Contacts of the strand formed by residues 23 - 28 (chain C) in PDB entry 3V4P


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 VAL 23 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20C  GLY*     3.6    22.4    -      -       -      +
     22C  SER*     1.3    82.2    -      -       -      +
     24C  VAL*     1.3    74.7    -      -       -      +
     25C  LEU*     5.1     2.2    -      -       +      +
     34C  LEU*     3.5    28.3    -      -       +      -
     35C  LEU      3.4     6.1    -      -       -      +
     36C  VAL*     4.6     7.2    -      -       +      -
     98C  LEU*     4.5     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 24 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  VAL*     1.3    81.5    -      -       -      +
     25C  LEU*     1.3    80.4    +      -       -      +
     26C  HIS*     3.7     3.7    +      -       +      -
     34C  LEU*     3.8     4.6    -      -       -      +
     35C  LEU*     2.9    45.2    +      -       +      +
     98C  LEU*     3.5    43.5    -      -       +      +
     99C  SER*     3.7     7.6    -      -       -      +
    100C  ARG*     3.5    25.6    -      -       +      +
    108C  ILE*     5.4     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 25 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  VAL*     5.9     1.8    -      -       +      -
     24C  VAL*     1.3    83.8    -      -       -      +
     26C  HIS*     1.3    59.4    +      -       -      +
     33C  TRP      3.8     1.1    -      -       -      +
     34C  LEU*     4.0    20.4    -      -       +      -
     60C  ILE*     4.1    22.7    -      -       +      -
    100C  ARG*     3.3    12.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 26 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24C  VAL*     3.7     1.3    +      -       +      -
     25C  LEU*     1.3    75.8    -      -       -      +
     27C  SER*     1.3    83.8    +      -       -      +
     28C  HIS*     3.9     6.3    +      -       +      +
     31C  ASN      3.9     0.3    -      -       -      +
     32C  ARG*     3.8     4.2    -      -       -      -
     33C  TRP*     2.9    50.8    +      +       +      +
     35C  LEU*     4.2    12.6    -      -       +      -
    100C  ARG*     3.0    31.9    +      -       -      +
    106C  GLY      3.6    12.3    -      -       -      -
    108C  ILE*     3.4    28.0    -      -       +      +
    137C  PRO*     3.3    27.0    +      -       +      +
    139C  LEU*     3.9    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 27 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  HIS*     1.3    87.8    +      -       -      +
     28C  HIS*     1.3    61.4    +      -       -      +
     29C  GLY      3.9     2.8    +      -       -      -
     31C  ASN      3.4     4.7    -      -       -      -
     32C  ARG*     3.8    28.0    -      -       -      -
    100C  ARG*     3.4    26.2    +      -       -      +
    104C  GLU*     4.8     4.7    -      -       -      +
    105C  ASN      4.0     7.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 28 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  HIS*     3.9    11.7    +      -       +      +
     27C  SER*     1.3    70.5    -      -       -      +
     29C  GLY*     1.3    54.7    +      -       -      +
     30C  ALA      2.6    18.2    +      -       -      -
     31C  ASN*     2.9    43.3    +      -       +      -
     33C  TRP*     4.9     5.8    -      -       +      +
    105C  ASN*     3.6    16.7    +      -       -      +
    137C  PRO*     3.4    40.8    -      -       +      +
    138C  ASP*     3.4    31.2    +      -       -      +
----------------------------------------------------------
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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