Contacts of the strand formed by residues 176 - 184 (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 LYS 176 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123C  GLU*     2.6    28.5    +      -       -      -
    169C  PRO      3.2    18.7    +      -       -      -
    170C  ASN*     3.3    33.4    -      -       +      +
    171C  ASN      5.4     0.4    -      -       -      +
    172C  ASP*     4.4     9.2    -      -       -      -
    174C  PHE*     4.1     4.9    -      -       +      -
    175C  ASP*     1.3    76.3    -      -       -      +
    177C  LEU*     1.3    60.4    +      -       -      +
    178C  TYR*     3.0    28.9    +      -       +      +
    235C  THR      3.8     0.3    -      -       -      +
    236C  ILE*     3.3     4.7    -      -       -      +
    237C  VAL*     2.8    35.5    +      -       +      +
    257C  TYR*     3.5    44.9    -      -       +      -
    258C  PHE      3.8     4.5    -      -       -      -
    260C  MET*     4.8     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 177 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70C  LEU*     4.7     7.2    -      -       +      -
    111C  LEU*     4.0    13.0    -      -       +      -
    112C  VAL*     4.8     8.7    -      -       +      -
    175C  ASP      4.3     0.2    -      -       -      -
    176C  LYS*     1.3    71.5    -      -       -      +
    178C  TYR*     1.3    62.5    +      -       -      +
    179C  ILE*     3.9    14.6    -      -       +      -
    234C  TRP*     3.9    28.5    -      -       +      -
    235C  THR      3.6     2.7    -      -       -      +
    236C  ILE*     3.9    17.9    -      -       +      +
    257C  TYR*     3.6     1.0    -      -       -      -
    258C  PHE*     3.0    60.6    +      -       +      +
    260C  MET*     3.7    33.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 178 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123C  GLU*     2.8    29.4    +      -       -      -
    125C  PHE*     4.0     7.2    -      +       -      -
    168C  MET*     3.5    12.6    +      -       +      +
    176C  LYS*     3.0    37.0    +      -       +      +
    177C  LEU*     1.3    74.0    -      -       -      +
    179C  ILE*     1.4    60.2    +      -       -      +
    180C  TRP*     3.8     9.5    -      -       +      -
    234C  TRP*     3.3     4.7    -      -       -      +
    235C  THR*     2.8    40.2    +      -       -      +
    237C  VAL*     3.5    34.3    -      -       +      +
    243C  LEU*     3.7    31.4    -      -       +      -
    254C  PRO*     4.2    15.9    -      -       +      -
    256C  GLY      3.2    28.3    -      -       -      -
    257C  TYR*     3.9     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 179 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70C  LEU*     4.0    11.0    -      -       +      -
     71C  LEU*     3.6    30.1    -      -       +      -
    108C  LEU*     3.7    23.1    -      -       +      -
    150C  ARG*     5.0     2.2    -      -       +      +
    151C  LEU*     3.5    15.2    -      -       +      +
    177C  LEU*     3.9    12.0    +      -       +      -
    178C  TYR*     1.4    71.7    -      -       -      +
    180C  TRP*     1.3    64.6    +      -       -      +
    232C  ILE*     3.6    16.6    -      -       +      -
    233C  TYR      3.4     2.0    -      -       -      +
    234C  TRP*     3.6    26.0    -      -       +      -
    254C  PRO*     3.4    18.5    -      -       -      +
    256C  GLY      5.0     1.4    +      -       -      -
    258C  PHE*     3.8    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 180 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151C  LEU*     4.1     8.5    -      -       -      -
    178C  TYR*     3.8    20.9    -      -       +      -
    179C  ILE*     1.3    75.2    -      -       -      +
    181C  GLY*     1.3    87.6    +      -       -      +
    182C  ILE*     5.3     0.4    -      -       +      -
    202C  VAL*     3.8    21.8    -      -       +      -
    204C  VAL*     3.4    36.3    -      -       +      +
    211C  GLN*     3.7    19.1    -      -       +      -
    213C  ILE*     3.4    31.9    -      -       +      -
    232C  ILE*     3.6     8.8    -      -       -      +
    233C  TYR*     2.8    55.9    +      +       +      +
    234C  TRP      4.1     1.0    -      -       -      -
    235C  THR*     2.9    23.5    +      -       -      +
    243C  LEU*     6.1     0.7    -      -       +      -
    245C  ILE*     5.9     1.1    -      -       +      -
    251C  LEU*     4.9     2.7    -      -       +      -
    252C  ILE      3.8    12.1    -      -       -      +
    254C  PRO*     3.9    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 181 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180C  TRP*     1.3    91.4    -      -       -      +
    182C  ILE*     1.3    62.3    +      -       -      +
    202C  VAL*     4.6     0.5    -      -       -      +
    230C  ILE*     5.9     0.7    -      -       -      -
    231C  SER      3.2    14.1    -      -       -      -
    232C  ILE*     4.4     3.6    -      -       -      -
    233C  TYR*     4.3     1.1    -      -       -      -
    251C  LEU*     3.7     9.0    -      -       -      +
    252C  ILE*     3.0    37.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 182 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180C  TRP*     5.3     0.7    -      -       +      -
    181C  GLY*     1.3    74.8    -      -       -      +
    183C  HIS*     1.3    63.2    +      -       -      +
    184C  HIS*     4.0    18.3    +      -       +      +
    201C  ARG      4.9     0.4    -      -       -      -
    202C  VAL*     3.7    18.2    -      -       +      +
    213C  ILE*     3.5    48.7    -      -       +      +
    215C  PRO*     3.5    27.4    -      -       +      -
    230C  ILE*     3.3     4.4    -      -       -      +
    231C  SER*     3.1    23.2    +      -       -      +
    233C  TYR*     4.0    13.7    -      -       +      -
    250C  ASN*     3.2    20.9    -      -       +      +
    252C  ILE*     4.1     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 183 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  TYR*     2.9    29.1    +      +       -      -
    153C  TRP*     3.8    12.5    -      +       -      -
    182C  ILE*     1.3    72.4    -      -       -      +
    184C  HIS*     1.3    59.2    +      -       -      +
    185C  PRO*     3.6    12.8    -      -       +      +
    190C  GLU*     3.3    22.8    +      -       -      -
    194C  LEU*     3.8    14.4    -      -       +      -
    195C  TYR*     2.8    36.4    +      -       +      +
    215C  PRO*     3.4     7.8    -      -       -      +
    228C  SER*     4.0     2.0    -      -       -      -
    229C  ARG      4.0     5.4    -      -       -      -
    230C  ILE*     3.7    23.1    -      -       +      -
    250C  ASN*     2.8    37.7    +      -       -      +
    252C  ILE*     4.1     8.5    -      -       +      +
    329C  SIA      3.8     4.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 184 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  ILE*     4.1    13.3    -      -       +      +
    183C  HIS*     1.3    74.7    -      -       -      +
    185C  PRO*     1.3    66.1    -      -       -      +
    213C  ILE*     5.2     2.2    -      -       +      -
    214C  ILE      4.3     2.7    -      -       -      -
    215C  PRO*     3.3    12.3    -      -       +      +
    216C  ASN*     2.7    56.6    +      -       -      +
    220C  ARG*     3.3    13.6    +      -       -      +
    228C  SER*     3.4    20.3    -      -       -      -
    229C  ARG      2.9    24.0    +      -       -      +
    231C  SER*     2.8    34.4    +      -       -      -
    233C  TYR*     5.9     0.2    -      -       -      -
    210E  GLN*     3.7    19.1    +      -       -      -
----------------------------------------------------------
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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