Contacts of the strand formed by residues 147 - 151 (chain C) in PDB entry 1VCB


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 ILE 147 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72C  SER*     4.2     3.1    -      -       -      +
     73C  GLN      3.0    13.0    +      -       -      +
     74C  VAL*     3.4     8.7    -      -       +      +
     75C  ILE*     2.9    27.1    +      -       -      +
    131C  ASN*     5.7     0.7    -      -       -      +
    136C  PHE*     3.6    31.6    -      -       +      -
    139C  SER*     3.8    41.1    -      -       -      +
    140C  LEU      4.1    14.6    -      -       -      +
    141C  ASN*     4.1     3.4    -      -       -      +
    145C  GLN      3.9    12.8    -      -       -      +
    146C  PRO*     1.3    73.7    -      -       -      +
    148C  PHE*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 148 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  ILE*     3.2    44.0    -      -       +      -
     77C  CYS*     3.5    26.9    -      -       +      -
     79C  ARG*     4.0    10.5    -      -       -      -
    131C  ASN*     3.0    22.9    +      -       -      +
    136C  PHE*     4.1     4.0    -      -       -      -
    146C  PRO      3.8     2.2    +      -       -      -
    147C  ILE*     1.3    77.0    -      -       -      +
    149C  ALA*     1.3    60.2    +      -       -      +
    150C  ASN*     3.3    28.8    +      -       -      +
     44K  ALA*     3.2    24.2    -      -       +      +
     45K  MET*     3.0    48.0    -      -       +      -
     48K  GLY*     5.6     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 149 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74C  VAL*     4.1     0.4    -      -       +      -
     75C  ILE      2.8    17.1    +      -       -      +
     76C  PHE*     3.8    21.1    -      -       +      -
     77C  CYS      3.0    25.2    +      -       -      +
    119C  PHE*     4.7     1.8    -      -       +      -
    130C  VAL*     3.8    19.7    -      -       +      -
    131C  ASN*     3.7     3.6    -      -       -      +
    136C  PHE*     4.0    18.6    -      -       +      -
    148C  PHE*     1.3    72.5    -      -       -      +
    150C  ASN*     1.3    64.1    +      -       -      +
    151C  ILE*     3.4     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 150 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77C  CYS*     3.7     3.9    -      -       -      +
     79C  ARG*     3.6    27.7    +      -       -      -
    129C  LEU      3.5     0.9    -      -       -      +
    130C  VAL*     3.1     3.5    -      -       -      -
    131C  ASN*     2.7    55.6    +      -       -      +
    148C  PHE*     3.3    32.5    +      -       -      +
    149C  ALA*     1.3    69.0    -      -       -      +
    151C  ILE*     1.3    62.5    -      -       -      +
    152C  THR*     3.8    13.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 151 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  PHE*     4.3     4.9    -      -       +      -
     77C  CYS      3.0    19.1    +      -       -      +
     78C  ASN*     4.1     5.4    -      -       -      +
     79C  ARG*     3.0    30.7    +      -       -      +
     80C  SER*     3.9     1.8    +      -       -      +
     84C  VAL*     3.8    30.3    -      -       +      -
    101C  LEU*     4.0    25.6    -      -       +      -
    119C  PHE*     3.6    44.0    -      -       +      -
    128C  LEU*     4.2    12.3    -      -       +      -
    129C  LEU      3.2    10.3    -      -       -      +
    130C  VAL*     4.6     1.8    -      -       +      -
    149C  ALA      3.7    11.0    -      -       -      +
    150C  ASN*     1.3    74.0    -      -       -      +
    152C  THR*     1.3    63.0    +      -       -      +
----------------------------------------------------------
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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