Contacts of the strand formed by residues 235 - 242 (chain C) in PDB entry 2VGB


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 GLY 235 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  LEU*     3.7     7.1    -      -       -      +
    185C  VAL      3.4    11.4    -      -       -      -
    186C  THR*     4.8     1.8    -      -       -      -
    187C  VAL*     5.6     0.4    -      -       -      -
    208C  VAL*     4.3    15.9    -      -       -      +
    231C  ILE*     5.4     0.2    -      -       -      -
    232C  GLY*     3.3    28.5    +      -       -      +
    233C  PRO      3.5     3.8    +      -       -      -
    234C  GLU*     1.3    80.7    -      -       -      +
    236C  LEU*     1.3    66.0    +      -       -      -
    237C  VAL*     3.7     3.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 236 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  LEU*     3.5     5.3    -      -       -      +
    185C  VAL*     3.0    37.5    +      -       +      +
    207C  ILE*     3.9    32.3    -      -       +      +
    208C  VAL*     3.9    24.9    -      -       +      +
    211C  VAL*     4.0    17.9    -      -       +      +
    217C  ILE*     4.2    22.4    -      -       +      -
    228C  VAL*     4.2    11.7    -      -       +      -
    230C  LYS      3.8     2.0    -      -       -      -
    231C  ILE*     3.9    27.8    -      -       +      -
    235C  GLY*     1.3    71.8    -      -       -      -
    237C  VAL*     1.3    63.1    +      -       -      +
    238C  THR*     3.2    16.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 237 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  GLN*     4.2    23.3    -      -       +      -
    183C  VAL      4.3     2.2    -      -       -      +
    184C  LEU*     4.7    10.3    -      -       +      +
    228C  VAL*     3.7     1.9    -      -       -      -
    229C  GLN*     2.8    31.8    +      -       +      +
    230C  LYS*     2.6    42.5    +      -       +      +
    231C  ILE      5.4     2.0    -      -       -      -
    232C  GLY*     5.9     2.0    -      -       -      -
    235C  GLY      3.7     5.3    +      -       -      +
    236C  LEU*     1.3    71.6    -      -       -      +
    238C  THR*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 238 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  GLN*     3.4    11.3    -      -       -      +
    183C  VAL*     2.4    63.6    +      -       -      +
    185C  VAL*     4.1    17.3    -      -       +      -
    217C  ILE*     4.5     5.6    -      -       +      -
    226C  LEU*     4.0    18.1    -      -       +      +
    227C  VAL      3.5     8.7    -      -       -      -
    228C  VAL*     4.2    15.7    -      -       +      +
    229C  GLN*     4.2     3.8    -      -       -      -
    236C  LEU*     3.4    24.0    -      -       +      +
    237C  VAL*     1.3    77.5    -      -       -      +
    239C  GLN*     1.3    59.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 239 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180C  GLY*     3.7    25.8    +      -       -      +
    181C  SER      3.3     9.0    -      -       -      +
    182C  GLN*     4.1     6.3    -      -       -      +
    226C  LEU*     3.7     2.4    -      -       -      -
    227C  VAL*     3.0    37.1    +      -       +      +
    229C  GLN*     3.4    32.3    +      -       -      +
    238C  THR*     1.3    73.4    -      -       -      +
    240C  VAL*     1.3    69.8    +      -       -      +
    241C  GLU*     3.2     1.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 240 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177C  LEU*     3.9    11.9    -      -       +      +
    178C  VAL      3.2    18.8    -      -       -      +
    179C  LYS*     3.8     1.3    -      -       -      +
    180C  GLY*     2.9    27.9    +      -       -      +
    181C  SER*     2.9    33.8    +      -       -      +
    183C  VAL*     3.4    27.6    -      -       +      -
    224C  ILE*     5.4     0.2    -      -       +      -
    225C  SER      4.1     2.0    -      -       -      +
    226C  LEU*     3.7    14.4    -      -       +      -
    239C  GLN*     1.3    71.2    -      -       -      +
    241C  GLU*     1.3    60.7    +      -       -      +
    242C  ASN      3.4    23.1    -      -       -      +
    243C  GLY*     3.7    14.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 241 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179C  LYS*     3.3    29.6    +      -       -      +
    216C  ARG*     2.6    38.3    +      -       -      -
    225C  SER*     2.5    38.8    +      -       -      +
    227C  VAL*     3.5    19.3    -      -       +      +
    239C  GLN      3.2     2.0    +      -       -      +
    240C  VAL*     1.3    73.2    -      -       -      +
    242C  ASN*     1.3    67.6    +      -       -      +
    243C  GLY      4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 242 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    381A  PRO*     4.8    14.0    -      -       +      +
    179C  LYS*     5.1     4.3    +      -       -      +
    218C  TYR*     6.0     0.8    -      -       -      -
    223C  LEU      4.1    11.9    -      -       -      +
    224C  ILE*     3.8     2.9    -      -       -      +
    225C  SER*     3.0    52.2    +      -       -      +
    240C  VAL*     3.4     7.3    -      -       -      +
    241C  GLU*     1.3    87.7    +      -       -      +
    243C  GLY*     1.3    61.6    +      -       -      +
----------------------------------------------------------
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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