Contacts of the strand formed by residues 124 - 131 (chain D) in PDB entry 1GN6


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 GLY 124 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120D  VAL*     3.8     8.9    -      -       -      +
    122D  GLY      3.9     1.6    +      -       -      -
    123D  SER*     1.3    76.3    -      -       -      +
    125D  TRP*     1.3    66.3    +      -       -      -
    142D  VAL      3.0    14.4    -      -       -      -
    144D  ASP      3.8     9.4    -      -       -      -
    161D  MET*     2.8    34.4    +      -       -      -
    162D  TRP*     3.5     7.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 125 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75D  ASN*     3.3    55.8    -      -       +      +
     76D  HIS*     3.8    28.0    -      +       -      -
     79D  TRP*     4.1     9.4    -      +       +      -
    120D  VAL*     4.5     5.9    -      -       -      +
    124D  GLY*     1.3    75.8    -      -       -      -
    126D  ALA*     1.3    64.3    +      -       -      +
    141D  GLN*     3.8     7.4    -      -       -      +
    142D  VAL*     3.0    42.9    +      -       +      +
    144D  ASP      3.1    20.3    +      -       -      -
    145D  HIS*     3.0    22.9    +      +       -      -
    158D  LEU*     3.8    22.9    -      -       +      -
    159D  LEU      3.1    11.2    -      -       -      -
    160D  ASP*     3.3    49.6    -      -       +      -
    161D  MET*     4.1     4.0    -      -       -      +
    162D  TRP*     3.9     2.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 126 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113D  PHE*     3.9    26.3    -      -       +      +
    116D  ALA*     4.2     7.9    -      -       +      -
    117D  ALA*     3.7    38.5    -      -       +      +
    125D  TRP*     1.3    75.0    -      -       -      +
    127D  ALA*     1.3    62.0    +      -       -      +
    139D  ILE*     5.2     0.2    -      -       +      -
    140D  PHE      3.8     2.9    -      -       -      -
    141D  GLN*     4.9     0.9    -      -       -      +
    158D  LEU*     3.4     5.0    -      -       -      +
    159D  LEU*     3.0    30.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 127 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  LEU*     5.1     7.4    -      -       +      -
    113D  PHE*     4.0     6.2    -      -       -      -
    126D  ALA*     1.3    76.4    -      -       -      +
    128D  LEU*     1.3    60.0    +      -       -      +
    129D  GLY*     3.9     1.2    +      -       -      +
    138D  LEU      3.8     0.3    -      -       -      +
    139D  ILE*     3.2     6.6    -      -       -      +
    140D  PHE*     2.7    50.4    +      -       +      +
    142D  VAL*     4.1    16.4    -      -       +      -
    155D  PRO*     5.8     0.9    -      -       +      -
    157D  LEU      3.6     3.1    -      -       -      -
    158D  LEU*     3.1    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 128 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95D  LEU*     5.2     0.9    -      -       +      -
     99D  ILE*     4.8    13.2    -      -       +      -
    103D  PHE*     3.8    20.4    -      -       +      -
    109D  PHE*     3.8    31.2    -      -       +      -
    113D  PHE*     3.8    10.2    -      -       +      -
    127D  ALA*     1.3    72.4    -      -       -      +
    129D  GLY*     1.3    59.5    +      -       -      +
    137D  LEU*     4.1    13.0    -      -       +      -
    138D  LEU      3.7    15.3    -      -       -      +
    139D  ILE*     4.1     2.5    -      -       +      +
    155D  PRO*     3.7     2.1    -      -       -      +
    156D  LEU*     2.7    51.8    +      -       +      -
    157D  LEU*     3.0    29.6    +      -       +      +
    187D  TRP*     5.6     0.2    -      -       +      -
    190D  VAL*     4.6     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 129 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127D  ALA*     3.9     2.0    +      -       -      -
    128D  LEU*     1.3    76.4    -      -       -      +
    130D  TRP*     1.3    60.7    +      -       -      -
    131D  ASP      4.0     0.4    +      -       -      -
    137D  LEU*     3.5    10.1    -      -       -      +
    138D  LEU      2.9    36.3    +      -       -      -
    140D  PHE*     4.5     5.2    -      -       -      -
    153D  ILE*     4.1    15.3    -      -       -      -
    154D  VAL      3.3    11.0    -      -       -      -
    155D  PRO*     4.3     1.3    -      -       -      -
    156D  LEU*     4.3     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 130 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129D  GLY*     1.3    75.0    -      -       -      -
    131D  ASP*     1.3    64.4    +      -       -      +
    132D  THR*     3.4    25.8    +      -       +      +
    135D  ASN*     3.2    47.6    -      -       +      +
    136D  LYS*     3.4    21.8    -      -       -      -
    137D  LEU*     3.9    17.9    -      -       +      -
    153D  ILE*     3.7     6.2    -      -       -      -
    154D  VAL*     2.9    36.7    +      -       +      +
    156D  LEU*     4.5     8.3    -      -       +      +
    194D  TYR*     4.5     9.9    -      +       +      -
    197D  ALA*     3.2    41.3    +      -       +      -
    198D  THR*     3.7    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 131 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  TYR*     2.7    26.8    +      -       -      +
     70B  LEU*     4.4    11.2    -      -       -      +
     74B  VAL*     5.0     4.0    -      -       -      +
    129D  GLY      4.0     1.0    +      -       -      -
    130D  TRP*     1.3    72.3    -      -       -      +
    132D  THR*     1.3    54.5    +      -       -      +
    133D  LEU*     3.1    16.6    +      -       -      +
    134D  GLY*     2.7    22.3    +      -       -      -
    135D  ASN*     2.7    37.8    +      -       -      -
    136D  LYS      2.7    20.9    +      -       -      +
    138D  LEU*     3.8    18.3    -      -       +      +
    153D  ILE*     3.8    16.5    -      -       +      +
----------------------------------------------------------
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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