Contacts of the strand formed by residues 309 - 314 (chain A) in PDB entry 1N0W


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 309 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305A  GLY*     3.0    18.5    +      -       -      +
    306A  ARG*     2.6    34.5    +      -       +      +
    308A  GLU*     1.3    99.4    -      -       +      +
    310A  ARG*     1.3    76.8    +      -       -      +
    326A  MSE      4.1    19.5    -      -       -      -
    327A  PHE      3.3     9.0    -      -       -      +
    328A  ALA*     4.2     0.9    -      -       +      +
    337A  ALA*     3.9    22.0    -      -       +      -
    338A  LYS      4.9     6.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 310 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  ARG*     2.7    33.3    +      -       -      +
    131A  THR*     3.3    20.3    -      -       -      +
    303A  ARG      3.6    11.4    -      -       -      +
    304A  LYS*     3.6    31.2    -      -       -      +
    305A  GLY      3.9     2.5    -      -       -      +
    307A  GLY      2.9    26.9    +      -       -      -
    308A  GLU*     3.4    13.4    -      -       -      +
    309A  THR*     1.3    85.0    +      -       -      +
    311A  ILE*     1.3    65.3    +      -       -      +
    326A  MSE      3.3     6.9    -      -       -      +
    327A  PHE*     2.7    54.2    +      -       +      +
    329A  ILE*     3.3    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 311 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  TYR      3.6     1.4    -      -       -      +
    302A  LEU*     3.2     5.5    -      -       -      +
    303A  ARG*     2.9    85.3    +      -       +      +
    304A  LYS      4.8     1.6    -      -       -      +
    305A  GLY*     4.8    14.4    -      -       -      -
    310A  ARG*     1.3    81.2    -      -       -      +
    312A  CYS*     1.3    68.4    +      -       -      +
    324A  GLU*     4.2     2.7    -      -       +      +
    325A  ALA      3.5     3.6    -      -       -      +
    326A  MSE      4.4    14.1    -      -       +      -
    327A  PHE*     4.0     3.1    -      -       -      -
    504A  EDO      3.7    36.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 312 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  LEU*     3.8    31.9    -      -       +      -
    112A  LEU*     3.7    10.1    -      -       +      +
    300A  LEU*     3.7    41.3    -      -       -      -
    301A  TYR      3.5     3.1    -      -       -      -
    302A  LEU*     3.5    17.7    -      -       +      -
    311A  ILE*     1.3    76.0    -      -       -      +
    313A  LYS*     1.3    63.9    +      -       -      +
    324A  GLU*     3.2     5.4    -      -       -      +
    325A  ALA      2.9    32.7    +      -       -      +
    327A  PHE*     3.9     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  LEU*     3.8     0.3    -      -       -      -
    301A  TYR*     2.8    47.2    +      -       +      +
    303A  ARG*     4.1     9.2    -      -       -      +
    312A  CYS*     1.3    75.1    -      -       -      +
    314A  ILE*     1.3    72.1    +      -       -      +
    315A  TYR*     3.4    39.9    +      -       +      +
    322A  GLU*     3.3    35.8    +      -       -      -
    323A  ALA      3.4     4.9    -      -       -      +
    324A  GLU*     3.4    36.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  LEU*     3.7    39.0    -      -       +      +
    113A  LEU*     4.0    11.4    -      -       +      -
    298A  THR*     4.5     9.4    -      -       +      -
    299A  ARG      3.8    12.8    -      -       -      +
    300A  LEU*     3.3    33.9    -      -       +      -
    312A  CYS*     4.5     0.4    -      -       -      -
    313A  LYS*     1.3    80.8    -      -       -      +
    315A  TYR*     1.3    77.5    +      -       -      +
    317A  SER*     4.2     9.1    +      -       -      +
    322A  GLU*     3.4     4.9    -      -       -      -
    323A  ALA*     3.0    33.5    +      -       +      +
----------------------------------------------------------
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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