Contacts of the strand formed by residues 210 - 216 (chain G) 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 ILE 210 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154G  LEU*     5.7     4.0    -      -       +      -
    163G  ALA      3.9     8.1    -      -       -      +
    164G  GLY*     3.7    36.6    -      -       -      +
    166G  ALA*     4.1    13.2    -      -       +      +
    198G  PHE*     4.2    17.5    -      -       +      -
    199G  ALA      3.6     8.1    -      -       -      +
    200G  SER*     4.6    10.8    -      -       -      -
    201G  THR*     3.9     0.2    -      -       -      -
    206G  GLN      3.7    13.2    -      -       -      +
    207G  ASN      4.3     2.3    +      -       -      +
    208G  LYS      3.7     1.6    -      -       -      -
    209G  SER*     1.3    79.1    -      -       -      +
    211G  SER*     1.3    66.3    +      -       -      +
    258G  GLY*     3.1    13.3    -      -       -      +
    260G  GLY*     2.8    41.3    +      -       -      -
    261G  PHE*     3.9    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 211 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198G  PHE*     3.4     4.2    -      -       -      -
    199G  ALA      2.8    30.6    +      -       -      -
    201G  THR*     3.1    23.4    +      -       -      +
    210G  ILE*     1.3    72.7    -      -       -      +
    212G  ALA*     1.3    59.4    +      -       -      +
    213G  PHE*     3.3    30.4    -      -       -      -
    253G  ILE*     4.0     7.8    -      -       -      +
    256G  GLU      5.1     0.9    -      -       -      -
    257G  PRO*     3.3    11.4    -      -       -      +
    258G  GLY      3.2    16.2    +      -       -      +
    259G  MET      5.0     0.2    -      -       -      +
    260G  GLY*     3.8     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 212 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196G  VAL*     4.7     2.2    -      -       +      -
    197G  VAL      3.5     4.3    -      -       -      +
    198G  PHE*     3.7    26.0    -      -       +      -
    211G  SER*     1.3    71.5    -      -       -      +
    213G  PHE*     1.3    62.6    +      -       -      +
    253G  ILE*     3.5     5.8    -      -       -      +
    254G  LEU*     2.7    58.6    +      -       +      +
    256G  GLU      5.5     0.6    +      -       -      -
    260G  GLY*     3.8     3.4    -      -       -      +
    263G  ILE*     4.0    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 213 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170G  ALA*     3.5    29.8    -      -       +      -
    177G  TRP*     3.6    42.6    -      +       +      -
    179G  LEU*     4.7     7.2    -      -       +      -
    195G  ALA      3.4     1.2    -      -       -      +
    196G  VAL*     3.3     7.2    -      -       -      -
    197G  VAL*     2.8    45.3    +      -       -      +
    199G  ALA*     4.0    11.9    -      -       +      -
    201G  THR*     4.0     5.8    -      -       +      -
    211G  SER*     3.3    41.3    -      -       -      -
    212G  ALA*     1.3    77.1    -      -       -      +
    214G  LEU*     1.3    62.6    +      -       -      +
    215G  VAL*     3.9     5.5    +      -       +      -
    248G  ILE*     4.1    22.9    -      -       +      -
    252G  SER      3.5     3.6    -      -       -      +
    253G  ILE*     4.0    18.6    -      -       +      -
    254G  LEU*     5.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 214 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123G  TYR*     5.2     0.2    -      -       +      -
    127G  ILE*     3.6    35.0    -      -       +      -
    135G  GLN*     3.8    32.1    -      -       +      +
    139G  TRP*     3.3    57.3    -      -       +      +
    195G  ALA      3.5     2.5    -      -       -      +
    196G  VAL*     4.0    14.4    -      -       +      -
    213G  PHE*     1.3    72.1    -      -       -      +
    215G  VAL*     1.3    62.0    +      -       -      +
    216G  PRO*     4.2     1.6    -      -       -      +
    248G  ILE*     4.2     1.6    -      -       -      +
    252G  SER*     2.9    36.6    +      -       -      +
    254G  LEU*     4.5    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 215 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139G  TRP*     3.8     4.8    -      -       -      -
    179G  LEU*     3.9    12.3    -      -       +      -
    194G  ALA*     3.3     1.9    -      -       -      -
    195G  ALA*     2.9    39.6    +      -       +      +
    197G  VAL*     3.7    27.6    -      -       +      -
    213G  PHE*     4.2     4.5    -      -       +      +
    214G  LEU*     1.3    77.7    -      -       -      +
    216G  PRO*     1.4    80.3    -      -       +      +
    217G  MET*     4.0     0.6    -      -       +      +
    219G  THR*     4.2     9.9    -      -       +      -
    222G  LEU*     4.6     3.8    -      -       +      -
    243G  PHE*     3.9    24.2    -      -       +      -
    246G  CYS*     5.1     0.4    -      -       -      -
    248G  ILE*     3.7    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 216 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139G  TRP*     3.5    21.1    -      -       +      -
    193G  SER      3.7     7.9    -      -       -      +
    214G  LEU      4.2     2.0    -      -       -      +
    215G  VAL*     1.4    90.0    -      -       +      +
    217G  MET*     1.3    63.3    +      -       -      +
    218G  PRO      3.9     7.0    -      -       -      +
    219G  THR*     3.2    41.8    -      -       -      +
    248G  ILE*     4.5    13.7    -      -       +      -
    249G  PRO*     6.1     2.9    -      -       +      -
    252G  SER*     5.9     0.7    -      -       -      +
----------------------------------------------------------
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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