Contacts of the strand formed by residues 314 - 319 (chain B) in PDB entry 1D0N


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 LYS 314 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  SER*     5.4     6.5    -      -       -      -
    309B  HIS*     2.8    49.2    +      -       +      +
    312B  ASP*     4.4     5.4    -      -       -      +
    313B  GLY*     1.3    79.9    -      -       -      +
    315B  ILE*     1.3    73.2    +      -       -      +
    316B  PHE*     3.7    35.3    -      -       +      -
    348B  THR*     3.9     2.0    -      -       -      +
    349B  GLN*     3.1    43.5    +      -       +      +
    350B  VAL      4.5     0.9    -      -       -      -
    351B  SER*     3.3    37.2    +      -       -      +
    361B  LEU*     5.0    11.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    306B  ILE*     4.7     7.6    -      -       +      -
    307B  LEU      3.4    10.8    -      -       -      +
    308B  ASP*     3.9    19.7    -      -       -      +
    309B  HIS      4.2     0.7    -      -       -      +
    310B  GLY*     4.4     2.7    -      -       -      +
    314B  LYS*     1.3    85.1    -      -       -      +
    316B  PHE*     1.3    65.0    +      -       -      +
    317B  VAL*     5.1     2.5    -      -       +      -
    335B  ALA*     3.9    17.3    -      -       +      +
    338B  PHE*     4.0    21.1    -      -       +      -
    339B  ILE*     3.7    27.6    -      -       +      -
    344B  TYR*     4.8     4.5    -      -       +      -
    348B  THR*     4.3    10.8    -      -       +      -
    349B  GLN      3.0     9.6    +      -       -      +
    350B  VAL*     3.7    23.3    -      -       +      +
    351B  SER      3.2    19.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305B  PHE      3.8     0.2    -      -       -      +
    306B  ILE*     3.3     6.3    -      -       -      +
    307B  LEU*     2.8    47.7    +      -       +      +
    309B  HIS*     4.6     5.6    -      -       +      -
    314B  LYS*     3.7    44.0    -      -       +      -
    315B  ILE*     1.3    76.9    -      -       -      +
    317B  VAL*     1.3    63.7    +      -       -      +
    351B  SER*     3.2    10.1    -      -       -      +
    353B  LEU*     4.3    15.0    -      -       +      -
    359B  THR*     5.0     3.4    -      -       -      -
    361B  LEU*     4.0    22.9    -      -       +      -
    362B  PHE*     3.9    46.4    -      +       +      -
    364B  GLN*     5.8     0.2    -      -       -      -
    365B  PHE*     3.9    21.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304B  CYS*     6.1     2.7    -      -       +      -
    305B  PHE      3.2     8.1    -      -       -      +
    306B  ILE*     4.5    13.2    -      -       +      -
    315B  ILE*     5.1     3.8    -      -       +      -
    316B  PHE*     1.3    78.0    -      -       -      +
    318B  TRP*     1.3    59.7    +      -       -      +
    319B  LYS*     4.4     6.5    -      -       +      -
    331B  ALA*     4.0    20.2    -      -       +      +
    334B  THR*     5.7     3.4    -      -       +      -
    335B  ALA*     3.9    31.4    -      -       +      +
    350B  VAL*     4.4     6.5    -      -       +      -
    351B  SER      2.9    10.2    +      -       -      +
    352B  VAL*     3.3    26.2    -      -       +      -
    353B  LEU*     2.9    24.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299B  LEU*     3.6    44.8    -      -       +      +
    300B  ARG      3.7    21.8    -      -       -      -
    304B  CYS*     3.2     8.3    -      -       -      +
    305B  PHE*     2.7    63.1    +      +       +      +
    307B  LEU      6.1     0.2    -      -       -      +
    316B  PHE      4.0     0.6    -      -       -      -
    317B  VAL*     1.3    73.5    -      -       -      +
    319B  LYS*     1.3    62.7    +      -       -      +
    320B  GLY*     3.9    10.1    -      -       -      -
    353B  LEU*     3.6    13.0    -      -       +      -
    354B  PRO      4.8     0.2    -      -       -      -
    355B  GLU*     3.3    51.3    -      -       +      +
    358B  GLU*     3.1    28.3    +      -       +      +
    362B  PHE*     3.7    36.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 319 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109B  ASP*     3.7    22.4    +      -       -      -
    114B  GLY*     5.1     3.4    +      -       -      -
    116B  ALA      5.7     1.8    +      -       -      -
    118B  GLN*     4.4     4.8    +      -       -      -
    304B  CYS*     4.2    16.2    -      -       -      -
    317B  VAL*     4.4     6.3    -      -       +      -
    318B  TRP*     1.3    80.0    -      -       -      +
    320B  GLY*     1.3    66.0    +      -       -      +
    328B  ARG*     4.1    40.6    +      -       +      +
    331B  ALA*     4.1    13.9    -      -       +      -
    352B  VAL*     3.9    30.7    -      -       +      +
    353B  LEU      3.0    23.8    +      -       -      +
    354B  PRO*     3.9    11.4    -      -       +      +
    355B  GLU*     2.9    29.5    +      -       -      +
----------------------------------------------------------
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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