Contacts of the strand formed by residues 86 - 93 (chain D) in PDB entry 1OGA


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 GLY 86 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  ARG*     4.6     2.7    -      -       -      -
     38D  GLN      3.7     9.0    -      -       -      -
     39D  GLU*     3.8     9.0    -      -       -      -
     40D  PRO*     5.8     1.3    -      -       -      -
     84D  ASP      3.3     3.1    +      -       -      -
     85D  THR*     1.3    78.6    -      -       -      +
     87D  LEU*     1.3    61.3    +      -       -      -
     88D  TYR*     3.6    10.5    -      -       -      -
    106D  LYS*     3.8     4.0    -      -       -      -
    107D  LEU      2.9    32.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 87 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36D  TYR      3.7     0.7    -      -       -      +
     37D  ARG*     3.3     3.1    -      -       -      -
     38D  GLN*     2.7    66.5    +      -       -      +
     86D  GLY*     1.3    71.9    -      -       -      -
     88D  TYR*     1.3    61.7    +      -       -      +
     89D  LEU*     3.9    24.3    +      -       +      +
    103D  LYS      4.6     3.4    -      -       -      +
    104D  GLY*     4.1     7.6    -      -       -      -
    105D  THR      3.6    29.2    -      -       -      +
    106D  LYS*     4.0    14.1    -      -       +      +
     39E  GLN*     4.1    10.5    -      -       -      +
     43E  GLN      4.1    11.9    -      -       -      +
     44E  GLY*     4.9     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 88 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  GLN*     2.9    17.8    +      -       -      -
     22D  VAL*     5.1     5.8    -      -       +      -
     35D  TRP*     4.6    14.6    -      +       +      -
     36D  TYR      3.3    13.2    -      -       -      -
     37D  ARG*     3.4    29.2    +      -       +      -
     47D  LEU*     4.2    15.0    -      -       +      -
     62D  LEU*     5.1     4.5    -      -       +      +
     75D  LEU*     4.4    15.9    -      -       +      -
     77D  ILE*     3.9    18.0    -      -       +      +
     84D  ASP*     2.6    43.2    +      -       -      +
     86D  GLY      3.6    18.8    -      -       -      -
     87D  LEU*     1.3    73.4    -      -       -      +
     89D  LEU*     1.3    61.3    +      -       -      +
    104D  GLY*     3.1     2.1    -      -       -      -
    105D  THR*     2.9    35.9    +      -       +      +
    107D  LEU*     3.8    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 89 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  GLN*     3.5     1.3    -      -       -      -
     35D  TRP*     3.3     7.2    -      -       -      -
     36D  TYR*     2.8    45.4    +      -       +      +
     38D  GLN*     4.7     5.8    -      -       +      +
     44D  PRO*     4.7    14.4    -      -       +      -
     87D  LEU*     4.2    26.2    -      -       +      +
     88D  TYR*     1.3    75.4    -      -       -      +
     90D  CYS*     1.3    61.3    +      -       -      +
    101D  PHE*     4.2    15.5    -      -       +      -
    102D  GLY      3.7    15.9    -      -       -      +
    103D  LYS      4.0     4.5    -      -       -      +
    104D  GLY*     3.7    23.6    -      -       -      +
     44E  GLY*     5.0     6.5    -      -       -      -
     45E  LEU*     3.9    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 90 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  LEU*     4.0     6.3    -      -       -      -
      7D  GLN*     3.0    27.4    +      -       -      -
     24D  CYS*     2.1    53.4    -      -       +      -
     33D  LEU*     4.7     2.5    -      -       +      -
     34D  GLN      3.2     9.6    -      -       -      +
     35D  TRP*     3.9    17.7    -      -       +      -
     89D  LEU*     1.3    75.7    -      -       -      +
     91D  ALA*     1.3    63.5    +      -       -      +
    101D  PHE*     3.6     4.0    -      -       -      -
    102D  GLY*     2.9    28.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 91 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  LEU*     3.6     5.8    -      -       -      -
     33D  LEU*     3.3     4.9    -      -       -      +
     34D  GLN*     2.8    35.3    +      -       +      +
     36D  TYR*     4.3     7.9    -      -       +      -
     90D  CYS*     1.3    77.1    -      -       -      +
     92D  GLY*     1.3    59.6    +      -       -      +
     99D  LEU*     4.2    14.8    -      -       +      -
    100D  ILE      3.0    12.3    -      -       -      +
    101D  PHE*     3.7    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 92 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  LEU*     3.4     4.4    -      -       -      +
     30D  PHE*     3.6    18.8    -      -       -      -
     32D  SER      3.5     9.2    -      -       -      -
     33D  LEU*     4.3     2.2    -      -       -      -
     34D  GLN*     4.6     0.4    -      -       -      -
     91D  ALA*     1.3    75.4    -      -       -      +
     93D  ALA*     1.3    66.1    +      -       -      -
     94D  GLY      3.1     0.2    +      -       -      -
     99D  LEU*     3.4     8.3    -      -       -      -
    100D  ILE*     2.8    34.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 93 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  GLN*     4.2    12.4    +      -       -      +
      3D  GLN*     3.1    19.9    +      -       -      -
     30D  PHE*     3.5     7.0    -      -       -      -
     31D  SER*     3.5    26.4    +      -       -      +
     32D  SER*     3.0    24.2    +      -       -      +
     34D  GLN*     4.8     0.2    +      -       -      -
     92D  GLY*     1.3    70.4    -      -       -      -
     94D  GLY*     1.3    60.3    +      -       -      +
     99D  LEU*     4.1     1.6    -      -       -      +
    100E  SER*     3.5    24.5    -      -       -      +
----------------------------------------------------------
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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