Contacts of the strand formed by residues 112 - 118 (chain A) 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 LEU 112 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  GLY*     3.2    23.1    -      -       -      -
     46A  GLN*     3.0    29.5    +      -       -      +
     98A  LEU*     4.0    22.4    -      -       +      -
    101A  MET*     4.0    34.2    -      -       +      +
    102A  ARG*     4.5     7.0    -      -       +      -
    110A  VAL      3.8     2.4    +      -       -      -
    111A  ARG*     1.3    71.2    -      -       -      +
    113A  ARG*     1.3    64.4    +      -       -      +
    114A  TYR      3.3    23.8    -      -       -      +
    115A  PHE*     4.3     6.5    -      -       +      -
    130A  LEU*     3.8    11.9    -      -       +      -
    131A  VAL      3.7    14.1    -      -       -      +
    132A  LEU*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  PRO*     3.5     2.1    -      -       -      +
     45A  GLY      2.8    21.5    +      -       -      -
     46A  GLN*     5.3     0.2    +      -       -      -
     75A  LEU*     4.0    22.0    -      -       +      +
     78A  SER*     4.0     6.9    +      -       -      -
     80A  GLU*     2.7    44.4    +      -       -      +
     82A  VAL*     4.3     6.1    -      -       +      +
    111A  ARG*     3.3    41.9    -      -       -      +
    112A  LEU*     1.3    71.2    -      -       -      +
    114A  TYR*     1.3    92.2    +      -       +      +
    131A  VAL*     2.9    22.9    +      -       +      +
    132A  LEU      4.4     4.9    -      -       -      +
    133A  ASP*     3.4    23.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ALA*     3.7    14.4    -      -       +      -
     43A  THR      3.0    21.3    -      -       -      +
     44A  PRO*     3.7     9.2    -      -       +      -
     45A  GLY      3.9     0.9    -      -       -      +
     52A  GLN*     3.4    40.1    +      -       -      -
     54A  VAL*     4.1    33.7    -      -       +      -
     75A  LEU*     4.9     9.0    -      -       +      -
    112A  LEU*     3.3     7.6    -      -       -      +
    113A  ARG*     1.3   113.1    +      -       +      +
    115A  PHE*     1.3    65.9    +      -       -      +
    131A  VAL*     2.9    38.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ALA*     4.1     0.2    -      -       -      -
     43A  THR*     3.0    65.5    +      -       +      -
     44A  PRO      4.3     2.7    -      -       -      -
     45A  GLY*     4.5     2.7    -      -       -      -
     49A  ASP*     5.2     1.3    -      -       -      -
     98A  LEU*     3.7    41.1    -      -       +      -
    102A  ARG*     3.7    36.3    -      -       -      -
    112A  LEU*     4.3    10.5    -      -       +      -
    114A  TYR*     1.3    81.3    -      -       -      +
    116A  PHE*     1.3    61.5    +      -       -      +
    117A  TYR*     3.7    19.2    -      +       -      -
    128A  LEU*     3.8    12.1    -      -       +      -
    129A  ASN      3.2    13.2    -      -       -      +
    130A  LEU*     4.4     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  VAL*     3.8    39.5    -      -       +      -
     41A  VAL      3.3    25.4    -      -       -      +
     42A  ALA*     3.9     7.6    -      -       +      -
     54A  VAL*     6.3     0.9    -      -       +      -
     56A  TYR*     4.1    23.6    -      +       -      -
     84A  ILE*     4.5     4.5    -      -       +      -
    115A  PHE*     1.3    75.5    -      -       -      +
    117A  TYR*     1.3    78.1    -      -       -      +
    118A  SER*     4.0     6.3    -      -       -      -
    128A  LEU*     3.7     2.9    -      -       -      +
    129A  ASN*     2.7    71.6    +      -       +      +
    131A  VAL*     3.6    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  VAL      5.2     0.2    +      -       -      -
     89A  GLN*     5.9     3.1    -      -       +      -
     95A  ASN*     6.0     0.2    -      -       -      +
     98A  LEU*     3.3    23.0    -      -       -      +
    115A  PHE*     3.7    24.4    -      +       -      -
    116A  PHE*     1.3    89.2    -      -       -      +
    118A  SER*     1.3    68.4    +      -       -      +
    126A  VAL*     4.2    28.7    -      -       +      -
    127A  TYR      3.4    10.8    -      -       -      -
    128A  LEU*     3.7    24.7    -      -       +      +
    129A  ASN*     4.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LYS*     4.3    13.5    +      -       -      -
    116A  PHE*     4.0     6.6    -      -       -      -
    117A  TYR*     1.3    77.2    +      -       -      +
    119A  SER*     1.3    66.8    +      -       -      +
    120A  GLY      3.1     3.3    +      -       -      -
    126A  VAL*     3.8     8.5    -      -       -      +
    127A  TYR*     2.9    42.5    +      -       -      -
    129A  ASN*     3.0    16.4    +      -       -      -
----------------------------------------------------------
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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