Contacts of the strand formed by residues 161 - 167 (chain D) in PDB entry 1VEW


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 PHE 161 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  VAL*     3.2     2.2    -      -       -      -
    133D  LEU*     2.8    47.0    +      -       +      +
    150D  LEU*     4.4    13.5    -      -       +      -
    160D  GLY*     1.3    73.2    -      -       -      -
    162D  PRO*     1.3    80.2    -      -       +      +
    163D  ILE*     3.4    14.4    +      -       +      -
    200D  ARG*     3.4    55.4    -      -       +      -
    204D  LYS*     3.6    25.4    -      -       -      +
    205D  LYS*     3.5    38.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 162 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  LEU*     4.0    19.1    -      -       +      -
    130D  TRP*     4.0    25.6    -      -       +      -
    131D  LEU      3.8     5.6    -      -       -      +
    132D  VAL*     4.1     4.3    -      -       +      -
    148D  SER*     4.7     3.6    -      -       -      +
    149D  PRO*     4.1    14.4    -      -       +      -
    150D  LEU*     3.6    30.3    -      -       +      -
    160D  GLY      3.6     6.0    -      -       -      +
    161D  PHE*     1.3    91.9    -      -       +      +
    163D  ILE*     1.3    61.5    +      -       -      +
    164D  MET      4.8     0.7    -      -       -      +
    200D  ARG*     2.8    34.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 163 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  LEU*     5.0     2.1    -      -       -      +
     98D  LEU*     4.7     9.0    -      -       +      -
    131D  LEU*     2.8    32.4    +      -       +      +
    133D  LEU*     4.2    16.4    -      -       +      +
    138D  LEU*     4.3    15.3    -      -       +      -
    161D  PHE*     3.9    28.9    -      -       +      +
    162D  PRO*     1.3    75.0    -      -       -      +
    164D  MET*     1.3    63.9    +      -       +      +
    197D  ALA*     3.5    37.0    -      -       +      +
    200D  ARG*     3.3    22.4    -      -       -      +
    201D  PHE*     3.9    29.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 164 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  LEU*     4.6     7.6    -      -       -      -
     87D  GLY*     5.5     7.0    -      -       -      +
    112D  PHE*     3.8    29.2    -      -       +      -
    116D  PHE*     3.9    24.2    -      -       +      -
    130D  TRP*     3.5     9.4    -      -       -      -
    131D  LEU*     2.9    40.2    +      -       +      +
    162D  PRO      3.6     0.4    -      -       -      -
    163D  ILE*     1.3    87.6    +      -       +      +
    165D  GLY*     1.3    61.6    +      -       -      +
    188D  PHE*     4.2    13.9    -      -       +      -
    189D  TRP*     4.9     4.7    -      -       +      -
    192D  VAL*     4.0    20.4    -      -       +      -
    194D  TRP*     4.1    20.0    -      -       +      -
    197D  ALA*     4.5     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 165 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  LEU*     4.2     8.5    -      -       -      +
     84D  PHE*     3.7    16.9    -      -       -      -
    116D  PHE*     4.5     1.1    -      -       -      -
    128D  TRP*     4.5     5.4    -      -       -      -
    129D  ALA      3.2    11.4    -      -       -      -
    130D  TRP*     3.7    17.3    -      -       -      -
    164D  MET*     1.3    79.5    -      -       -      +
    166D  LEU*     1.3    60.7    +      -       -      +
    188D  PHE*     3.8    13.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 166 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  PHE*     4.6     0.7    -      -       +      -
     84D  PHE*     4.0     6.1    -      -       +      -
    116D  PHE*     3.9    24.7    -      -       +      -
    120D  ALA*     4.3     4.0    -      -       +      -
    128D  TRP*     3.3     9.1    -      -       -      -
    129D  ALA*     2.8    31.0    +      -       +      +
    165D  GLY*     1.3    74.5    -      -       -      +
    167D  ASP*     1.3    68.2    +      -       -      +
    168D  VAL*     3.5    17.1    +      -       +      +
    184D  TYR*     3.4    31.2    -      -       +      +
    185D  ILE*     4.1    22.7    -      -       +      -
    188D  PHE*     3.5    44.2    -      -       +      -
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Residues in contact with ASP 167 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26D  HIS*     3.0     7.8    +      -       -      -
     81D  HIS*     3.4     2.4    +      -       -      -
     84D  PHE*     3.8    16.2    -      -       +      -
    127D  GLY      3.7     0.5    -      -       -      +
    128D  TRP*     3.5    28.4    -      -       +      -
    166D  LEU*     1.3    75.6    -      -       -      +
    168D  VAL*     1.3    63.1    +      -       -      +
    169D  TRP*     3.2    15.7    +      -       -      +
    172D  ALA*     3.8    13.6    -      -       +      +
    184D  TYR*     2.7    32.2    +      -       -      -
    206D   MN      2.0    35.2    +      -       -      -
    207D   OH      2.8    14.6    +      -       -      -
----------------------------------------------------------
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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