Contacts of the strand formed by residues 409 - 416 (chain A) in PDB entry 2OIV


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 HIS 409 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    405A  GLN*     2.7    44.2    +      -       +      +
    408A  ALA*     1.3    82.1    +      -       +      +
    410A  TRP*     1.3    81.4    +      -       -      +
    429A  ASP*     2.5    30.7    +      -       -      -
    430A  SER*     3.9     2.9    -      -       -      -
    431A  MET*     3.3    30.6    +      -       -      -
    438A  GLN*     3.4    40.0    +      -       +      +
    470A  CYS*     3.5    22.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  TRP*     5.4     4.7    -      +       +      -
    339A  LEU*     2.9    28.7    +      -       +      -
    341A  ASP*     3.4    34.3    -      -       -      -
    344A  LEU*     3.6    30.1    -      -       +      +
    369A  SER*     3.5    22.9    -      -       -      -
    402A  PRO*     3.6    14.6    -      -       +      -
    403A  ILE      3.3    22.7    -      -       -      -
    404A  ASN*     3.5    34.7    +      -       +      -
    409A  HIS*     1.3    93.3    +      -       -      +
    411A  SER*     1.3    59.9    +      -       -      +
    430A  SER*     4.6     2.4    +      -       -      -
    438A  GLN*     3.9     1.1    -      -       -      -
    470A  CYS*     3.2    25.8    -      -       -      +
    471A  GLY*     3.6    24.5    -      -       -      +
    474A  VAL*     3.7    17.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  PRO*     3.7     1.6    -      -       -      +
    403A  ILE*     2.8    34.1    +      -       -      +
    410A  TRP*     1.3    75.1    -      -       -      +
    412A  LEU*     1.3    62.1    +      -       -      +
    427A  HIS*     2.7    25.7    +      -       -      -
    428A  TYR      3.3    15.3    -      -       -      -
    429A  ASP*     4.0     9.9    -      -       -      +
    438A  GLN*     2.9    27.9    +      -       -      +
    474A  VAL*     3.6    12.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400A  PHE*     4.2     4.7    -      -       +      -
    401A  LEU      3.7    22.4    -      -       -      +
    411A  SER*     1.3    76.0    -      -       -      +
    413A  LEU*     1.3    66.8    +      -       -      +
    414A  VAL*     3.8    20.2    -      -       +      -
    426A  TYR      3.5     1.7    -      -       -      +
    427A  HIS*     3.4     5.5    -      -       -      -
    428A  TYR*     2.9    54.9    +      -       +      +
    461A  ILE*     5.6     1.8    -      -       +      -
    474A  VAL*     4.2    17.9    -      -       +      +
    477A  GLY*     4.2     9.2    -      -       -      -
    478A  ILE*     3.8    49.1    -      -       +      +
    481A  LEU*     4.5     4.0    -      -       +      -
    498A  LEU*     4.8     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400A  PHE*     3.7     0.9    -      -       -      -
    401A  LEU*     2.7    68.4    +      -       +      +
    403A  ILE*     4.1    13.7    -      -       +      +
    412A  LEU*     1.3    74.5    -      -       -      +
    414A  VAL*     1.3    61.6    +      -       -      +
    415A  VAL*     4.2     9.2    -      -       +      -
    425A  ALA*     4.4     5.2    -      -       +      -
    426A  TYR      3.3    18.2    -      -       -      +
    427A  HIS*     4.2     8.1    -      -       +      -
    442A  ALA*     3.6    26.7    -      -       +      +
    445A  ALA*     4.0    16.6    -      -       +      -
    446A  ALA*     4.1     9.0    -      -       +      +
    449A  LEU*     5.1     0.2    -      -       +      -
    456A  THR*     3.7    29.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398A  ILE*     4.5    11.0    -      -       +      -
    399A  VAL      3.3     7.4    -      -       -      +
    400A  PHE*     3.7    35.0    -      -       +      -
    412A  LEU*     3.8    13.2    -      -       +      -
    413A  LEU*     1.3    78.7    -      -       -      +
    415A  VAL*     1.3    71.0    +      -       -      +
    416A  ASP      5.0     0.4    -      -       -      +
    425A  ALA*     3.2     5.7    -      -       -      +
    426A  TYR*     2.7    53.5    +      -       +      +
    428A  TYR*     3.8    10.1    -      -       +      -
    481A  LEU*     3.8    20.2    -      -       +      -
    490A  PHE*     4.7    10.3    -      -       +      -
    496A  ARG*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 415 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  PRO      3.3     3.1    -      -       -      +
    398A  ILE*     3.3     2.9    -      -       -      +
    399A  VAL*     2.7    47.3    +      -       +      +
    401A  LEU*     3.5    24.0    -      -       +      -
    413A  LEU*     4.2     9.9    -      -       +      -
    414A  VAL*     1.3    76.6    -      -       -      +
    416A  ASP*     1.3    64.5    +      -       -      +
    417A  ARG*     4.3    21.3    -      -       +      +
    423A  VAL*     3.8    23.8    -      -       +      -
    424A  ALA      3.6     3.1    -      -       -      +
    425A  ALA*     4.4     3.4    -      -       +      -
    449A  LEU*     4.3     8.3    -      -       +      -
    451A  LEU*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397A  PRO      3.5     2.7    -      -       -      -
    398A  ILE*     3.8     9.7    -      -       +      +
    414A  VAL*     4.2     0.6    -      -       +      -
    415A  VAL*     1.3    71.2    -      -       -      +
    417A  ARG*     1.3    60.0    +      -       -      +
    418A  ARG*     2.8    58.8    +      -       -      +
    419A  ASN      5.0     0.6    +      -       -      -
    422A  ALA      4.4     1.9    -      -       -      +
    423A  VAL*     3.4     3.1    -      -       -      +
    424A  ALA*     2.8    48.2    +      -       +      +
    426A  TYR*     4.7    10.8    +      -       +      -
    490A  PHE*     4.2    11.8    -      -       +      -
----------------------------------------------------------
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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