Contacts of the strand formed by residues 313 - 317 (chain D) in PDB entry 5Y1Z


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 ARG 313 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  LYS*     4.0    11.1    +      -       -      +
    247D  HIS*     5.7     0.6    +      -       -      -
    250D  ASN*     4.2     9.9    -      -       -      +
    251D  GLU*     3.0    37.1    +      -       -      -
    254D  VAL*     3.9     8.7    -      -       -      +
    296D  LEU*     3.5    21.8    -      -       -      -
    297D  ARG*     3.2     4.9    -      -       -      +
    304D  ASP*     2.3    43.0    +      -       -      +
    305D  ALA      3.1    14.4    -      -       -      +
    306D  ARG*     3.6    26.3    -      -       +      +
    307D  PHE*     4.8     1.1    -      -       -      -
    312D  ASP*     1.3    80.1    -      -       -      +
    314D  ALA*     1.3    63.2    +      -       -      +
    504D  SO4      3.1    26.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 314 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  SER*     6.2     4.0    -      -       -      -
     10B  ARG*     5.6     1.3    -      -       -      +
    285D  LEU*     4.0    20.4    -      -       +      -
    303D  VAL      3.5     0.3    -      -       -      +
    304D  ASP*     4.2     3.8    +      -       -      -
    305D  ALA*     2.9    35.4    +      -       -      +
    307D  PHE*     3.9    19.1    -      -       +      -
    312D  ASP*     5.4     2.5    -      -       -      +
    313D  ARG*     1.3    78.8    -      -       -      +
    315D  TRP*     1.3    63.6    +      -       -      +
    316D  VAL*     3.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 315 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285D  LEU*     4.4     7.3    -      -       -      +
    297D  ARG*     3.6    38.6    -      -       +      -
    299D  LYS*     4.0    26.5    -      -       +      -
    302D  GLN*     3.5    46.4    +      -       +      +
    303D  VAL      3.4     3.6    -      -       -      -
    304D  ASP*     3.5    43.9    +      -       +      -
    314D  ALA*     1.3    73.5    -      -       -      +
    316D  VAL*     1.3    62.3    +      -       -      +
    317D  PRO*     4.4     2.8    -      -       -      +
    504D  SO4      2.6    29.4    +      -       -      -
    505D  SO4      3.3    26.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 316 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283D  ALA*     4.2     7.2    -      -       +      -
    284D  LYS      3.6    28.9    -      -       -      +
    285D  LEU*     3.7    23.1    -      -       +      -
    302D  GLN*     3.9     2.7    -      -       -      -
    303D  VAL*     2.8    37.4    +      -       -      +
    305D  ALA*     4.2    14.1    -      -       +      -
    307D  PHE*     4.4     2.7    -      -       +      -
    314D  ALA      3.8     9.9    -      -       -      +
    315D  TRP*     1.3    80.3    -      -       -      +
    317D  PRO*     1.3    80.5    -      -       +      +
    320D  ASN*     3.8     8.3    -      -       +      -
    321D  CYS*     4.0    14.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 317 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284D  LYS      5.2     1.1    -      -       -      +
    301D  GLY      3.6     1.6    -      -       -      +
    302D  GLN*     3.1    26.0    -      -       -      +
    315D  TRP      4.4     3.4    -      -       -      +
    316D  VAL*     1.3    87.8    -      -       +      +
    318D  ILE*     1.3    61.5    +      -       -      +
    319D  ASN*     3.1     6.3    -      -       +      +
    320D  ASN*     2.8    48.6    +      -       -      +
    321D  CYS*     4.2     0.5    -      -       -      -
----------------------------------------------------------
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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