
     27C  ARG*     2.8    52.1    +      -       +      +
     31C  ALA      3.9     1.5    +      -       -      +
     32C  ASN*     1.3    79.3    -      -       -      +
     34C  TRP*     1.3    68.1    +      -       -      +
     35C  PRO*     3.2    12.2    -      -       +      +
     13D  VAL      4.6     0.5    -      -       -      +
     16D  HIS*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 34 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  ASN*     3.7    33.8    +      -       +      +
      5C  ILE      2.8    14.7    +      -       -      +
      6C  LEU*     3.4    20.9    -      -       +      +
      7C  ALA      2.9    24.2    +      -       -      -
     32C  ASN*     4.5     4.9    -      -       +      +
     33C  VAL*     1.3    79.9    -      -       -      +
     35C  PRO*     1.3    63.0    -      -       -      +
     36C  LEU      3.2     5.1    +      -       -      -
     67C  ILE*     4.1    32.5    -      -       +      -
     72C  LYS      3.5    10.8    -      -       -      -
     73C  LEU*     4.5     5.6    -      -       +      -
     75C  THR*     3.3    27.1    -      -       -      -
     76C  CYS*     3.6    27.1    -      -       +      -
     13D  VAL*     3.2    25.1    -      -       +      +
     14D  TYR*     3.6    27.8    -      +       -      -
     15D  GLY      5.1     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 35 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  ALA      3.6     5.8    -      -       -      +
     19C  ASN*     3.9    11.0    -      -       +      +
     23C  GLU*     4.8     8.3    -      -       +      -
     27C  ARG*     4.1    15.9    -      -       -      +
     33C  VAL*     3.2    22.9    -      -       +      +
     34C  TRP*     1.3    79.2    -      -       -      +
     36C  LEU*     1.3    60.8    +      -       -      +
     37C  ASN*     3.1    21.2    +      -       -      +
     11D  HIS*     2.8    44.1    +      -       +      +
     12D  VAL      4.6     1.1    -      -       -      +
     13D  VAL*     3.6    15.0    -      -       -      +
     20D  SER*     6.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 36 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  LEU*     3.8    18.2    -      -       +      -
      7C  ALA      2.8    12.2    +      -       -      +
      8C  ILE*     3.2    43.2    -      -       +      +
      9C  GLN      3.5     0.5    +      -       -      -
     19C  ASN*     3.8     0.7    -      -       -      -
     34C  TRP      3.2     3.6    +      -       -      -
     35C  PRO*     1.3    67.9    -      -       -      +
     37C  ASN*     1.3    64.0    +      -       -      +
     38C  THR      3.4     1.9    +      -       -      -
     59C  HIS*     4.5     0.2    -      -       -      +
     60C  LEU*     3.6    52.0    -      -       +      +
     63C  ILE*     3.9    31.0    -      -       +      -
     64C  VAL*     4.1    15.0    -      -       +      -
     96C  ILE*     4.3     0.4    -      -       +      -
     13D  VAL*     3.8     8.1    -      -       +      -
     40D  GLN*     3.9    10.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 37 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  GLN      3.3     4.7    -      -       -      -
     11C  HIS*     3.3    41.0    +      -       +      +
     19C  ASN*     3.1    24.4    +      -       -      +
     35C  PRO*     3.1    16.9    +      -       -      +
     36C  LEU*     1.3    72.0    -      -       -      +
     38C  THR*     1.3    63.1    +      -       -      +
     39C  VAL      3.7     5.8    -      -       -      +
     40C  GLN*     5.9     0.9    -      -       +      +
     55C  MSE      3.5     7.3    -      -       -      +
     60C  LEU*     4.2     3.6    -      -       -      +
     11D  HIS*     3.9     9.7    +      -       -      -
     37D  ASN*     3.7    18.6    -      -       -      +
     40D  GLN*     3.1    33.3    +      -       -      +
----------------------------------------------------------
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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