Contacts of the strand formed by residues 21 - 28 (chain A) 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 ARG 21 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR      3.5     2.3    -      -       -      +
     11A  SER*     3.3     3.0    -      -       -      -
     12A  VAL*     2.9    42.8    +      -       +      +
     14A  ARG*     3.7    20.4    -      -       -      +
     19A  GLU      3.6     1.6    +      -       -      -
     20A  PRO*     1.3    71.4    -      -       -      +
     22A  PHE*     1.3    60.2    +      -       -      +
     23A  ILE*     4.4    24.6    -      -       +      +
     37A  ASP*     2.8    41.6    +      -       -      -
     38A  SER*     3.8     2.5    -      -       -      -
     39A  ASP*     3.1    36.6    +      -       -      +
     51B  HIS*     6.0     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  PHE*     3.5    37.0    -      +       +      -
     10A  THR      3.3    12.3    -      -       -      -
     11A  SER*     3.9    15.9    -      -       -      +
     20A  PRO*     3.6     3.3    +      -       +      +
     21A  ARG*     1.3    72.5    -      -       -      +
     23A  ILE*     1.3    65.5    +      -       -      +
     24A  ALA*     4.1     4.9    -      -       +      -
     36A  PHE*     3.8    11.5    -      +       -      +
     37A  ASP*     3.5     3.3    -      -       -      +
     38A  SER*     2.9    43.5    +      -       -      +
     67A  VAL*     3.9    21.3    -      -       +      -
     70A  HIS*     4.0     5.4    -      -       +      -
     71A  SER*     3.4    55.6    -      -       -      +
     74A  HIS*     3.7    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  PHE      3.8     0.7    -      -       -      +
      9A  PHE*     3.4     2.6    -      -       -      +
     10A  THR*     2.9    39.5    +      -       -      +
     21A  ARG*     4.4    29.6    -      -       +      +
     22A  PHE*     1.3    82.9    -      -       -      +
     24A  ALA*     1.3    66.6    -      -       -      +
     25A  VAL*     4.3     5.2    -      -       +      -
     35A  ARG*     6.1     0.7    -      -       +      -
     36A  PHE      3.3     9.0    -      -       -      +
     37A  ASP*     4.4    14.1    -      -       +      +
     53B  ASP*     5.1     2.9    -      -       +      -
     54B  LEU*     3.7    56.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  TYR*     6.3     0.9    -      -       +      -
      8A  PHE      3.3     5.4    -      -       -      -
      9A  PHE*     3.6    29.8    -      -       +      -
     22A  PHE*     4.1     3.6    -      -       +      -
     23A  ILE*     1.3    73.6    -      -       -      +
     25A  VAL*     1.3    67.2    +      -       -      +
     35A  ARG*     3.2     5.7    -      -       -      +
     36A  PHE*     2.9    35.2    +      -       +      +
     45A  MET*     5.3     4.9    -      -       +      -
     67A  VAL*     3.8    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  TYR*     3.4     7.7    -      -       -      +
      8A  PHE*     2.9    52.1    +      -       +      +
     23A  ILE*     4.3     3.8    -      -       +      -
     24A  ALA*     1.3    79.9    -      -       -      +
     26A  GLY*     1.3    60.2    +      -       -      +
     27A  TYR*     3.8    23.6    -      -       +      +
     32A  GLN*     3.7    11.9    -      -       -      +
     34A  VAL*     3.4     8.5    -      -       -      +
     35A  ARG*     4.4     1.3    -      -       +      +
     53B  ASP*     3.6    31.9    -      -       +      +
     54B  LEU      3.6    17.7    -      -       -      +
     55B  SER*     3.8     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ARG      3.4     7.6    -      -       -      -
      7A  TYR*     3.6    21.3    -      -       -      -
     25A  VAL*     1.3    75.2    -      -       -      +
     27A  TYR*     1.3    57.8    +      -       -      -
     32A  GLN*     3.4     7.1    -      -       -      +
     33A  PHE*     2.8    36.9    +      -       -      -
     34A  VAL*     3.1    16.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  MET*     3.3     8.0    -      -       -      +
      6A  ARG*     2.8    37.7    +      -       +      +
      8A  PHE*     3.6    22.7    -      +       +      -
     25A  VAL*     3.8    14.6    -      -       +      -
     26A  GLY*     1.3    76.9    -      -       -      -
     28A  VAL*     1.3    59.3    -      -       -      +
     29A  ASP      3.8    12.1    -      -       -      +
     30A  ASP*     4.2     9.9    -      -       -      -
     31A  THR      3.3    13.2    -      -       -      -
     32A  GLN*     3.5    45.0    +      -       +      +
     33A  PHE*     3.5     6.0    -      -       -      -
     53B  ASP      5.0     2.8    +      -       -      -
     55B  SER*     3.5    25.3    -      -       -      -
     63B  TYR*     3.3    27.6    +      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  SER      3.3     2.7    -      -       -      +
      5A  MET*     4.5     3.6    -      -       +      -
     27A  TYR*     1.3    74.7    -      -       -      +
     29A  ASP*     1.3    77.3    +      -       -      +
     31A  THR*     2.9    26.4    +      -       -      +
     33A  PHE*     3.8    19.7    -      -       +      -
     51A  TRP*     4.0     8.7    -      -       +      -
    168A  LEU*     3.7    26.5    -      -       +      -
    171A  TYR*     4.0    23.8    -      -       +      -
    172A  LEU*     4.0    19.7    -      -       +      -
    179A  LEU*     4.0    19.8    -      -       +      +
    209A  TYR*     4.1     0.3    +      -       -      -
----------------------------------------------------------
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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