Contacts of the strand formed by residues 33 - 39 (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 33 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31J  HIS*     3.5     0.7    -      -       -      +
     32J  ASP*     1.3    76.6    -      -       -      +
     34J  MET*     1.3    65.9    +      -       -      +
     35J  TYR*     3.8     9.2    -      -       -      +
     51J  SER      3.2    10.1    -      -       -      +
     52J  GLN      3.9     5.4    -      -       -      +
     95J  SER*     3.2     6.9    -      -       -      -
     96J  SER*     3.1    40.6    +      -       -      +
     99J  ALA*     3.6    34.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 34 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25J  CYS*     5.0     9.6    -      -       -      +
     27J  GLN*     3.9    22.7    -      -       -      +
     31J  HIS      5.4     0.2    -      -       -      +
     33J  ALA*     1.3    77.6    -      -       -      +
     35J  TYR*     1.3    64.5    +      -       -      +
     50J  TYR*     3.3     4.7    -      -       -      +
     51J  SER*     2.8    38.8    +      -       -      +
     70J  ARG*     2.6    39.6    -      -       -      +
     73J  LYS      2.6    31.0    -      -       -      +
     74J  GLU      4.4     1.3    -      -       -      +
     75J  SER      3.5    20.6    -      -       -      +
     76J  PHE*     3.6    31.7    -      -       +      -
     93J  CYS*     5.1     1.6    -      -       -      -
     94J  ALA      3.3     8.5    -      -       -      +
     95J  SER*     4.1    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 35 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97I  GLY      2.7    22.9    +      -       -      -
     98I  ASN*     3.9    10.5    -      -       +      -
     33J  ALA*     3.8    15.9    -      -       +      +
     34J  MET*     1.3    76.4    -      -       -      +
     36J  TRP*     1.3    59.9    +      -       -      +
     37J  TYR*     3.8    23.6    -      -       +      -
     47J  LEU*     4.3    11.2    -      -       +      -
     49J  TYR      3.8     4.5    -      -       -      -
     50J  TYR*     3.4    37.1    -      +       +      -
     51J  SER      5.1     0.8    +      -       -      -
     52J  GLN*     5.4     0.2    -      -       -      +
     76J  PHE*     4.0     2.2    -      -       -      -
     92J  LEU      4.7     0.4    -      -       -      -
     93J  CYS*     3.3    11.3    -      -       -      -
     94J  ALA*     2.9    35.6    +      -       +      +
     95J  SER*     4.6     0.2    -      -       -      -
     96J  SER*     3.5    19.5    -      -       -      -
     99J  ALA*     3.4    20.4    -      -       -      +
    100J  SER      3.7     3.5    +      -       -      -
    103J  GLN*     3.6    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 36 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8J  GLN*     3.3    31.2    -      -       -      -
     23J  LEU*     3.9    29.4    -      -       +      -
     24J  SER      4.0     7.6    -      -       -      -
     25J  CYS*     3.6    18.8    -      -       +      -
     35J  TYR*     1.3    71.8    -      -       -      +
     37J  TYR*     1.3    64.4    +      -       -      +
     47J  LEU*     3.6     8.8    -      -       -      +
     48J  ILE*     3.0    35.5    +      -       +      +
     49J  TYR*     3.1    14.2    +      -       +      +
     68J  VAL*     4.4     7.2    -      -       +      -
     76J  PHE*     2.8    51.4    +      +       -      -
     78J  LEU*     3.5    37.3    -      -       +      +
     91J  TYR*     3.9    19.3    -      -       +      -
     92J  LEU      3.6    22.7    -      -       -      -
     93J  CYS*     4.0    13.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 37 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98I  ASN*     6.1     0.2    -      -       -      +
     99I  LEU*     4.9     4.6    +      -       -      +
    101I  PHE*     3.6    28.9    -      +       -      -
     35J  TYR*     3.8    21.7    -      -       +      +
     36J  TRP*     1.3    76.5    -      -       -      +
     38J  ARG*     1.3    60.4    +      -       -      +
     45J  LEU*     4.0    27.8    -      -       +      -
     46J  ARG      3.2     8.7    -      -       -      +
     47J  LEU*     3.9    33.3    -      -       +      +
     48J  ILE*     3.8     5.3    -      -       -      +
     91J  TYR*     3.7     8.1    -      -       -      +
     92J  LEU*     2.9    43.8    +      -       +      +
     94J  ALA*     4.2     2.7    -      -       +      -
    103J  GLN*     2.6    40.2    +      -       -      -
    105J  PHE*     3.7    24.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 38 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37J  TYR*     1.3    76.3    -      -       -      +
     39J  GLN*     1.3    62.6    +      -       -      +
     40J  ASP*     2.9    31.1    +      -       -      -
     44J  GLY      4.0     0.5    -      -       -      +
     45J  LEU*     3.8     2.6    -      -       -      -
     46J  ARG*     2.9    64.5    +      -       +      +
     48J  ILE*     3.8    15.9    -      -       +      +
     62J  ILE*     4.6    15.9    -      -       +      +
     66J  TYR*     3.1    29.1    +      -       -      -
     84J  GLN      5.5     0.6    +      -       -      -
     86J  ASN*     3.0    38.7    +      -       -      +
     88J  THR      3.6     9.7    +      -       -      -
     89J  ALA*     3.8    10.5    -      -       +      +
     90J  PHE      3.4     7.0    -      -       -      +
     91J  TYR*     3.8    12.7    +      -       +      -
     92J  LEU*     6.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 39 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38I  GLN*     3.1    39.4    +      -       -      -
     41I  GLY      5.7     0.9    +      -       -      -
     87I  LEU*     4.3     6.5    -      -       -      +
     89I  LEU*     6.2     0.2    -      -       -      +
     38J  ARG*     1.3    77.6    -      -       -      +
     40J  ASP*     1.3    74.5    +      -       -      +
     41J  PRO*     4.7     0.9    -      -       -      +
     42J  GLY      6.0     0.2    -      -       -      +
     43J  GLN      2.8    23.7    +      -       -      +
     44J  GLY*     3.5    18.6    -      -       -      +
     45J  LEU*     4.3    15.2    -      -       +      +
     89J  ALA*     4.2     1.6    -      -       -      +
     90J  PHE*     2.8    57.3    +      -       +      +
     92J  LEU*     4.2     2.3    -      -       +      +
----------------------------------------------------------
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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