Contacts of the strand formed by residues 109 - 118 (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 PHE 109 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  CYS*     4.7     0.7    -      -       +      -
    102A  ASP      3.9     5.2    -      -       -      -
    103A  VAL*     4.2     1.4    -      -       -      +
    107A  TRP      4.1     0.6    +      -       -      -
    108A  ARG*     1.3    76.9    -      -       -      +
    110A  LEU*     1.3    72.4    +      -       -      +
    111A  ARG*     3.3    36.8    -      -       -      -
    112A  GLY*     3.5     7.4    -      -       -      -
    128A  GLU      5.9     0.4    -      -       -      -
    130A  LEU*     3.9    10.5    -      -       +      -
    160A  LEU      3.5    26.7    -      -       -      -
    161A  GLU*     3.8    41.7    -      -       +      +
    165A  VAL*     3.8    22.4    -      -       +      +
    169A  ARG*     4.6     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  SER*     4.5     9.0    -      -       -      +
    102A  ASP*     2.8    29.8    +      -       +      +
    103A  VAL*     4.1     8.5    -      -       -      +
    104A  GLY*     4.1    20.4    -      -       -      +
    108A  ARG      3.3     0.4    +      -       -      +
    109A  PHE*     1.3    87.3    -      -       -      +
    111A  ARG*     1.3    64.9    +      -       +      +
    128A  GLU*     4.9     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  CYS*     3.3     3.1    -      -       -      -
    102A  ASP*     2.8    34.1    +      -       +      +
    109A  PHE*     3.3    14.6    -      -       -      -
    110A  LEU*     1.3    84.5    -      -       +      +
    112A  GLY*     1.3    69.0    +      -       -      +
    113A  TYR*     3.3    44.2    +      -       +      +
    128A  GLU*     3.5    48.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  GLY      3.5     8.5    -      -       -      -
    109A  PHE*     3.5    16.3    -      -       -      -
    111A  ARG*     1.3    83.7    +      -       -      +
    113A  TYR*     1.3    67.7    +      -       -      -
    126A  LEU      5.3     2.1    -      -       -      +
    127A  LYS      5.2     0.2    -      -       -      +
    128A  GLU*     5.0     6.4    +      -       -      -
    130A  LEU*     3.8    24.6    -      -       -      +
    160A  LEU*     4.4     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  ARG*     3.0    35.3    +      -       -      -
     98A  MET*     4.0    29.8    -      -       +      -
     99A  TYR*     3.1     4.1    -      -       -      +
    100A  GLY      2.9    37.1    +      -       -      +
    102A  ASP*     2.6    29.8    +      -       -      -
    111A  ARG*     3.3    49.8    +      -       +      -
    112A  GLY*     1.3    76.6    -      -       -      -
    114A  HIS*     1.3    66.0    +      -       -      +
    115A  GLN*     4.5    12.3    -      -       -      +
    126A  LEU      5.4     3.1    -      -       -      -
    130A  LEU*     5.4     0.7    -      -       -      -
    160A  LEU*     3.6     8.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ARG*     3.0    32.2    +      -       -      -
     98A  MET      3.3     7.2    -      -       -      -
     99A  TYR*     3.8    20.9    -      +       +      -
    113A  TYR*     1.3    78.1    -      -       -      +
    115A  GLN*     1.3    63.0    +      -       -      +
    116A  TYR*     3.5    26.4    -      +       -      -
    125A  ALA*     3.7     0.5    -      -       -      -
    126A  LEU*     2.9    45.7    +      -       +      +
    133A  TRP*     3.9    14.2    -      +       -      -
    147A  TRP*     4.4     0.4    -      +       -      -
    156A  LEU*     3.6    33.0    -      -       +      +
    160A  LEU*     4.4     6.5    -      -       +      -
      3C  LEU*     4.5     0.2    -      -       +      -
      7C  PHE*     3.6    13.1    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLN 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ARG*     3.3     4.9    -      -       -      +
     98A  MET*     2.9    60.4    +      -       +      +
    113A  TYR*     4.5    17.3    -      -       -      +
    114A  HIS*     1.3    78.1    +      -       -      +
    116A  TYR*     1.3    67.6    +      -       -      +
    122A  ASP*     5.6     2.6    -      -       -      +
    124A  ILE      3.4     4.9    -      -       -      -
    125A  ALA*     3.6    24.8    -      -       +      +
    126A  LEU      5.1     3.8    +      -       -      -
     58B  LYS*     5.1     5.4    -      -       -      +
     60B  TRP*     3.5    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  HIS*     3.6    25.1    +      +       -      -
     77A  ASP*     4.6     0.3    +      -       -      -
     95A  VAL*     4.2     8.3    -      -       +      -
     96A  GLN      3.2    13.7    -      -       -      -
     97A  ARG*     3.3    35.4    +      -       +      -
    114A  HIS*     3.5    26.2    -      +       -      -
    115A  GLN*     1.3    83.0    -      -       -      +
    117A  ALA*     1.3    60.6    +      -       -      +
    122A  ASP*     3.8     1.9    -      -       -      +
    123A  TYR*     2.9    28.5    +      -       +      -
    124A  ILE*     2.8    30.2    +      -       +      +
    147A  TRP*     3.5    15.3    -      +       -      -
     60B  TRP*     3.6    10.3    -      -       -      -
      7C  PHE*     4.0    11.8    +      -       -      -
      9C  LEU*     3.6    33.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  LEU*     5.8     0.2    -      -       -      +
     94A  THR      3.9     0.7    -      -       -      +
     95A  VAL*     3.5     6.9    -      -       -      +
     96A  GLN*     2.9    35.9    +      -       +      +
    116A  TYR*     1.3    73.1    -      -       -      +
    118A  TYR*     1.3    60.0    +      -       -      +
    119A  ASP      4.2     0.2    -      -       -      -
    120A  GLY      4.4     1.6    -      -       -      -
    121A  LYS      3.1    19.3    -      -       -      +
    123A  TYR*     3.9     4.0    -      -       -      +
     60B  TRP*     3.3    46.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LEU*     4.5     5.6    +      -       +      -
     81A  LEU*     3.6    36.8    -      -       +      -
     82A  ARG*     3.9     9.9    +      -       -      +
     85A  TYR*     3.5    38.1    -      +       -      +
     87A  GLN*     2.6    28.5    +      -       -      -
     93A  HIS*     3.3    30.4    +      -       +      +
     94A  THR      3.3    13.0    -      -       -      -
     95A  VAL*     4.1     6.1    -      -       +      -
    117A  ALA*     1.3    73.2    -      -       -      +
    119A  ASP*     1.3    85.9    +      -       +      +
    120A  GLY      3.1     1.0    +      -       -      -
    121A  LYS*     2.9    24.3    +      -       -      +
    123A  TYR*     4.1    17.6    -      -       +      +
----------------------------------------------------------
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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