Contacts of the strand formed by residues 383 - 388 (chain D) in PDB entry 6OY5


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 GLY 383 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213D  VAL*     4.6     2.5    -      -       -      -
    214D  GLU      3.3    13.2    -      -       -      -
    215D  TYR*     3.9     6.5    -      -       -      -
    216D  VAL*     4.0    10.1    -      -       -      -
    359D  ALA      3.7     1.9    -      -       -      +
    360D  ARG*     4.0     4.5    +      -       -      +
    361D  VAL*     3.3    35.9    +      -       -      +
    381D  ALA      3.4     3.3    +      -       -      -
    382D  GLU*     1.3    78.9    -      -       -      +
    384D  VAL*     1.3    59.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 384 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    213D  VAL*     3.5     5.6    -      -       -      +
    214D  GLU*     2.9    45.6    +      -       +      +
    216D  VAL*     4.9     3.9    -      -       +      +
    340D  THR*     6.0     2.9    -      -       +      -
    358D  GLY*     3.6    22.0    -      -       -      +
    359D  ALA      3.5    13.0    -      -       -      +
    360D  ARG*     5.6     3.1    -      -       +      -
    383D  GLY*     1.3    73.9    -      -       -      -
    385D  VAL*     1.3    63.1    +      -       -      +
    386D  HIS*     3.3    25.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 385 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211D  VAL*     3.9    24.5    -      -       +      -
    212D  ARG      4.2     1.6    -      -       -      -
    213D  VAL*     4.8     9.9    -      -       +      +
    353D  VAL*     6.0     0.2    -      -       +      -
    355D  VAL*     3.6    34.1    -      -       +      -
    356D  PRO      4.0     8.7    -      -       -      +
    357D  GLU*     4.0     0.9    -      -       -      +
    358D  GLY*     2.7    30.3    +      -       -      -
    359D  ALA*     3.5    15.1    +      -       +      +
    361D  VAL*     4.5    17.7    -      -       +      -
    367D  ILE*     4.8     6.7    -      -       +      -
    384D  VAL*     1.3    81.1    -      -       -      +
    386D  HIS*     1.3    74.3    +      -       -      +
    387D  LEU*     5.0     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 386 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180D  LYS*     5.0     5.0    +      -       -      +
    211D  VAL*     3.7     7.6    -      -       -      +
    212D  ARG*     3.1    44.5    +      -       +      +
    214D  GLU*     3.8    19.0    -      -       +      +
    357D  GLU*     3.6    18.2    +      -       -      +
    358D  GLY*     6.1     1.3    -      -       -      -
    384D  VAL*     3.3    29.0    -      -       +      +
    385D  VAL*     1.3    81.6    +      -       -      +
    387D  LEU*     1.3    64.1    +      -       -      +
    388D  HIS*     3.6    23.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 387 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180D  LYS*     3.8     7.1    +      -       -      -
    181D  ASP*     5.3     5.2    -      -       -      +
    205D  TYR*     3.4    36.5    +      -       +      -
    208D  PRO*     3.6    29.6    -      -       +      -
    210D  ARG      4.4     0.4    -      -       -      -
    211D  VAL*     3.9    21.5    -      -       +      -
    353D  VAL*     4.1    11.4    -      -       +      -
    355D  VAL      3.9    11.9    -      -       -      +
    356D  PRO*     4.4     1.3    -      -       +      -
    357D  GLU*     3.1    49.4    +      -       +      +
    385D  VAL*     5.0     3.4    -      -       +      -
    386D  HIS*     1.3    72.9    -      -       -      +
    388D  HIS*     1.3    65.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 388 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176D  ASP*     3.1    19.9    +      -       -      -
    180D  LYS*     3.0    28.7    +      -       -      -
    205D  TYR*     5.0     0.9    -      -       -      -
    208D  PRO*     3.5     5.6    -      -       -      +
    209D  ARG      3.4     7.3    +      -       -      -
    210D  ARG*     3.1    55.5    +      -       -      +
    212D  ARG*     4.0    25.6    +      -       +      +
    386D  HIS*     3.6    28.9    +      -       +      +
    387D  LEU*     1.3    77.2    +      -       -      +
    389D  GLU*     1.3    72.6    +      -       -      +
    390D  PRO*     3.6     4.3    -      -       -      -
----------------------------------------------------------
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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