Contacts of the strand formed by residues 176 - 185 (chain A) in PDB entry 5GGR


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 TYR 176 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  THR*     5.8     2.3    -      -       -      +
    110A  THR*     4.1    20.6    +      -       -      +
    144A  ASP      3.2     8.0    +      -       -      -
    145A  TYR*     2.9    50.0    +      +       +      +
    146A  PHE*     3.5    33.6    -      +       -      -
    147A  PRO*     4.3     0.9    -      -       +      -
    148A  GLU*     3.8    46.8    -      -       +      +
    168A  ALA*     4.3     3.8    -      -       +      -
    169A  VAL      3.6     5.4    -      -       -      +
    170A  LEU*     3.9    36.4    -      -       +      +
    174A  GLY      5.2     1.3    -      -       -      -
    175A  LEU*     1.3    72.2    -      -       -      +
    177A  SER*     1.3    70.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  LEU*     5.6     3.1    -      -       -      -
    142A  VAL      3.4    11.0    -      -       -      -
    143A  LYS*     3.1    12.3    -      -       -      +
    144A  ASP      3.0    11.1    +      -       -      -
    145A  TYR*     4.0     2.0    -      -       -      -
    168A  ALA*     4.1     2.7    -      -       -      -
    169A  VAL*     3.0    38.6    +      -       -      +
    171A  GLN*     2.5    38.3    +      -       -      -
    176A  TYR*     1.3    77.7    +      -       -      +
    178A  LEU*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  LEU*     3.4     8.4    -      -       -      +
    142A  VAL*     2.9    50.3    +      -       +      +
    145A  TYR*     3.7     1.7    -      -       +      +
    148A  GLU*     6.0     0.7    -      -       +      -
    150A  VAL*     3.6    28.7    -      -       +      +
    152A  VAL*     4.6     5.2    -      -       +      -
    165A  THR*     4.0    17.9    -      -       +      -
    166A  PHE      3.7    16.2    -      -       -      +
    167A  PRO      4.4     1.6    -      -       -      +
    168A  ALA*     3.5    30.5    -      -       +      +
    177A  SER*     1.3    75.8    -      -       -      +
    179A  SER*     1.3    91.2    +      -       -      +
    180A  SER*     3.9     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  LEU*     4.7    13.2    -      -       -      -
    140A  CYS      3.4     7.6    -      -       -      -
    141A  LEU*     3.4    19.3    -      -       -      +
    166A  PHE*     3.2    37.1    +      -       -      +
    178A  LEU*     1.3    82.8    -      -       -      +
    180A  SER*     1.3    60.6    +      -       -      +
    181A  VAL*     4.1     4.7    -      -       -      -
    133B  VAL*     4.5     6.2    -      -       -      +
    176B  SER*     4.2    15.8    +      -       -      -
    178B  THR*     4.1    12.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 180 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  GLY*     3.2     0.7    -      -       -      -
    140A  CYS*     2.5    45.6    +      -       -      -
    142A  VAL*     5.7     1.1    -      -       -      -
    152A  VAL*     3.6    20.9    -      -       -      +
    154A  TRP*     3.0    25.8    +      -       -      -
    163A  VAL*     4.7     0.3    -      -       -      +
    164A  HIS      3.5     5.0    +      -       -      -
    165A  THR*     2.9    29.3    +      -       -      +
    178A  LEU*     3.9     5.0    -      -       -      +
    179A  SER*     1.3    73.7    -      -       -      +
    181A  VAL*     1.3    58.1    +      -       -      +
    196A  CYS*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  LEU*     4.4    11.0    -      -       +      -
    138A  LEU      4.3     1.6    -      -       -      +
    139A  GLY*     3.6    22.2    -      -       -      +
    154A  TRP*     4.6     2.5    -      -       -      -
    162A  GLY      3.7     0.3    -      -       -      +
    163A  VAL*     3.7     2.6    -      -       -      +
    164A  HIS*     2.7    56.0    +      -       +      +
    166A  PHE*     3.8    24.7    -      -       +      -
    179A  SER*     4.9     4.5    -      -       -      -
    180A  SER*     1.3    79.7    -      -       -      +
    182A  VAL*     1.3    60.5    +      -       -      +
    118B  PHE*     5.0     2.0    -      -       +      -
    133B  VAL*     5.7     2.5    -      -       +      -
    135B  LEU*     3.8    34.3    -      -       +      -
    137B  ASN*     4.3     5.6    -      -       -      +
    176B  SER*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ALA      3.9     0.9    -      -       -      +
    137A  ALA*     3.7     1.4    -      -       -      -
    138A  LEU*     3.0    49.2    +      -       +      +
    154A  TRP*     3.7    32.5    -      -       +      -
    159A  LEU*     3.9    25.1    -      -       +      -
    161A  SER      4.1     2.0    -      -       -      +
    162A  GLY      3.2     8.3    -      -       -      +
    163A  VAL*     3.7    26.9    -      -       +      -
    181A  VAL*     1.3    76.7    -      -       -      +
    183A  THR*     1.3    73.3    +      -       -      +
    184A  VAL*     4.0     5.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  THR*     3.9    17.9    -      -       +      +
    136A  ALA      3.5     2.9    -      -       -      -
    137A  ALA*     4.3    13.5    -      -       +      -
    161A  SER      3.5    14.7    -      -       -      +
    162A  GLY*     2.9    26.4    +      -       -      +
    182A  VAL*     1.3    74.5    -      -       -      +
    184A  VAL*     1.3    69.1    +      -       -      +
    116B  PHE*     5.5     3.1    -      -       +      -
    135B  LEU*     5.4     0.2    -      -       +      -
    137B  ASN*     3.4    34.1    -      -       +      +
    138B  ASN*     5.8     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  THR*     2.9     5.5    +      -       -      -
    136A  ALA      2.4    50.1    +      -       -      +
    138A  LEU*     3.6    23.6    -      -       +      -
    159A  LEU*     4.4     9.4    -      -       +      -
    182A  VAL*     4.2    18.4    -      -       +      -
    183A  THR*     1.3    80.3    -      -       -      +
    185A  PRO*     1.3    70.5    -      -       +      +
    189A  LEU*     4.1     6.3    -      -       +      -
    194A  TYR*     3.3    42.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  GLY      4.1     8.5    -      -       -      +
    135A  THR*     4.3     2.2    -      -       -      +
    136A  ALA*     4.6     0.4    -      -       -      -
    184A  VAL*     1.3    93.0    -      -       +      +
    186A  SER*     1.3    65.1    +      -       -      +
    187A  SER*     4.6     8.7    -      -       -      +
    188A  SER*     2.3    47.5    +      -       -      +
    189A  LEU*     4.0     1.6    +      -       -      +
    194A  TYR*     4.9     0.9    -      -       -      +
----------------------------------------------------------
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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