Contacts of the strand formed by residues 108 - 115 (chain F) in PDB entry 6NMY


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 108 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104F  TRP*     3.6    39.7    -      -       -      -
    106F  GLY      3.7     4.8    +      -       -      +
    107F  ALA*     1.3    80.1    -      -       -      +
    109F  ASN*     1.3    75.1    +      -       -      +
    110F  LEU*     3.2     4.1    +      -       -      -
    124F  TRP*     3.4     1.7    -      -       -      +
    125F  ALA*     2.7    44.7    +      -       +      +
    127F  GLY*     5.4     1.6    -      -       -      -
    128F  PRO*     4.0    19.9    -      -       +      +
    196F  THR*     4.9     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 109 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108F  GLU*     1.3    85.9    -      -       -      +
    110F  LEU*     1.3    62.6    +      -       -      +
    111F  THR*     3.4     8.5    +      -       -      +
    123F  SER*     3.2    12.8    +      -       -      +
    124F  TRP*     3.6     2.5    -      -       -      -
    125F  ALA*     4.5    12.8    -      -       +      -
    196F  THR*     5.7     0.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 110 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107F  ALA*     5.7     0.7    -      -       +      -
    108F  GLU*     3.2     1.9    -      -       -      +
    109F  ASN*     1.3    75.2    -      -       -      +
    111F  THR*     1.3    55.1    +      -       -      +
    112F  CYS*     4.0    18.8    -      -       -      -
    123F  SER      3.4     7.4    -      -       -      +
    124F  TRP*     3.9    20.9    -      -       +      -
    138F  LEU*     5.1     0.7    -      -       +      -
    182F  ILE*     4.7    11.7    -      -       +      +
    184F  VAL*     3.6    35.4    -      -       +      -
    196F  THR*     4.3    25.7    -      -       +      +
    197F  ASP      5.0     1.3    -      -       -      -
    198F  LYS*     2.7    67.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 111 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109F  ASN      3.8     7.5    +      -       -      +
    110F  LEU*     1.3    79.6    -      -       -      +
    112F  CYS*     1.3    63.5    +      -       -      +
    113F  TRP*     3.4    13.0    -      -       -      -
    123F  SER*     2.9    42.6    +      -       -      -
    198F  LYS*     3.7    13.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 112 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110F  LEU*     4.0    17.5    -      -       -      -
    111F  THR*     1.3    75.7    -      -       -      +
    113F  TRP*     1.3    63.5    +      -       -      +
    120F  LEU*     4.3     5.4    -      -       +      -
    121F  SER      3.2     4.7    -      -       -      +
    122F  CYS*     2.0    48.9    -      -       -      -
    182F  ILE*     3.4    24.9    -      -       +      -
    198F  LYS*     4.9     5.6    -      -       -      +
    200F  VAL*     4.6    11.0    -      -       +      +
    205F  ILE*     3.6    21.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 113 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111F  THR*     3.4    27.8    -      -       -      -
    112F  CYS*     1.3    78.1    -      -       -      +
    114F  ILE*     1.3    57.9    +      -       -      +
    115F  HIS*     3.1    30.0    +      +       +      +
    120F  LEU*     3.6     6.3    -      -       -      +
    121F  SER*     2.9    65.3    +      -       -      -
    122F  CYS      4.4     1.1    -      -       -      -
    123F  SER*     3.7    26.7    -      -       -      -
    205F  ILE*     3.3    16.8    -      -       +      +
    207F  ILE*     3.6    27.1    -      -       +      -
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Residues in contact with ILE 114 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113F  TRP*     1.3    73.5    -      -       -      +
    115F  HIS*     1.3    58.7    +      -       -      +
    116F  ASP      5.8     0.2    -      -       -      -
    117F  VAL      3.9    19.3    -      -       -      +
    119F  PHE      3.2    17.7    -      -       -      +
    120F  LEU*     3.7    22.2    -      -       +      -
    170F  ILE*     4.5     3.8    -      -       +      -
    202F  PHE*     3.4    54.1    -      -       +      +
    205F  ILE*     2.9    10.3    +      -       +      +
    206F  GLU*     3.3    18.1    -      -       +      -
    207F  ILE*     2.7    34.3    +      -       -      +
    232F  PHE*     3.5    24.7    -      -       +      -
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Residues in contact with HIS 115 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113F  TRP*     3.1    34.3    -      +       +      +
    114F  ILE*     1.3    75.3    -      -       -      +
    116F  ASP*     1.3    83.3    +      -       -      +
    117F  VAL*     2.9    11.1    +      -       -      -
    119F  PHE*     2.9    48.6    +      +       +      +
    121F  SER*     2.3    31.9    +      -       -      -
    166F  ARG*     4.3     8.4    -      -       -      +
    207F  ILE*     4.2    13.9    -      -       +      -
----------------------------------------------------------
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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