Contacts of the strand formed by residues 193 - 198 (chain A) in PDB entry 4NTX


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 GLY 193 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159A  TYR*     3.5    29.2    -      -       -      -
    189A  PHE*     3.2    13.3    -      -       -      -
    190A  THR      2.9    37.2    +      -       -      -
    191A  ARG      3.2     1.6    +      -       -      -
    192A  TYR*     1.3    79.5    -      -       -      +
    194A  LYS*     1.3    61.7    +      -       -      -
    195A  CYS*     3.4     3.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  CYS*     5.1     2.6    -      -       -      -
     95A  ASN*     5.2     2.9    +      -       -      +
     98A  GLU      5.5     1.2    +      -       -      -
    100A  ARG*     5.8     1.6    -      -       -      +
    159A  TYR*     3.8    21.7    -      -       -      +
    160A  ASP*     2.8    45.3    +      -       -      +
    163A  GLY*     4.4    14.6    +      -       -      +
    164A  HIS*     4.0    12.6    +      -       -      +
    165A  ASP*     5.4     6.7    +      -       -      +
    169A  MET*     5.9     0.2    -      -       -      +
    187A  VAL*     4.2    26.0    -      -       +      -
    188A  VAL      4.4     0.2    -      -       -      -
    189A  PHE*     4.0    16.8    -      -       +      -
    192A  TYR      4.0     2.2    +      -       -      -
    193A  GLY*     1.3    67.5    -      -       -      -
    195A  CYS*     1.3    64.2    +      -       -      +
    196A  TYR*     3.5    34.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  THR*     4.5     2.0    -      -       +      -
     93A  PHE      3.2     6.1    -      -       -      +
     94A  CYS*     2.0    50.9    -      -       -      +
    187A  VAL*     3.5     6.2    -      -       -      +
    188A  VAL*     2.9    45.5    +      -       +      +
    190A  THR*     3.2    18.4    -      -       +      -
    192A  TYR*     4.0     5.4    -      -       -      -
    193A  GLY      3.7     5.6    -      -       -      -
    194A  LYS*     1.3    79.4    -      -       -      +
    196A  TYR*     1.3    73.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  VAL      3.5     1.9    -      -       -      +
     92A  THR*     3.2     2.9    -      -       -      -
     93A  PHE*     2.9    58.5    +      +       +      -
     94A  CYS*     6.1     0.2    -      -       -      -
    164A  HIS      2.7    29.9    +      -       -      -
    165A  ASP*     3.4     3.8    +      -       -      -
    166A  ILE*     3.1    49.6    +      -       +      +
    169A  MET*     3.8    16.8    -      -       +      -
    185A  PHE*     3.9    17.5    -      -       +      -
    186A  LYS      3.5     2.0    -      -       -      -
    187A  VAL*     3.7    28.5    -      -       +      -
    194A  LYS*     3.5    31.8    +      -       +      -
    195A  CYS*     1.3    83.7    -      -       -      +
    197A  THR*     1.3    63.5    +      -       -      +
    198A  PHE      4.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  ALA*     3.9    14.6    -      -       +      -
     91A  VAL      3.3     4.5    -      -       -      +
     92A  THR*     2.9    25.0    +      -       -      +
    184A  ASP      3.8     1.0    -      -       -      +
    185A  PHE*     3.4     4.5    -      -       -      -
    186A  LYS*     2.8    42.4    +      -       -      +
    188A  VAL*     3.3    20.7    -      -       -      +
    196A  TYR*     1.3    73.9    -      -       -      +
    198A  PHE*     1.3    72.6    +      -       -      +
    199A  ASN      3.8     0.3    +      -       -      -
    200A  ALA*     3.8    23.6    +      -       +      -
    202A  GLN*     6.0     1.1    -      -       -      +
    251A  HIS*     4.5     3.7    -      -       +      +
    257A  PRO*     5.2     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  PHE*     4.3    11.0    -      +       -      -
     90A  ALA*     3.5     0.9    -      -       -      -
     91A  VAL*     2.6    46.0    +      -       +      +
    175A  PHE*     3.9    26.2    -      +       +      -
    180A  CYS*     4.0    21.8    -      -       +      -
    184A  ASP*     3.9    22.2    -      -       +      -
    185A  PHE*     3.7    34.2    -      +       +      -
    197A  THR*     1.3    73.3    -      -       -      +
    199A  ASN*     1.3    78.7    +      -       +      +
    200A  ALA      3.3     0.7    +      -       -      -
    208A  LEU*     3.5    32.8    -      -       +      -
    219A  LEU*     3.9    28.0    -      -       +      -
----------------------------------------------------------
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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