Contacts of the helix formed by residues 82 - 91 (chain D) in PDB entry 2V5Q


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 THR 82 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  HIS*     3.7     2.0    -      -       -      -
     73D  VAL      4.5     3.8    -      -       -      -
     74D  ASP*     3.6    32.7    +      -       +      +
     75D  ALA      3.3     3.6    -      -       -      +
     76D  ALA*     4.7     3.8    -      -       +      -
     80D  GLY      3.5     3.3    +      -       -      +
     81D  PHE*     1.3    78.5    -      -       -      +
     83D  PRO*     1.4    76.4    -      -       -      +
     84D  LEU*     3.4    11.2    +      -       -      +
     85D  HIS*     2.9    41.7    +      -       +      +
     86D  LEU*     3.2    11.3    +      -       -      +
    105D  ASP      5.3     0.2    +      -       -      -
    108D  ALA*     4.0    25.0    -      -       +      +
    109D  PHE      6.2     0.2    -      -       -      +
    116D  PRO*     4.7     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49D  THR*     4.6     0.7    -      -       -      +
     51D  LEU*     3.8    42.4    -      -       +      +
     52D  HIS*     3.7    31.6    -      -       +      +
     55D  ALA*     3.6    12.0    -      -       +      +
     72D  ASP      4.7     1.1    -      -       -      +
     73D  VAL      3.3    19.5    -      -       -      +
     75D  ALA      3.3    13.5    -      -       -      +
     82D  THR*     1.4    82.2    -      -       -      +
     84D  LEU*     1.3    55.0    +      -       -      +
     86D  LEU*     3.2     3.5    +      -       +      +
     87D  ALA*     3.0    25.3    +      -       -      +
     99D  LEU*     3.6    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 84 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73D  VAL      5.2     0.8    +      -       -      +
     74D  ASP*     5.9     0.7    -      -       -      +
     82D  THR*     3.1    10.6    +      -       -      +
     83D  PRO*     1.3    75.6    -      -       -      +
     85D  HIS*     1.3    64.6    +      -       -      +
     88D  ALA*     3.0    27.4    +      -       +      +
     96D  VAL*     3.8    47.1    -      -       +      +
     99D  LEU*     3.5    15.1    -      -       +      +
    100D  LEU*     3.9    22.4    -      -       +      -
    104D  ALA*     4.1    16.4    -      -       +      -
    105D  ASP      3.6    22.9    -      -       -      +
    106D  VAL*     4.0     4.7    -      -       -      -
    116D  PRO*     3.7    17.9    -      -       +      -
    132D  LEU*     4.1     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 85 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80D  GLY      3.7     9.0    -      -       -      -
     81D  PHE*     3.6    21.0    -      +       +      -
     82D  THR*     2.9    39.2    +      -       +      +
     84D  LEU*     1.3    77.5    -      -       -      +
     86D  LEU*     1.3    58.2    +      -       -      +
     88D  ALA*     3.4     1.6    +      -       -      +
     89D  MET*     3.0    33.2    +      -       -      +
    108D  ALA*     3.0    29.0    +      -       +      -
    109D  PHE      4.0     0.4    -      -       -      -
    110D  ASP*     3.6    16.5    +      -       +      -
    114D  SER      2.9    22.0    +      -       -      -
    116D  PRO*     3.5    22.7    -      -       +      +
    119D  LEU*     3.4    25.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 86 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  THR*     4.0    16.4    -      -       +      +
     48D  LEU*     4.0    13.0    -      -       +      -
     52D  HIS*     3.7    43.5    -      -       +      +
     56D  VAL*     3.8    27.3    -      -       +      +
     81D  PHE*     3.7    32.5    -      -       +      -
     82D  THR      3.8     8.7    -      -       -      +
     83D  PRO*     3.2     7.9    +      -       +      +
     85D  HIS*     1.3    79.7    -      -       -      +
     87D  ALA*     1.3    61.1    +      -       -      +
     89D  MET*     3.5    16.6    -      -       +      +
     90D  THR*     2.8    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55D  ALA*     4.2    10.5    -      -       +      +
     83D  PRO      3.0    15.2    +      -       -      +
     84D  LEU      4.0     1.8    -      -       -      +
     86D  LEU*     1.3    74.5    -      -       -      +
     88D  ALA*     1.3    61.0    +      -       -      +
     90D  THR*     3.3     5.6    +      -       -      -
     91D  GLY*     3.0    23.0    +      -       -      -
     92D  HIS*     3.0    14.8    +      -       +      +
     95D  ILE*     3.6    33.2    -      -       +      -
     96D  VAL*     3.8    16.3    -      -       +      +
     99D  LEU*     4.2     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84D  LEU*     3.0    19.6    +      -       +      +
     85D  HIS      3.8     3.4    -      -       -      +
     87D  ALA*     1.3    78.0    -      -       -      +
     89D  MET*     1.3    61.2    +      -       -      +
     91D  GLY*     3.4     9.4    +      -       -      -
     96D  VAL*     3.8    10.9    -      -       +      +
    116D  PRO*     3.6    31.2    -      -       +      +
    120D  ALA*     3.5    12.0    -      -       +      +
    125D  HIS*     3.4    11.3    -      -       -      +
    128D  ILE*     3.8    19.9    -      -       +      +
    132D  LEU*     4.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316A  ILE*     3.9    11.9    -      -       +      +
    317A  THR*     3.5    44.3    -      -       +      +
    320A  THR*     5.5     0.9    -      -       -      -
     56D  VAL*     5.8     0.9    -      -       -      -
     81D  PHE*     3.5    22.2    -      -       +      -
     85D  HIS      3.0    19.6    +      -       -      +
     86D  LEU*     3.5    31.2    -      -       +      +
     88D  ALA*     1.3    76.5    -      -       -      +
     90D  THR*     1.3    61.5    +      -       +      +
     91D  GLY      3.4     0.2    -      -       -      -
    119D  LEU*     3.5    36.6    -      -       +      -
    120D  ALA*     4.8     0.2    -      -       -      +
    123D  GLU*     3.4    22.6    -      -       +      +
    125D  HIS*     2.9    20.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  THR*     3.8    20.2    -      -       +      -
    321A  ILE*     4.0    13.2    -      -       +      -
     55D  ALA      4.3     0.2    +      -       -      -
     56D  VAL*     3.7    27.7    +      -       +      +
     86D  LEU      2.8    23.1    +      -       -      +
     87D  ALA*     3.3     4.7    +      -       -      -
     89D  MET*     1.3    76.3    -      -       +      +
     91D  GLY*     1.3    60.6    +      -       -      +
     92D  HIS*     2.9    40.1    +      -       -      -
    125D  HIS*     3.5    10.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 91 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87D  ALA      3.0     6.4    +      -       -      -
     88D  ALA      3.4     6.2    +      -       -      -
     89D  MET      3.4     0.8    -      -       -      -
     90D  THR*     1.3    78.5    -      -       -      +
     92D  HIS*     1.3    60.1    +      -       -      +
     93D  LEU*     3.1     9.9    +      -       -      +
    125D  HIS*     3.5    26.0    -      -       -      -
    128D  ILE*     4.1    12.2    -      -       -      +
----------------------------------------------------------
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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