Contacts of the strand formed by residues 125 - 133 (chain B) in PDB entry 1GNG


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 GLU 125 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  LEU*     3.4    43.6    -      -       +      +
     89B  GLN      3.2     9.4    -      -       -      +
     90B  ASP*     5.4     3.1    -      -       +      -
     91B  LYS*     3.7     9.7    -      -       -      -
    120B  GLY*     3.8     8.4    +      -       -      -
    121B  GLU*     4.8     7.6    +      -       -      +
    122B  LYS*     3.4    62.8    +      -       +      +
    124B  ASP*     1.3    83.3    -      -       +      +
    126B  VAL*     1.3    65.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  LEU*     3.5     4.6    -      -       -      +
     89B  GLN*     2.6    55.8    +      -       +      +
     91B  LYS*     4.1    28.0    -      -       +      +
    117B  TYR*     4.0    30.3    -      -       +      -
    118B  SER      3.2    15.0    -      -       -      +
    119B  SER*     5.0     0.9    -      -       -      -
    120B  GLY*     3.6    11.6    -      -       -      +
    125B  GLU*     1.3    77.2    -      -       -      +
    127B  TYR*     1.3    67.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 127 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  LYS*     3.5    41.5    -      -       +      -
     87B  VAL*     3.2    16.4    -      -       -      -
     88B  LEU*     3.4    37.7    -      -       +      +
    117B  TYR*     3.1    12.1    -      -       -      +
    118B  SER*     2.8    45.4    +      -       -      -
    119B  SER      3.5    23.6    -      -       -      -
    120B  GLY*     3.9     9.9    -      -       -      -
    121B  GLU*     3.5    29.5    +      -       -      -
    126B  VAL*     1.3    77.2    -      -       -      +
    128B  LEU*     1.3    60.1    +      -       -      +
    129B  ASN*     3.5     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 128 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  LYS      3.3     2.9    -      -       -      +
     86B  LYS*     3.3     0.7    -      -       -      -
     87B  VAL*     2.8    39.8    +      -       +      +
     89B  GLN*     4.6     9.6    -      -       +      +
     95B  ASN*     3.5    35.4    -      -       +      +
     98B  LEU*     3.5    31.6    -      -       +      -
    115B  PHE*     4.0    11.2    -      -       +      -
    116B  PHE      3.8     6.5    -      -       -      +
    117B  TYR*     3.7    32.8    -      -       +      +
    126B  VAL      4.1     0.4    +      -       -      -
    127B  TYR*     1.3    73.3    -      -       -      +
    129B  ASN*     1.3    69.3    +      -       -      +
    130B  LEU*     3.5    20.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 129 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  TYR*     5.7     0.2    +      -       -      -
     84B  ILE*     4.0    11.2    -      -       +      +
     85B  LYS      3.2     3.1    -      -       -      -
     86B  LYS*     3.1    38.2    -      -       -      +
    115B  PHE*     3.0    28.5    -      -       -      +
    116B  PHE*     2.8    64.8    +      -       +      +
    118B  SER*     3.4    14.5    +      -       -      -
    127B  TYR      3.5     8.3    -      -       -      +
    128B  LEU*     1.3    74.2    -      -       -      +
    130B  LEU*     1.3    62.2    +      -       -      +
    131B  VAL      3.8     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 130 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  ALA      3.2     3.3    -      -       -      +
     84B  ILE*     3.2     3.9    -      -       -      -
     85B  LYS*     2.7    56.3    +      -       +      +
     87B  VAL*     4.9     7.9    -      -       +      -
     95B  ASN*     5.7     0.4    -      -       -      +
     97B  GLU*     3.7    41.5    -      -       +      +
     98B  LEU*     4.8     9.4    -      -       +      +
    101B  MET*     4.9     6.1    -      -       +      -
    112B  LEU*     3.9    17.7    -      -       +      -
    114B  TYR      4.1     4.3    -      -       -      -
    115B  PHE*     4.5     3.6    -      -       +      -
    128B  LEU*     3.5    31.4    -      -       +      +
    129B  ASN*     1.3    78.1    -      -       -      +
    131B  VAL*     1.3    60.4    +      -       -      +
    132B  LEU*     3.6    13.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  VAL*     5.9     4.5    -      -       +      -
     56B  TYR*     5.9     0.9    -      -       +      -
     75B  LEU*     4.9     4.0    -      -       +      -
     82B  VAL*     4.0    28.5    -      -       +      -
     83B  ALA      3.4     4.0    -      -       -      -
     84B  ILE*     4.2    13.2    -      -       +      -
    112B  LEU*     3.8     0.4    -      -       -      +
    113B  ARG*     2.8    32.3    +      -       +      +
    114B  TYR*     3.1    43.6    +      -       +      +
    116B  PHE*     3.7    33.2    -      -       +      -
    129B  ASN      4.5     0.2    -      -       -      +
    130B  LEU*     1.3    71.0    -      -       -      +
    132B  LEU*     1.3    61.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  VAL*     6.2     0.9    -      -       +      -
     82B  VAL*     3.0    11.2    -      -       -      +
     83B  ALA*     2.7    47.0    +      -       +      +
     85B  LYS*     4.7    18.2    -      -       +      -
     97B  GLU*     5.9     1.1    -      -       -      +
    101B  MET*     4.0    22.9    -      -       +      -
    110B  VAL*     4.4    13.5    -      -       +      -
    111B  ARG      4.0     7.0    -      -       -      +
    112B  LEU*     3.9    28.5    -      -       +      -
    113B  ARG*     4.3     3.1    -      -       -      -
    130B  LEU*     3.9    18.2    -      -       +      +
    131B  VAL*     1.3    74.8    -      -       -      +
    133B  ASP*     1.3    65.5    +      -       -      +
    199B  CYS*     6.3     1.8    -      -       +      -
    200B  ASP*     6.2     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  LEU      4.4     4.1    -      -       -      +
     83B  ALA*     4.4     3.9    -      -       -      +
    110B  VAL*     4.4    13.9    -      -       +      +
    111B  ARG*     3.1    51.5    +      -       -      +
    113B  ARG*     2.9    31.8    +      -       -      +
    132B  LEU*     1.3    81.5    -      -       -      +
    134B  TYR*     1.3    62.0    +      -       -      +
    135B  VAL*     3.6    12.3    +      -       +      +
    188B  LEU*     5.2     2.8    -      -       -      +
    197B  LYS*     6.1     1.0    -      -       -      +
----------------------------------------------------------
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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