Contacts of the strand formed by residues 288 - 292 (chain D) in PDB entry 4RYD


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 288 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248D  HIS      3.2    17.0    +      -       -      +
    249D  ILE*     3.5    12.5    -      -       +      -
    250D  TYR*     2.8    30.1    +      -       -      +
    282D  ARG*     3.7    27.8    -      -       -      +
    286D  GLY      3.9     0.2    -      -       -      +
    287D  SER*     1.3    73.0    -      -       -      +
    289D  PHE*     1.3    61.3    +      -       -      +
    290D  VAL*     4.1    11.0    -      -       +      -
    315D  LEU*     3.7    22.9    -      -       +      -
    378D  ILE*     4.0    23.8    -      -       +      -
    382D  LEU*     4.8     3.8    -      -       +      -
    389D  THR      4.5     0.4    -      -       -      +
    390D  TRP*     3.7    25.1    -      -       +      +
    393D  MET*     4.1    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 289 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240D  LEU*     3.7    42.0    -      -       +      -
    250D  TYR*     3.7    34.3    -      +       +      -
    273D  ALA      4.3     1.3    -      -       -      -
    274D  PHE*     3.6    44.2    -      +       +      -
    277D  GLY*     4.3     9.0    -      -       -      -
    278D  VAL*     4.2     7.6    -      -       +      -
    287D  SER*     3.7    27.5    +      -       -      -
    288D  ILE*     1.3    72.8    -      -       -      +
    290D  VAL*     1.3    56.5    +      -       -      +
    291D  TRP*     4.8     3.8    -      +       +      -
    313D  TYR      3.7    21.4    +      -       -      +
    314D  THR*     3.2    15.6    -      -       +      -
    315D  LEU*     2.8    35.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 290 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249D  ILE*     3.9    18.6    -      -       +      -
    250D  TYR      2.8    15.6    +      -       -      +
    251D  SER*     3.6     5.5    -      -       -      -
    252D  ALA*     2.9    29.3    +      -       -      +
    288D  ILE*     4.1     4.7    -      -       +      -
    289D  PHE*     1.3    75.2    -      -       -      +
    291D  TRP*     1.3    64.5    +      -       -      +
    315D  LEU*     3.7     6.3    -      -       +      +
    317D  ILE*     4.0    20.9    -      -       +      -
    371D  ALA*     3.4    30.2    -      -       +      +
    374D  ALA*     4.0     6.3    -      -       +      -
    375D  ALA*     4.1     5.6    -      -       +      +
    378D  ILE*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 291 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240D  LEU*     3.9    13.5    -      -       +      -
    250D  TYR*     6.5     0.4    -      -       +      -
    252D  ALA*     3.6    28.0    -      -       +      -
    254D  TRP*     2.8    50.5    +      +       -      -
    255D  GLY*     4.5     0.4    -      -       -      -
    274D  PHE*     3.5    24.7    -      +       -      -
    289D  PHE*     4.0     5.6    +      +       +      -
    290D  VAL*     1.3    77.9    -      -       -      +
    292D  ALA*     1.3    81.2    +      -       -      +
    308D  TYR*     3.4    43.7    -      +       +      +
    309D  THR*     3.7    20.0    -      -       +      -
    314D  THR*     3.7    29.2    -      -       +      +
    315D  LEU      3.0     9.1    +      -       -      +
    316D  SER*     3.5     2.5    -      -       -      -
    317D  ILE*     2.8    31.4    +      -       -      +
    371D  ALA*     3.9     4.5    -      -       -      -
      5K  00S      4.0     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 292 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252D  ALA      3.1    15.3    +      -       -      +
    253D  SER*     3.9     7.9    -      -       -      -
    291D  TRP*     1.3    78.5    -      -       -      +
    293D  SER*     1.3    58.4    +      -       -      +
    294D  GLY      3.3     0.2    -      -       -      -
    309D  THR*     3.4     0.4    -      -       -      +
    317D  ILE      3.9     3.6    -      -       -      -
    367D  THR*     3.3    29.6    -      -       -      +
    371D  ALA*     3.7    11.3    -      -       +      +
      5K  00S      2.9    44.2    +      -       +      -
----------------------------------------------------------
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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