Contacts of the strand formed by residues 312 - 316 (chain B) in PDB entry 5WN0


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 ILE 312 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  CYS*     3.2     3.3    -      -       -      -
     66B  SER*     2.8    50.6    +      -       -      +
    209B  GLY      4.8     0.7    -      -       -      +
    265B  THR*     3.6    31.2    -      -       +      -
    283B  ASP*     3.7    14.8    -      -       +      +
    284B  TYR*     3.4    41.1    -      -       -      +
    285B  PHE*     3.5    20.3    -      -       +      -
    299B  LYS      3.4    15.9    -      -       -      +
    300B  ILE*     4.4     6.5    -      -       +      -
    301B  ARG      4.8     0.2    -      -       -      +
    310B  CYS      4.7     0.4    -      -       -      +
    311B  PRO*     1.3    77.3    -      -       -      +
    313B  THR*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 313 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  LYS*     4.9     7.6    -      -       -      -
     64B  ILE      3.0     4.3    -      -       -      +
     65B  CYS*     3.5    29.6    -      -       +      -
     87B  GLU*     3.3    26.5    -      -       +      +
    285B  PHE*     3.5     6.5    -      -       -      -
    298B  SER*     3.6     3.1    -      -       -      -
    299B  LYS*     2.8    39.6    +      -       -      +
    301B  ARG*     2.9    33.3    +      -       +      +
    312B  ILE*     1.3    80.5    -      -       -      +
    314B  LEU*     1.3    61.3    +      -       -      +
    315B  TYR*     5.3     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  LEU      3.4     1.0    -      -       -      +
     63B  LYS*     3.2     7.8    -      -       -      +
     64B  ILE*     2.6    44.4    +      -       +      +
    206B  VAL*     3.9    15.7    -      -       +      -
    252B  SER*     3.9    14.4    -      -       -      +
    285B  PHE*     3.6    47.8    -      -       +      -
    287B  LEU*     4.0     8.7    -      -       +      -
    295B  LEU*     4.0    23.8    -      -       +      -
    297B  ASP      3.8     2.7    -      -       -      +
    298B  SER*     4.4     1.6    -      -       -      +
    313B  THR*     1.3    74.1    -      -       -      +
    315B  TYR*     1.3    62.2    +      -       -      +
    316B  LEU*     3.7    31.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  ASP*     2.7    38.4    +      -       +      -
     51B  GLN      4.1    11.4    -      -       -      -
     52B  LYS*     3.8    27.0    -      -       +      -
     60B  ALA*     4.1    16.2    -      -       +      -
     62B  LEU      3.3     5.2    -      -       -      -
     63B  LYS*     3.0    54.7    +      -       +      -
    295B  LEU*     3.9     1.0    -      -       -      +
    296B  CYS*     3.0    39.1    +      -       +      +
    297B  ASP*     3.0    23.6    +      -       +      +
    299B  LYS*     4.3     7.6    -      -       +      -
    301B  ARG*     3.7     5.8    +      -       -      -
    313B  THR*     5.0     2.7    -      -       -      -
    314B  LEU*     1.3    75.9    -      -       -      +
    316B  LEU*     1.3    67.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  ALA*     4.0     3.8    -      -       -      -
     61B  THR      3.1    19.9    +      -       -      -
     62B  LEU*     2.9    32.2    +      -       +      +
    165B  PHE*     5.9     0.9    -      -       +      -
    206B  VAL*     4.2    20.2    -      -       +      -
    287B  LEU*     4.1    18.2    -      -       +      -
    291B  LEU*     4.6    11.0    -      -       +      +
    294B  ALA*     3.8     7.9    -      -       +      +
    295B  LEU*     3.7    23.3    -      -       +      +
    314B  LEU*     3.7    27.3    -      -       +      -
    315B  TYR*     1.3    80.6    -      -       -      +
    317B  ALA*     1.3    59.1    +      -       -      +
    318B  LEU*     3.3    28.5    +      -       +      -
----------------------------------------------------------
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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