Contacts of the strand formed by residues 312 - 316 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  CYS*     3.3     2.4    -      -       -      -
     66A  SER*     3.0    44.2    +      -       -      +
    265A  THR*     3.6    28.5    -      -       +      -
    283A  ASP*     3.6    24.9    -      -       +      +
    284A  TYR      3.5    27.8    -      -       -      +
    285A  PHE*     3.3    28.4    -      -       +      -
    298A  SER*     5.9     0.2    -      -       -      +
    299A  LYS      3.3    16.2    -      -       -      +
    300A  ILE*     4.3     6.1    -      -       +      -
    301A  ARG*     4.7     0.9    -      -       -      +
    310A  CYS      4.6     0.4    -      -       -      +
    311A  PRO*     1.3    79.2    -      -       -      +
    313A  THR*     1.3    67.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  LYS*     3.8    30.3    -      -       +      -
     64A  ILE      3.4     6.7    -      -       -      +
     65A  CYS*     3.7    12.0    -      -       +      +
     87A  GLU*     2.7    30.2    +      -       -      +
    285A  PHE*     3.6     3.9    -      -       -      -
    297A  ASP      3.9     0.2    -      -       -      +
    298A  SER*     3.4     2.4    -      -       -      -
    299A  LYS*     2.7    41.6    +      -       -      +
    301A  ARG*     3.8    19.6    +      -       -      +
    312A  ILE*     1.3    79.0    +      -       -      +
    314A  LEU*     1.3    63.2    +      -       -      +
    315A  TYR*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  LEU      3.8     0.5    -      -       -      +
     63A  LYS*     3.3     9.2    -      -       -      +
     64A  ILE*     2.8    41.7    +      -       +      +
    206A  VAL*     4.0    15.3    -      -       +      -
    252A  SER*     4.2     9.0    -      -       -      +
    285A  PHE*     3.6    45.1    -      -       +      -
    287A  LEU*     4.3     6.1    -      -       +      -
    295A  LEU*     3.6    30.7    -      -       +      -
    297A  ASP      3.4     4.9    -      -       -      +
    298A  SER*     4.5     1.1    -      -       -      -
    313A  THR*     1.3    74.6    -      -       -      +
    315A  TYR*     1.3    62.3    +      -       -      +
    316A  LEU*     3.7    33.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  ASP*     2.9    37.8    +      -       +      -
     51A  GLN      4.3     4.9    -      -       -      +
     52A  LYS*     3.9    27.5    -      -       +      -
     60A  ALA*     4.1    15.9    -      -       +      -
     62A  LEU      3.5     2.7    -      -       -      -
     63A  LYS*     3.3    51.6    +      -       +      -
    295A  LEU*     4.1     0.2    -      -       -      +
    296A  CYS*     2.8    36.0    +      -       +      -
    297A  ASP*     2.8    38.5    +      -       +      +
    299A  LYS*     4.0    12.8    -      -       +      -
    301A  ARG*     3.4     3.0    +      -       -      -
    313A  THR*     4.2     3.1    -      -       +      -
    314A  LEU*     1.3    73.2    -      -       -      +
    316A  LEU*     1.3    65.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ALA*     3.2     6.7    -      -       -      +
     61A  THR      2.9    21.1    +      -       -      -
     62A  LEU*     2.9    38.3    +      -       +      +
    165A  PHE*     5.9     0.4    -      -       +      -
    206A  VAL*     4.4    18.4    -      -       +      -
    287A  LEU*     4.7     8.5    -      -       +      -
    291A  LEU*     4.5    15.9    -      -       +      +
    294A  ALA*     3.4     7.9    -      -       +      +
    295A  LEU*     3.6    23.8    -      -       +      +
    296A  CYS*     4.0     0.7    -      -       -      -
    314A  LEU*     3.7    36.8    -      -       +      -
    315A  TYR*     1.3    82.3    -      -       -      +
    317A  ALA*     1.3    60.3    +      -       -      +
    318A  LEU*     4.1    17.5    -      -       +      -
----------------------------------------------------------
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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