Contacts of the strand formed by residues 210 - 216 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154E  LEU*     5.5     3.4    -      -       +      -
    163E  ALA      3.8     7.6    -      -       -      +
    164E  GLY*     3.4    39.9    -      -       -      +
    166E  ALA*     4.3    14.6    -      -       +      +
    198E  PHE*     3.9    21.3    -      -       +      -
    199E  ALA      3.4    13.5    -      -       -      +
    200E  SER*     4.5     4.5    -      -       -      -
    209E  SER*     1.3    87.6    -      -       -      +
    211E  SER*     1.3    68.7    +      -       -      +
    258E  GLY*     3.1    12.7    +      -       -      +
    260E  GLY*     2.7    36.5    +      -       -      -
    261E  PHE*     4.0    22.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 211 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198E  PHE*     3.4     5.1    -      -       -      -
    199E  ALA      2.9    30.0    +      -       -      +
    201E  THR*     2.7    37.1    +      -       -      +
    210E  ILE*     1.3    72.7    -      -       -      +
    212E  ALA*     1.3    59.5    +      -       -      +
    213E  PHE*     3.7    16.4    -      -       -      -
    253E  ILE*     3.9    12.3    -      -       -      -
    256E  GLU      4.7     1.1    -      -       -      -
    257E  PRO*     3.2     7.6    -      -       -      +
    258E  GLY      2.9    17.5    +      -       -      +
    259E  MET      4.9     0.2    -      -       -      +
    260E  GLY*     3.8     8.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 212 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196E  VAL*     4.4     2.2    -      -       +      -
    197E  VAL      3.4     5.6    -      -       -      +
    198E  PHE*     3.7    26.9    -      -       +      -
    211E  SER*     1.3    73.5    -      -       -      +
    213E  PHE*     1.3    58.3    +      -       -      +
    253E  ILE*     3.4    10.2    -      -       -      +
    254E  LEU*     2.7    60.3    +      -       +      +
    260E  GLY*     4.0     3.0    -      -       -      +
    263E  ILE*     4.2    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 213 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170E  ALA*     3.3    33.9    -      -       +      -
    177E  TRP*     3.6    34.3    -      +       +      -
    179E  LEU*     4.7     6.5    -      -       +      -
    195E  ALA      3.3     4.2    -      -       -      +
    196E  VAL*     3.4     3.4    -      -       -      -
    197E  VAL*     2.8    45.1    +      -       +      +
    199E  ALA*     4.1    11.0    -      -       +      -
    201E  THR*     3.9     7.6    -      -       +      -
    211E  SER*     3.7    35.9    -      -       -      -
    212E  ALA*     1.3    74.3    -      -       -      +
    214E  LEU*     1.3    63.1    +      -       -      +
    215E  VAL*     3.7     8.0    +      -       +      +
    248E  ILE*     4.0    24.9    -      -       +      -
    252E  SER      3.4     2.2    -      -       -      -
    253E  ILE*     3.7    26.0    -      -       +      -
    254E  LEU*     5.1     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 214 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123E  TYR*     5.1     1.1    -      -       +      -
    127E  ILE*     3.8    31.0    -      -       +      -
    135E  GLN*     3.9    32.3    -      -       +      +
    139E  TRP*     3.7    55.7    -      -       +      +
    195E  ALA      3.5     3.4    -      -       -      +
    196E  VAL*     3.9    18.6    -      -       +      -
    213E  PHE*     1.3    71.7    -      -       -      +
    215E  VAL*     1.3    58.1    +      -       -      +
    216E  PRO*     4.2     1.9    -      -       -      +
    248E  ILE*     3.7     3.8    -      -       -      +
    252E  SER*     2.8    37.6    +      -       -      +
    254E  LEU*     4.5    16.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 215 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139E  TRP*     3.8     4.1    -      -       -      -
    179E  LEU*     4.0    21.5    -      -       +      -
    194E  ALA*     3.3     2.4    -      -       -      -
    195E  ALA*     2.9    40.8    +      -       +      +
    197E  VAL*     3.6    25.6    -      -       +      -
    213E  PHE*     4.0     5.6    -      -       +      +
    214E  LEU*     1.3    77.7    -      -       -      +
    216E  PRO*     1.4    80.0    -      -       +      +
    217E  MET*     5.1     1.1    -      -       +      -
    219E  THR*     4.2     9.9    -      -       +      -
    222E  LEU*     4.4     4.5    -      -       +      -
    243E  PHE*     4.0    21.5    -      -       +      -
    248E  ILE*     4.1    15.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 216 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139E  TRP*     3.7    21.1    -      -       +      -
    193E  SER      3.8     8.1    -      -       -      +
    214E  LEU      4.2     2.2    -      -       -      +
    215E  VAL*     1.4    91.8    -      -       +      +
    217E  MET*     1.3    65.5    +      -       -      +
    218E  PRO      3.6     7.2    -      -       -      +
    219E  THR*     3.3    40.5    -      -       -      +
    222E  LEU*     3.9     0.5    -      -       -      +
    248E  ILE*     4.7     9.9    -      -       +      -
    249E  PRO*     6.0     3.8    -      -       +      -
    252E  SER*     5.9     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page


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