Contacts of the strand formed by residues 89 - 96 (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 ALA 89 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38J  ARG*     3.8    28.3    -      -       +      +
     39J  GLN      4.2     6.1    -      -       -      +
     40J  ASP*     4.1     6.7    -      -       -      +
     87J  PRO      3.3     3.1    +      -       -      +
     88J  THR*     1.3    78.6    -      -       -      +
     90J  PHE*     1.3    63.0    +      -       -      +
     91J  TYR*     3.6    24.7    -      -       +      -
    110J  ARG*     3.9     5.0    +      -       -      +
    111J  LEU      3.1    31.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 90 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38I  GLN*     4.2     0.4    -      -       -      -
     41I  GLY*     3.5    33.9    -      -       -      -
     42I  GLU      3.7    22.4    -      -       -      -
     38J  ARG*     3.4     3.8    -      -       -      -
     39J  GLN*     2.8    68.0    +      -       +      +
     89J  ALA*     1.3    72.9    -      -       -      +
     91J  TYR*     1.3    59.5    +      -       -      +
     92J  LEU*     3.8    21.9    +      -       +      +
    107J  PRO      3.9     4.5    -      -       -      -
    108J  GLY*     3.7    31.0    -      -       -      -
    109J  THR      3.6    13.5    -      -       -      -
    110J  ARG*     3.7    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 91 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8J  GLN*     3.7     3.1    +      -       -      -
     23J  LEU*     3.5    28.9    -      -       +      -
     36J  TRP*     3.9     6.1    -      +       +      -
     37J  TYR      3.7    11.4    -      -       -      -
     38J  ARG*     3.8    13.2    +      -       +      -
     48J  ILE*     3.9     8.7    -      -       +      -
     66J  TYR*     2.7    38.6    +      +       -      -
     78J  LEU*     3.9    17.5    -      -       +      -
     80J  VAL*     4.6     5.9    -      -       +      +
     87J  PRO*     2.8    29.9    +      -       -      +
     89J  ALA*     3.6    26.4    -      -       +      +
     90J  PHE*     1.3    72.2    -      -       -      +
     92J  LEU*     1.3    61.3    +      -       -      +
    108J  GLY*     3.3     7.1    -      -       -      -
    109J  THR*     2.9    37.5    +      -       -      +
    111J  LEU*     4.1    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 92 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38I  GLN*     3.9     6.1    -      -       -      +
     43I  GLY*     3.8    15.5    -      -       -      -
     44I  PRO*     3.8    19.1    -      -       +      -
      8J  GLN*     3.9     0.9    -      -       -      -
     36J  TRP*     3.6     6.9    -      -       -      -
     37J  TYR*     2.9    48.0    +      -       +      +
     38J  ARG      6.3     0.2    -      -       -      -
     39J  GLN*     4.2     3.4    -      -       +      +
     45J  LEU*     3.7    27.4    -      -       +      -
     90J  PHE*     3.8    34.0    +      -       +      +
     91J  TYR*     1.3    71.0    -      -       -      +
     93J  CYS*     1.3    58.1    +      -       -      +
    105J  PHE*     4.2    13.9    -      -       +      -
    106J  GLY      3.6    23.8    -      -       -      +
    108J  GLY*     3.9    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 93 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  ILE*     4.4     2.5    -      -       +      -
      8J  GLN*     3.2    18.9    +      -       +      +
     25J  CYS*     2.0    52.9    -      -       +      -
     34J  MET*     5.1     2.9    -      -       -      -
     35J  TYR      3.3    14.1    -      -       -      +
     36J  TRP*     4.1    16.4    -      -       +      -
     76J  PHE*     4.9     7.9    -      -       -      -
     92J  LEU*     1.3    74.2    -      -       -      +
     94J  ALA*     1.3    75.0    +      -       -      +
    105J  PHE*     3.5     4.9    -      -       -      -
    106J  GLY      3.0    25.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 94 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  ILE*     4.0     5.6    -      -       -      -
     34J  MET*     3.3     5.9    -      -       -      +
     35J  TYR*     2.9    33.5    +      -       +      +
     37J  TYR*     4.2     7.0    -      -       +      -
     93J  CYS*     1.3    76.8    -      -       -      +
     95J  SER*     1.3    61.8    +      -       -      +
    103J  GLN*     3.7    29.4    -      -       +      +
    104J  TYR      3.3    17.3    -      -       -      +
    105J  PHE*     4.1    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 95 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  ILE*     3.9     9.7    -      -       -      +
     27J  GLN*     4.0    18.0    -      -       -      +
     29J  LEU*     3.9    13.5    -      -       -      +
     31J  HIS*     2.8    34.3    +      -       -      -
     33J  ALA      3.2    13.7    -      -       -      -
     34J  MET*     4.1     4.7    -      -       -      -
     35J  TYR*     4.6     0.9    -      -       -      -
     94J  ALA*     1.3    75.0    -      -       -      +
     96J  SER*     1.3    58.8    +      -       -      +
    102J  GLU      4.1     0.2    -      -       -      +
    103J  GLN*     3.5     5.9    -      -       -      -
    104J  TYR      3.0    30.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 96 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31J  HIS*     3.0    20.3    -      -       -      +
     33J  ALA*     3.1    21.6    +      -       -      +
     35J  TYR*     3.5    21.9    +      -       -      -
     95J  SER*     1.3    72.6    -      -       -      +
     97J  SER*     1.3    65.9    +      -       -      +
     98J  ARG      3.2    19.9    +      -       -      -
     99J  ALA*     4.1     0.2    -      -       -      -
    100J  SER      4.6     0.3    +      -       -      -
    101J  TYR*     3.7    13.1    +      -       -      -
    102J  GLU      3.3    22.2    -      -       -      -
    103J  GLN*     4.1     3.2    -      -       -      +
----------------------------------------------------------
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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