Contacts of the strand formed by residues 194 - 200 (chain B) in PDB entry 2VIG


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 ALA 194 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  TYR*     3.2    30.7    -      -       +      +
    139B  TRP*     3.7    20.2    -      -       +      -
    143B  PHE*     3.5    13.0    -      -       +      -
    150B  GLY*     3.3     4.9    -      -       -      -
    151B  CYS*     3.1    26.2    +      -       -      -
    192B  ALA*     3.5     2.6    -      -       -      +
    193B  SER*     1.3    81.8    -      -       -      +
    195B  ALA*     1.3    61.7    +      -       -      +
    215B  VAL      3.2     7.4    -      -       -      -
    217B  MET*     3.7     5.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123B  TYR*     4.5     3.2    -      -       -      -
    139B  TRP*     5.2     0.2    -      -       -      -
    151B  CYS*     3.2    28.5    -      -       -      -
    153B  ALA*     5.0     2.2    -      -       +      -
    194B  ALA*     1.3    72.4    -      -       -      +
    196B  VAL*     1.3    64.0    +      -       -      +
    197B  VAL*     3.7    19.4    +      -       +      +
    213B  PHE      3.4     1.9    -      -       -      +
    214B  LEU*     3.6     4.2    -      -       -      +
    215B  VAL*     2.9    34.3    +      -       +      +
    217B  MET*     3.7    10.3    -      -       -      -
    241B  LEU*     4.2     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  LEU      4.1    11.0    -      -       -      +
    123B  TYR*     3.7    39.0    -      -       +      +
    126B  PRO*     4.4     9.0    -      -       +      -
    127B  ILE*     4.5     0.9    -      -       +      -
    151B  CYS      2.8    12.6    +      -       -      +
    152B  PHE*     3.6     3.7    -      -       +      -
    153B  ALA*     2.8    32.7    +      -       -      +
    195B  ALA*     1.3    71.2    -      -       -      +
    197B  VAL*     1.3    56.3    +      -       -      +
    198B  PHE*     4.1    24.3    -      -       +      -
    212B  ALA*     4.5     6.5    -      -       +      -
    213B  PHE      3.4     7.0    -      -       -      +
    214B  LEU*     4.2    11.4    -      -       +      -
    254B  LEU*     4.2    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  ALA*     3.5    11.9    -      -       +      +
    168B  THR*     5.1     3.8    -      -       +      -
    179B  LEU*     4.6    11.0    -      -       +      -
    183B  LYS*     4.2    11.2    -      -       +      -
    195B  ALA*     3.7    20.2    -      -       +      +
    196B  VAL*     1.3    77.2    -      -       -      +
    198B  PHE*     1.3    70.7    +      -       -      +
    199B  ALA*     5.3     0.9    -      -       +      -
    211B  SER      3.6     1.6    -      -       -      +
    212B  ALA*     3.5     2.6    -      -       -      -
    213B  PHE*     2.8    36.1    +      -       +      +
    215B  VAL*     3.2    32.8    -      -       +      -
    243B  PHE*     3.9    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126B  PRO*     5.9     0.2    -      -       +      -
    152B  PHE*     3.4    34.1    -      +       -      -
    153B  ALA      3.0    22.1    +      -       -      +
    154B  LEU*     3.7    25.6    -      -       +      -
    166B  ALA*     4.5     4.4    -      -       +      +
    168B  THR*     4.3     1.9    -      -       -      -
    183B  LYS*     2.9    31.2    +      -       -      +
    196B  VAL*     4.1    21.5    -      -       +      -
    197B  VAL*     1.3    73.8    -      -       -      +
    199B  ALA*     1.3    62.0    +      -       -      +
    210B  ILE*     4.1     8.5    -      -       +      -
    211B  SER      3.3     6.3    -      -       -      +
    212B  ALA*     3.8    18.8    -      -       +      -
    260B  GLY*     3.1    33.4    -      -       -      -
    263B  ILE*     4.2     7.2    -      -       +      -
    264B  ALA*     3.3    26.7    -      -       +      -
    267B  THR*     5.2     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  ALA*     5.4     0.9    -      -       -      -
    168B  THR*     3.7    15.5    -      -       +      +
    169B  THR      4.0     5.8    -      -       -      +
    170B  ALA*     3.7    31.2    -      -       +      +
    179B  LEU*     4.8     5.6    -      -       +      -
    197B  VAL*     3.9     2.0    +      -       +      +
    198B  PHE*     1.3    76.0    -      -       -      +
    200B  SER*     1.3    61.5    +      -       -      +
    201B  THR*     3.4     2.8    +      -       -      +
    210B  ILE*     3.5     4.6    -      -       -      +
    211B  SER*     2.8    38.2    +      -       -      +
    213B  PHE*     3.9    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166B  ALA*     3.6    20.2    +      -       -      +
    167B  SER*     5.1     0.9    -      -       -      -
    168B  THR      2.7    19.0    +      -       -      -
    169B  THR*     3.4    13.9    -      -       -      +
    170B  ALA      3.1    20.8    +      -       -      +
    199B  ALA*     1.3    70.1    -      -       -      +
    201B  THR*     1.3    63.2    +      -       -      +
    209B  SER*     3.4    13.7    +      -       -      -
    210B  ILE*     4.4     7.8    -      -       -      +
----------------------------------------------------------
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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