Contacts of the strand formed by residues 229 - 237 (chain C) in PDB entry 5HMG


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 229 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  TYR*     4.4     1.1    -      -       -      -
     99C  PRO*     3.3    29.4    -      -       +      +
    100C  TYR      4.7     5.2    -      -       -      +
    101C  ASP*     4.1    13.9    -      -       +      +
    183C  HIS*     4.0     1.6    -      -       -      -
    184C  HIS*     2.9    32.8    +      -       +      +
    220C  ARG*     3.6    28.6    -      -       -      +
    221C  PRO      2.7    30.9    +      -       -      -
    223C  VAL*     3.2    21.0    -      -       -      +
    226C  LEU      3.4    13.1    +      -       -      -
    227C  SER      3.8     3.2    -      -       -      -
    228C  SER*     1.3   102.8    +      -       -      +
    230C  ILE*     1.3    66.3    +      -       -      +
    206E  THR      4.0    10.5    +      -       -      -
    207E  ARG*     3.8    15.2    +      -       -      +
    209E  SER      5.3     3.6    +      -       -      +
    210E  GLN*     3.3    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 230 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  TYR*     4.2    11.4    -      -       +      -
     99C  PRO      3.0     7.4    +      -       -      +
    100C  TYR*     2.9    21.2    -      -       +      +
    101C  ASP*     2.8    25.1    +      -       -      +
    147C  PHE*     3.8    18.8    -      -       +      -
    148C  PHE*     3.5    31.4    -      -       +      -
    151C  LEU*     4.8     1.8    -      -       +      -
    181C  GLY*     5.9     0.2    -      -       -      -
    182C  ILE      3.3     9.0    -      -       -      +
    183C  HIS*     3.7    31.2    -      -       +      -
    184C  HIS*     4.6     0.2    -      -       -      -
    229C  ARG*     1.3    80.6    -      -       -      +
    231C  SER*     1.3    62.8    +      -       -      +
    232C  ILE*     4.6    11.9    -      -       +      -
    252C  ILE*     4.3    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 231 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101C  ASP*     3.0    29.9    +      -       -      -
    103C  PRO*     4.3     3.6    -      -       -      -
    181C  GLY*     3.2    23.6    -      -       -      -
    182C  ILE*     3.1    11.2    +      -       -      -
    184C  HIS*     2.8    28.2    +      -       -      -
    230C  ILE*     1.3    73.0    -      -       -      +
    232C  ILE*     1.3    60.4    +      -       -      +
    233C  TYR*     3.6    26.7    -      -       -      -
    210E  GLN*     4.5     1.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 232 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  LEU*     3.8    26.7    -      -       +      -
    100C  TYR*     3.9    33.7    -      -       +      -
    101C  ASP      2.8     6.9    +      -       -      -
    102C  VAL*     3.7    17.1    -      -       +      +
    103C  PRO*     3.3    21.3    -      -       -      +
    108C  LEU*     4.0    21.8    -      -       +      -
    151C  LEU*     3.9    17.5    -      -       +      -
    179C  ILE*     3.6    23.3    -      -       +      -
    180C  TRP      3.6     7.0    -      -       -      +
    181C  GLY*     4.9     2.5    -      -       -      -
    230C  ILE*     4.6     8.7    -      -       +      -
    231C  SER*     1.3    76.6    -      -       -      +
    233C  TYR*     1.3    67.9    +      -       -      +
    234C  TRP*     5.6     0.2    -      -       -      -
    252C  ILE*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 233 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103C  PRO*     3.6    31.4    -      -       +      +
    179C  ILE*     3.4     8.1    -      -       -      +
    180C  TRP*     2.8    69.6    +      +       +      +
    181C  GLY*     4.3     0.9    -      -       -      -
    182C  ILE*     4.0     9.0    -      -       +      -
    184C  HIS*     5.7     0.5    +      -       -      -
    211C  GLN*     4.4     9.9    -      -       -      +
    213C  ILE*     3.5    40.0    -      -       +      +
    231C  SER*     3.6    32.2    -      -       -      -
    232C  ILE*     1.3    77.0    -      -       -      +
    234C  TRP*     1.3    65.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 234 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  GLU*     5.5     3.1    -      -       -      -
     73B  VAL      3.5    19.5    -      -       -      -
     74B  GLU*     4.3    12.8    -      -       -      -
    102C  VAL*     5.6     2.5    -      -       +      -
    103C  PRO      5.5     4.0    +      -       -      -
    104C  ASP*     4.9     8.9    +      -       -      +
    107C  SER*     4.9     5.8    -      -       -      -
    108C  LEU*     3.7    31.6    -      -       +      +
    111C  LEU*     3.6    23.3    -      -       +      -
    177C  LEU*     3.9    10.3    -      -       +      -
    178C  TYR      3.3     5.6    -      -       -      -
    179C  ILE*     3.6    20.6    -      -       +      -
    180C  TRP*     4.1     0.4    -      -       -      +
    211C  GLN*     3.7    12.5    +      -       -      +
    232C  ILE      5.6     0.7    -      -       -      -
    233C  TYR*     1.3    81.1    -      -       -      +
    235C  THR*     1.3    65.0    +      -       -      +
    236C  ILE*     3.7    40.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 235 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176C  LYS      3.8     0.3    -      -       -      +
    177C  LEU*     3.6     0.7    -      -       -      -
    178C  TYR*     2.8    36.2    +      -       -      +
    180C  TRP*     2.9    25.0    +      -       -      -
    204C  VAL*     3.5     9.1    -      -       +      +
    205C  SER      5.6     0.9    -      -       -      -
    206C  THR*     4.0    13.5    -      -       +      -
    209C  SER*     5.2     5.2    -      -       -      +
    211C  GLN*     3.2    22.8    +      -       -      +
    234C  TRP*     1.3    71.4    -      -       -      +
    236C  ILE*     1.3    72.6    +      -       -      +
    237C  VAL*     3.9     2.4    +      -       +      -
    243C  LEU*     3.9    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 236 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  GLU*     4.6    10.4    -      -       -      +
     73B  VAL*     3.7    28.3    -      -       +      +
    111C  LEU*     4.5     2.5    -      -       +      -
    175C  ASP*     4.0    30.3    -      -       +      +
    176C  LYS      3.3     8.1    -      -       -      +
    177C  LEU*     3.9    12.1    -      -       +      -
    206C  THR*     4.4     5.0    +      -       -      +
    234C  TRP*     3.7    30.8    -      -       +      -
    235C  THR*     1.3    78.7    -      -       -      +
    237C  VAL*     1.3    64.8    +      -       -      +
    238C  LYS*     4.1    10.6    +      -       +      +
    260C  MET*     3.4    32.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 237 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168C  MET      5.1     0.9    -      -       -      +
    170C  ASN*     2.9    28.6    +      -       +      +
    176C  LYS*     2.8    24.9    +      -       +      +
    178C  TYR*     3.5    36.3    -      -       +      -
    206C  THR*     3.7    18.6    -      -       +      -
    235C  THR*     4.0     2.5    -      -       +      -
    236C  ILE*     1.3    76.6    -      -       -      +
    238C  LYS*     1.3    63.0    +      -       -      +
    241C  ASP*     3.7    31.4    -      -       +      -
    242C  VAL      4.1    11.0    -      -       -      +
    243C  LEU*     4.0    13.7    -      -       +      +
----------------------------------------------------------
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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