Contacts of the strand formed by residues 199 - 208 (chain F) in PDB entry 2VLR


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 199 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191F  HIS*     3.7    31.2    -      -       +      +
    193F  ALA*     4.1     9.6    -      -       +      +
    198F  GLU*     1.3    76.7    -      -       -      +
    200F  THR*     1.3    62.8    +      -       -      +
    201F  LEU*     3.8     3.5    +      -       -      +
    247F  VAL      4.8     1.0    -      -       -      +
    248F  VAL*     5.9     0.4    -      -       -      -
    249F  VAL*     4.4    14.5    +      -       -      +
    251F  SER*     4.2    12.4    -      -       -      +
    254F  GLU*     4.2    17.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 200 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190F  THR      3.4     5.0    -      -       -      +
    191F  HIS*     3.5     2.4    +      -       -      -
    192F  HIS*     2.9    49.4    +      -       -      +
    194F  VAL*     3.7    15.3    -      -       +      +
    199F  ALA*     1.3    70.5    -      -       -      +
    201F  LEU*     1.3    65.8    +      -       -      +
    202F  ARG*     5.2     2.9    -      -       +      +
    246F  ALA*     5.1     6.3    -      -       +      -
    247F  VAL      3.3    20.2    -      -       -      +
    248F  VAL*     3.3    36.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 201 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189F  MET*     5.0     9.6    -      -       +      -
    190F  THR      3.4    14.8    -      -       -      +
    191F  HIS*     3.5    25.4    -      -       +      -
    199F  ALA      3.8     4.1    +      -       -      +
    200F  THR*     1.3    73.8    -      -       -      +
    202F  ARG*     1.3    61.0    +      -       -      +
    217F  TRP*     4.1    21.8    -      -       +      -
    247F  VAL*     2.9    38.1    +      -       +      +
    254F  GLU*     3.3    25.1    -      -       -      +
    257F  TYR*     4.8    20.6    -      -       +      -
    274F  TRP*     3.8    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 202 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188F  HIS      4.0    12.1    -      -       -      +
    189F  MET*     4.9     3.5    -      -       -      +
    190F  THR*     3.4    29.7    +      -       -      +
    200F  THR*     5.2     4.0    -      -       +      +
    201F  LEU*     1.3    75.4    -      -       -      +
    203F  CYS*     1.3    58.8    +      -       -      +
    204F  TRP*     3.3    48.4    +      -       +      +
    217F  TRP*     4.2     4.0    -      -       -      -
    229F  GLU*     3.5     6.6    +      -       -      -
    244F  TRP*     3.2    52.3    -      -       -      +
    245F  ALA      4.0     0.2    -      -       -      -
    246F  ALA*     3.0    42.7    -      -       +      +
     98G  ASP*     4.4     5.9    +      -       -      +
     99G  MET*     3.5    25.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 203 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187F  THR*     5.3     7.2    -      -       -      -
    188F  HIS      5.4     0.7    -      -       -      -
    189F  MET*     5.4     6.3    -      -       +      -
    202F  ARG*     1.3    69.5    -      -       -      +
    204F  TRP*     1.3    68.9    +      -       -      +
    215F  LEU*     4.0    15.9    -      -       -      +
    217F  TRP*     3.2    18.9    -      -       +      +
    244F  TRP*     3.4     5.5    -      -       -      +
    245F  ALA*     2.8    44.8    +      -       +      +
    259F  CYS*     2.0    50.5    -      -       -      -
    261F  VAL*     5.5     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 204 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186F  LYS      4.3     0.2    -      -       -      -
    187F  THR*     3.2    27.9    -      -       -      +
    188F  HIS*     3.3    44.5    +      +       +      +
    189F  MET*     5.9     0.2    -      -       -      +
    190F  THR*     4.5     2.7    -      -       -      -
    202F  ARG*     3.3    36.7    +      -       +      +
    203F  CYS*     1.3    76.1    -      -       -      +
    205F  ALA*     1.3    58.4    +      -       -      +
    206F  LEU*     3.8    38.4    -      -       +      -
    234F  ARG*     3.6    25.8    -      -       -      -
    242F  GLN*     4.7     1.8    -      -       +      -
    243F  LYS      3.9    12.1    -      -       -      -
    244F  TRP*     3.4    28.5    -      +       +      -
     98G  ASP*     3.5    36.4    +      -       -      -
     99G  MET*     3.9    14.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 205 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185F  PRO*     4.6     4.9    -      -       +      -
    186F  LYS      3.8     2.9    -      -       -      -
    187F  THR*     4.4     4.3    -      -       +      -
    203F  CYS      3.9     0.2    +      -       -      -
    204F  TRP*     1.3    74.1    -      -       -      +
    206F  LEU*     1.3    63.0    +      -       -      +
    208F  PHE*     3.2    19.4    -      -       +      -
    213F  ILE*     3.9    14.8    -      -       +      -
    215F  LEU*     3.9    22.9    -      -       +      -
    242F  GLN*     3.4     1.7    -      -       -      +
    243F  LYS*     2.8    46.3    +      -       +      +
    261F  VAL*     4.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 206 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185F  PRO*     3.4     3.1    -      -       -      +
    186F  LYS*     2.8    41.8    +      -       +      +
    188F  HIS*     3.8    31.9    -      -       +      +
    204F  TRP*     3.8    34.1    -      -       +      -
    205F  ALA*     1.3    74.4    -      -       -      +
    207F  SER*     1.3    68.5    +      -       -      +
    208F  PHE*     3.3     5.0    +      -       -      -
    241F  PHE      4.0     3.6    -      -       -      -
    242F  GLN*     3.8    38.6    -      -       +      +
     12G  ARG      5.9     0.4    -      -       -      +
     14G  PRO*     4.9    12.6    -      -       +      -
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Residues in contact with SER 207 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183F  ASP*     3.8    15.2    -      -       -      +
    184F  ALA      4.0     6.0    -      -       -      +
    186F  LYS*     3.7    38.2    +      -       -      +
    206F  LEU*     1.3    78.9    -      -       -      +
    208F  PHE*     1.3    60.3    +      -       -      +
    240F  THR*     4.0    22.4    +      -       -      +
    241F  PHE      3.2     8.7    +      -       -      -
    242F  GLN*     5.2     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 208 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183F  ASP      3.2    13.7    -      -       -      +
    184F  ALA      4.6     0.2    -      -       -      -
    185F  PRO*     4.1    13.5    -      -       +      -
    205F  ALA*     3.2    34.5    -      -       +      -
    206F  LEU      3.7    11.0    -      -       -      -
    207F  SER*     1.3    78.2    -      -       -      +
    209F  TYR*     1.3    63.7    +      -       -      +
    210F  PRO      3.6    14.8    -      -       -      -
    211F  ALA      3.6    20.0    -      -       -      -
    213F  ILE*     3.9    22.2    -      -       +      -
    233F  THR*     4.0     2.7    -      -       +      -
    240F  THR*     3.6     4.8    -      -       -      -
    241F  PHE*     3.1    52.1    +      -       +      -
    242F  GLN      3.7    16.8    -      -       -      -
    243F  LYS*     3.8    10.3    -      -       +      -
    263F  HIS*     3.8    13.7    -      -       +      +
----------------------------------------------------------
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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