Contacts of the strand formed by residues 116 - 121 (chain B) in PDB entry 6ZGI


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 SER 116 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  PHE      3.5    11.4    +      -       -      -
    107B  GLY*     4.0     2.6    -      -       -      -
    108B  THR      4.8     0.3    +      -       -      -
    110B  LEU*     3.8    26.7    +      -       -      +
    114B  THR*     4.6     4.0    +      -       -      -
    115B  GLN*     1.3    76.6    +      -       -      +
    117B  LEU*     1.3    60.1    +      -       -      +
    130B  VAL*     3.3     4.8    -      -       -      +
    131B  CYS      2.9    32.8    +      -       -      +
    133B  PHE*     3.6    13.3    +      -       -      -
    135B  PHE*     3.5    26.9    -      -       -      -
    233B  ILE*     4.2     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105B  ILE*     3.4     6.4    -      -       -      +
    106B  PHE*     2.9    57.0    +      -       +      +
    116B  SER*     1.3    74.3    -      -       -      +
    118B  LEU*     1.3    62.1    +      -       -      +
    119B  ILE*     4.2    11.7    -      -       +      -
    128B  ILE*     3.9    23.6    -      -       +      -
    129B  LYS      3.5    14.6    -      -       -      +
    130B  VAL*     3.7    19.3    -      -       +      +
    133B  PHE*     4.9     0.2    -      -       -      -
    135B  PHE*     5.2     0.7    -      -       -      -
    201B  PHE*     4.2    21.5    -      -       +      -
    229B  LEU*     4.7     1.6    -      -       +      -
    231B  ILE*     3.9    26.5    -      -       +      -
    233B  ILE*     4.1    12.7    -      -       +      +
    235B  ILE*     4.6     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  TRP      3.9     3.8    -      -       -      +
    105B  ILE*     3.7    24.2    -      -       +      -
    116B  SER      4.2     0.2    -      -       -      -
    117B  LEU*     1.3    73.1    -      -       -      +
    119B  ILE*     1.3    66.5    +      -       -      +
    120B  VAL*     4.0    31.2    -      -       +      -
    127B  VAL*     3.5     4.0    -      -       +      +
    128B  ILE*     3.3     5.7    -      -       -      +
    129B  LYS*     2.9    48.3    +      -       +      +
    133B  PHE*     4.1    20.0    -      -       +      -
    135B  PHE*     4.7     2.5    -      -       +      -
    157B  PHE*     5.0     3.8    -      -       +      -
    159B  VAL*     4.3     8.5    -      -       +      -
    160B  TYR*     4.2    24.9    -      -       +      -
    241B  LEU*     4.1     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103B  GLY*     3.3     5.1    -      -       -      -
    104B  TRP*     2.9    57.5    +      -       +      +
    106B  PHE*     4.0    22.0    -      -       +      -
    117B  LEU*     4.2    12.3    -      -       +      -
    118B  LEU*     1.3    76.8    -      -       -      +
    120B  VAL*     1.3    63.0    +      -       -      +
    126B  VAL*     5.2     6.3    -      -       +      -
    127B  VAL      3.6     2.2    -      -       -      -
    128B  ILE*     4.1    27.4    -      -       +      -
    194B  PHE*     5.3     1.3    -      -       +      -
    201B  PHE*     4.2     8.5    -      -       +      -
    203B  ILE*     4.1    25.6    -      -       +      -
    229B  LEU*     4.7     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  ARG      4.0     6.7    -      -       -      +
    118B  LEU*     4.0    23.6    -      -       +      -
    119B  ILE*     1.3    77.1    -      -       -      +
    121B  ASN*     1.3    70.1    +      -       -      +
    122B  ASN*     4.1     5.1    +      -       +      +
    126B  VAL*     3.6     6.7    -      -       -      +
    127B  VAL*     2.9    56.4    +      -       +      +
    141B  LEU*     4.6    10.5    -      -       +      -
    157B  PHE*     4.2    29.2    -      -       +      -
    241B  LEU*     4.0    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  ARG*     3.2    46.2    +      -       -      +
    120B  VAL*     1.3    77.6    -      -       -      +
    122B  ASN*     1.3    84.9    +      -       -      +
    125B  ASN      3.7     3.1    -      -       -      -
    126B  VAL*     4.2    16.9    -      -       +      +
    141B  LEU*     5.5     0.2    -      -       -      +
    175B  PHE*     3.6    11.7    -      -       -      -
    177B  MET*     3.4    31.6    -      -       -      +
----------------------------------------------------------
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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