Contacts of the strand formed by residues 203 - 212 (chain F) in PDB entry 1NZB


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 LEU 203 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198F  GLY      4.1     5.6    -      -       -      +
    199F  ARG*     3.4     2.9    -      -       -      +
    200F  THR*     2.9    43.1    +      -       +      +
    201F  LYS      3.6     2.6    +      -       -      -
    202F  THR*     1.3    82.9    -      -       -      +
    204F  VAL*     1.3    63.3    +      -       -      +
    205F  SER*     4.0    19.7    -      -       -      +
    208F  GLY*     4.4    20.0    -      -       -      +
    209F  VAL*     5.4     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 204 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ARG*     3.0    37.9    +      -       -      +
    122A  LYS*     4.0    22.0    -      -       +      -
    125A  VAL*     3.6    24.0    -      -       +      -
    199F  ARG*     3.6    31.6    -      -       +      -
    203F  LEU*     1.3    77.7    -      -       -      +
    205F  SER*     1.3    60.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 205 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  ARG*     5.1     5.6    -      -       -      +
    125A  VAL*     3.5    27.4    -      -       -      +
    129A  GLU      4.7     1.6    -      -       -      +
    198F  GLY*     4.3     9.8    +      -       -      +
    203F  LEU*     4.0    15.3    -      -       -      +
    204F  VAL*     1.3    78.1    -      -       -      +
    206F  THR*     1.3    64.3    +      -       -      +
    207F  ALA*     3.5    14.7    +      -       -      +
    208F  GLY      3.6    13.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 206 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  VAL*     4.3    16.6    -      -       +      -
     86A  LYS*     5.3     9.7    -      -       +      +
    121A  ARG*     6.6     0.2    -      -       +      -
    125A  VAL*     5.1     4.0    -      -       +      -
    129A  GLU*     3.2    44.6    -      -       +      +
    130A  ARG*     3.3    11.1    -      -       -      +
    131A  ALA*     2.8    40.4    +      -       -      +
    114D    A      5.5     2.4    +      -       -      +
    196F  HIS*     5.2     0.4    -      -       -      -
    205F  SER*     1.3    74.9    -      -       -      +
    207F  ALA*     1.3    62.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 207 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  ALA*     4.7     8.5    -      -       +      -
    323A  ASN*     5.0    14.3    +      -       -      +
    326A  ARG*     3.8     7.9    +      -       -      +
    196F  HIS*     3.4    15.9    +      -       -      -
    205F  SER*     3.3     8.1    +      -       -      +
    206F  THR*     1.3    82.5    +      -       -      +
    208F  GLY*     1.3    72.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 208 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  ARG*     3.2    16.5    +      -       -      -
    196F  HIS*     4.4     4.3    -      -       -      -
    197F  ILE      3.5    13.7    -      -       -      -
    198F  GLY*     4.2    11.0    -      -       -      -
    203F  LEU*     4.4    14.7    -      -       -      +
    205F  SER*     3.6     9.8    +      -       -      -
    206F  THR      3.8     0.6    -      -       -      -
    207F  ALA*     1.3    90.7    -      -       -      +
    209F  VAL*     1.3    61.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 209 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326A  ARG*     4.0     9.9    -      -       -      +
    196F  HIS*     3.8     3.2    -      -       -      -
    197F  ILE*     3.0    42.7    +      -       +      +
    200F  THR*     5.4     7.4    -      -       +      -
    203F  LEU*     5.9     5.4    -      -       +      -
    208F  GLY*     1.3    76.0    -      -       -      +
    210F  GLU*     1.3    85.0    +      -       -      +
    211F  LYS*     4.0    21.3    +      -       -      +
    311F  GLN*     5.9     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 210 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ARG*     3.3    12.6    +      -       -      -
    326A  ARG*     3.5    46.4    +      -       +      +
    327A  ASN*     5.8     1.6    -      -       +      +
    186F  SER*     5.3     2.9    +      -       -      -
    194F  LEU*     4.3    28.6    -      -       +      +
    195F  ILE      3.7     2.5    -      -       -      +
    196F  HIS*     3.1    48.7    +      -       -      +
    209F  VAL*     1.3    87.3    -      -       -      +
    211F  LYS*     1.3    61.0    +      -       -      +
    212F  ALA*     4.0     2.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 211 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170F  THR*     3.2    50.5    -      -       +      +
    171F  LEU      5.6     0.2    -      -       -      -
    172F  LEU*     4.3    12.6    -      -       +      +
    194F  LEU*     3.5     2.1    -      -       -      -
    195F  ILE*     2.8    48.2    +      -       +      +
    197F  ILE*     4.2    19.5    -      -       +      -
    209F  VAL*     4.0    22.0    +      -       +      +
    210F  GLU*     1.3    73.7    -      -       -      +
    212F  ALA*     1.3    63.0    +      -       -      +
    213F  LEU*     4.0     1.4    +      -       -      +
    311F  GLN      4.1    10.5    +      -       -      -
    312F  ALA*     3.4    19.0    +      -       -      +
    313F  GLY      5.0     1.7    -      -       -      -
    314F  GLY*     4.7     7.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 212 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332A  THR*     3.7    40.9    +      -       +      +
    336A  VAL*     3.5    12.9    -      -       +      +
    169F  ASN*     3.9     9.7    +      -       -      +
    170F  THR*     4.8     1.6    -      -       -      +
    188F  THR*     5.2     0.2    -      -       +      -
    192F  ARG*     5.6     0.4    -      -       +      -
    193F  MET      3.6     2.5    -      -       -      +
    194F  LEU*     3.3    26.2    -      -       +      -
    210F  GLU      4.0     2.6    +      -       -      +
    211F  LYS*     1.3    75.6    -      -       -      +
    213F  LEU*     1.3    68.5    +      -       -      +
----------------------------------------------------------
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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