Contacts of the strand formed by residues 728 - 734 (chain C) in PDB entry 3N1G


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 THR 728 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    723C  ALA*     3.7     0.3    -      -       -      -
    724C  VAL*     2.9    46.8    +      -       +      -
    725C  ASN*     3.0    22.7    +      -       -      +
    727C  THR*     1.3    89.2    +      -       -      +
    729C  ILE*     1.3    67.6    +      -       -      +
    776C  SER*     2.7    31.0    -      -       -      +
    777C  ILE      3.2     8.5    -      -       -      +
    778C  SER*     3.9    14.0    +      -       -      +
    780C  LEU*     4.5     0.2    -      -       -      -
    809C  THR*     4.2     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 729 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    721C  THR*     4.6     1.1    -      -       -      -
    722C  ASP      3.7    11.2    -      -       -      +
    723C  ALA*     4.3     5.2    -      -       -      -
    724C  VAL*     4.3     1.6    -      -       -      -
    728C  THR*     1.3    79.4    -      -       -      +
    730C  MET*     1.3    71.3    +      -       -      +
    731C  LEU*     5.6     0.4    -      -       +      -
    775C  HIS      4.0     0.2    -      -       -      +
    776C  SER*     3.4     2.1    -      -       -      -
    777C  ILE*     2.7    43.4    +      -       +      +
    780C  LEU*     3.5    24.0    -      -       +      -
    786C  TYR*     3.9     9.2    -      -       +      -
    788C  ILE*     3.9    27.6    -      -       +      -
    807C  CYS*     3.8    44.0    -      -       +      +
    809C  THR*     3.8    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 730 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    720C  PHE*     4.3    16.8    -      -       +      -
    721C  THR*     3.3     3.8    -      -       -      -
    722C  ASP*     2.9    33.9    +      -       +      +
    724C  VAL*     3.4    22.5    -      -       +      +
    729C  ILE*     1.3    76.5    -      -       -      +
    731C  LEU*     1.3    68.3    +      -       -      +
    732C  LYS*     4.8     5.4    -      -       +      -
    774C  TRP*     3.0    46.9    -      -       +      -
    775C  HIS      3.3    12.6    -      -       -      +
    776C  SER*     3.6    21.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 731 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718C  ILE*     4.2    18.8    -      -       +      -
    720C  PHE      3.1    11.0    -      -       -      +
    721C  THR*     3.9    11.7    -      -       +      -
    729C  ILE*     4.6     2.5    -      -       +      +
    730C  MET*     1.3    77.3    -      -       -      +
    732C  LYS*     1.3    64.6    +      -       -      +
    733C  TRP*     4.1    17.5    -      -       +      -
    750C  ILE*     4.0    26.7    -      -       +      -
    774C  TRP*     3.3     6.6    -      -       -      +
    775C  HIS*     2.9    52.4    +      -       +      +
    777C  ILE*     3.9    31.4    -      -       +      -
    788C  ILE*     4.1    13.9    -      -       +      -
    790C  MET*     4.3     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 732 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718C  ILE*     3.4     7.3    -      -       -      +
    719C  THR*     2.8    33.6    +      -       -      +
    720C  PHE*     2.9    37.3    +      -       +      -
    730C  MET*     4.8     6.3    -      -       +      -
    731C  LEU*     1.3    80.6    -      -       -      +
    733C  TRP*     1.3    66.5    +      -       -      +
    773C  TYR*     3.5    35.1    +      -       +      +
    774C  TRP*     4.1    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 733 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    716C  PRO*     4.0    12.8    -      -       +      -
    717C  TYR      3.2    16.2    -      -       -      +
    718C  ILE*     4.1     0.4    -      -       -      -
    719C  THR*     4.1     3.8    -      -       -      -
    731C  LEU*     4.1    14.8    -      -       +      -
    732C  LYS*     1.3    80.7    -      -       -      +
    734C  MET*     1.3    76.1    +      -       -      +
    735C  TYR*     4.3     2.1    +      -       +      -
    748C  PHE*     3.4    33.7    -      +       -      -
    750C  ILE*     4.2     3.8    -      -       +      -
    768C  VAL*     4.0    13.5    -      -       +      -
    772C  LYS*     3.2    32.6    +      -       +      -
    773C  TYR*     2.9    31.3    +      -       +      +
    774C  TRP*     3.5    34.5    -      -       -      -
    775C  HIS*     3.6    17.5    -      -       +      -
    790C  MET*     3.4    37.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 734 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    715C  GLY      4.9     0.2    -      -       -      +
    716C  PRO*     3.4     1.9    -      -       -      +
    717C  TYR*     2.9    40.3    +      -       +      +
    719C  THR*     3.6    26.2    -      -       +      +
    733C  TRP*     1.3    80.1    -      -       -      +
    735C  TYR*     1.3    62.7    +      -       -      +
    736C  ILE*     5.6     6.3    -      -       +      -
    773C  TYR*     6.3     1.3    -      -       -      -
----------------------------------------------------------
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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