Contacts of the strand formed by residues 155 - 161 (chain J) 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 VAL 155 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12J  TYR*     3.5    11.7    +      -       -      -
    123J  PRO*     4.7     1.6    -      -       +      -
    150J  PHE*     3.7    47.1    -      -       +      -
    153J  ASP*     3.9     6.1    +      -       -      +
    154J  HIS*     1.3    80.2    -      -       -      +
    156J  GLU*     1.3    71.5    +      -       -      +
    157J  LEU      5.6     0.2    -      -       -      +
    190J  LEU*     4.6    15.5    -      -       +      -
    212J  VAL*     4.1    20.2    -      -       +      -
    213J  GLN      3.2    12.1    -      -       -      +
    214J  PHE*     4.0    14.8    -      -       +      -
    215J  TYR*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 156 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11J  LYS*     4.2    15.3    +      -       -      +
     12J  TYR*     3.9    20.8    -      -       +      +
    155J  VAL*     1.3    81.9    -      -       -      +
    157J  LEU*     1.3    63.6    +      -       -      +
    158J  SER*     5.2     0.7    +      -       -      -
    211J  GLN*     3.5     2.4    +      -       -      +
    212J  VAL*     3.5     5.0    -      -       -      -
    213J  GLN*     3.0    44.6    +      -       +      +
    215J  TYR*     3.6    28.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 157 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145J  CYS*     4.4    16.6    -      -       +      +
    147J  ALA*     4.7     7.9    -      -       +      -
    155J  VAL*     5.4     1.4    -      -       +      +
    156J  GLU*     1.3    75.1    -      -       -      +
    158J  SER*     1.3    73.2    +      -       -      +
    159J  TRP*     4.0    13.2    -      -       +      +
    172J  THR*     4.6    13.7    -      -       +      +
    190J  LEU*     4.1    26.6    -      -       +      +
    192J  SER*     3.5    39.0    -      -       -      +
    210J  CYS*     3.9    20.0    -      -       -      -
    211J  GLN      3.3     5.6    -      -       -      +
    212J  VAL*     4.3    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 158 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156J  GLU      5.2     0.6    +      -       -      -
    157J  LEU*     1.3    80.0    -      -       -      +
    159J  TRP*     1.3    64.8    +      -       -      +
    160J  TRP*     2.8    27.9    +      -       -      -
    165J  GLU*     3.7    21.5    -      -       -      -
    210J  CYS*     3.6     4.0    -      -       -      -
    211J  GLN*     2.8    54.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 159 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127J  VAL*     4.3    13.5    -      -       +      -
    143J  LEU*     3.9    31.0    -      -       +      -
    144J  VAL      4.2     1.6    -      -       -      -
    145J  CYS*     3.4    42.2    -      -       +      -
    157J  LEU*     4.0     8.6    -      -       +      +
    158J  SER*     1.3    73.3    -      -       -      +
    160J  TRP*     1.3    63.7    +      -       -      +
    161J  VAL*     4.2     0.9    -      -       +      -
    165J  GLU*     3.2    11.3    +      -       -      +
    166J  VAL*     3.1    43.7    +      -       +      +
    170J  VAL*     3.6    33.0    -      -       +      -
    192J  SER*     2.9    25.2    +      -       -      -
    193J  ARG      4.0     5.7    +      -       -      -
    194J  LEU*     3.7    29.6    -      -       +      -
    208J  PHE*     5.1     4.3    -      -       +      -
    209J  ARG      3.6    20.9    -      -       -      -
    210J  CYS*     4.0    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 160 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158J  SER*     2.8    33.2    +      -       -      -
    159J  TRP*     1.3    78.6    -      -       -      +
    161J  VAL*     1.3    63.2    +      -       -      +
    162J  ASN      4.0     0.6    +      -       -      -
    163J  GLY*     4.0    10.7    +      -       -      +
    164J  LYS*     3.6    19.1    -      -       -      +
    165J  GLU*     3.5    43.5    -      -       +      +
    207J  HIS*     3.7     2.4    +      -       -      +
    208J  PHE      3.7     0.7    -      -       -      -
    209J  ARG*     2.8    73.4    +      -       +      +
    211J  GLN*     3.9    25.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 161 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159J  TRP*     4.2     0.8    -      -       +      -
    160J  TRP*     1.3    73.9    -      -       -      +
    162J  ASN*     1.3    83.9    +      -       -      +
    163J  GLY      3.4     1.3    -      -       -      -
    164J  LYS*     2.9    27.6    +      -       -      +
    166J  VAL*     3.9    31.8    -      -       +      +
    194J  LEU*     4.3    10.3    -      -       +      -
    196J  VAL*     6.2     0.4    -      -       +      -
    200J  PHE*     4.2    20.0    -      -       +      -
    207J  HIS      3.4    10.8    -      -       -      +
    208J  PHE*     4.0    28.5    -      -       +      -
----------------------------------------------------------
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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