Contacts of the strand formed by residues 193 - 199 (chain B) in PDB entry 2NUE


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 TYR 193 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  ARG*     4.9     9.7    +      -       -      -
    164B  TRP*     4.8    13.0    -      +       -      -
    188B  ALA      3.8     0.2    -      -       -      +
    189B  LYS*     3.2     4.9    -      -       -      -
    190B  ILE*     3.1    39.1    +      -       +      +
    191B  LYS*     3.4     8.1    +      -       +      -
    192B  GLU*     1.3    93.7    -      -       +      +
    194B  ARG*     1.3    63.1    +      -       -      +
    213B  LEU*     3.5    22.2    -      -       +      +
    216B  LEU*     4.5    27.6    -      -       +      -
    217B  LEU*     4.0    24.0    -      -       +      -
    220B  SER      5.8     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  ARG*     6.0     1.4    -      -       -      +
    187B  GLU*     3.7    24.1    +      -       +      -
    188B  ALA      3.2     7.2    -      -       -      +
    189B  LYS*     3.9    37.3    -      -       +      +
    191B  LYS      5.4     0.2    +      -       -      -
    192B  GLU*     5.0     9.6    +      -       -      -
    193B  TYR*     1.3    82.1    -      -       -      +
    195B  THR*     1.3    72.9    +      -       -      +
    196B  LEU*     5.3     3.6    -      -       +      -
    213B  LEU*     4.5     0.4    -      -       -      +
    216B  LEU*     3.6     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187B  GLU*     3.4     9.0    -      -       -      +
    188B  ALA*     3.1    33.2    +      -       -      +
    194B  ARG*     1.3    85.2    -      -       -      +
    196B  LEU*     1.3    70.7    +      -       -      +
    209B  ALA      2.5    28.2    +      -       -      -
    212B  GLU*     3.9    15.7    -      -       +      -
    213B  LEU*     3.8    19.1    -      -       +      +
    216B  LEU*     3.3    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173B  ILE*     3.6    31.6    -      -       +      -
    185B  ILE*     4.5    12.6    -      -       +      -
    186B  VAL      3.6    11.0    -      -       -      +
    187B  GLU*     4.0     6.1    -      -       +      -
    194B  ARG*     5.3     2.5    -      -       +      -
    195B  THR*     1.3    89.2    -      -       -      +
    197B  GLY*     1.3    59.4    +      -       -      +
    208B  ARG*     4.6     1.2    -      -       -      +
    209B  ALA*     3.7    12.8    +      -       -      -
    212B  GLU*     4.7     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  ILE*     3.4     8.0    -      -       -      +
    186B  VAL      3.2    29.0    +      -       -      -
    196B  LEU*     1.3    78.6    -      -       -      +
    198B  GLU*     1.3    61.2    +      -       -      -
    205B  ALA*     3.5    24.3    -      -       -      +
    208B  ARG*     3.7    13.5    -      -       -      -
    209B  ALA*     3.8     1.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  GLU*     4.1    14.1    -      -       -      +
    215A  LYS*     3.6    30.4    -      -       -      +
    183B  LYS*     3.4    42.9    -      -       +      +
    184B  PHE      3.4     5.8    -      -       -      +
    185B  ILE*     4.8     4.9    -      -       +      +
    197B  GLY*     1.3    72.4    -      -       -      -
    199B  GLY*     1.3    64.0    +      -       -      +
    204B  GLU*     4.2     1.6    -      -       -      +
    205B  ALA*     4.1     1.6    -      -       -      -
    208B  ARG*     2.9    47.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  LYS*     3.5     5.9    -      -       -      -
    184B  PHE      2.7    40.6    +      -       -      +
    198B  GLU*     1.3    79.4    -      -       -      +
    200B  LYS*     1.3    59.2    +      -       -      -
    201B  SER      3.0     9.1    +      -       -      +
    204B  GLU*     3.1    14.6    -      -       -      -
    205B  ALA*     3.8    15.0    -      -       -      +
----------------------------------------------------------
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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