Contacts of the strand formed by residues 288 - 292 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248E  HIS      3.1    18.5    +      -       -      +
    249E  ILE*     3.5    13.3    -      -       +      +
    250E  TYR*     2.8    30.0    +      -       -      +
    282E  ARG*     3.5    25.6    -      -       -      +
    286E  GLY      3.8     0.7    -      -       -      +
    287E  SER*     1.3    72.6    -      -       -      +
    289E  PHE*     1.3    59.3    +      -       -      +
    290E  VAL*     4.2     4.9    -      -       +      -
    315E  LEU*     3.5    26.5    -      -       +      -
    378E  ILE*     4.0    25.8    -      -       +      -
    382E  LEU*     4.6     8.3    -      -       +      -
    389E  THR      4.5     0.4    -      -       -      +
    390E  TRP*     3.7    24.9    -      -       +      +
    393E  MET*     4.2    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 289 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240E  LEU*     3.6    45.8    -      -       +      -
    250E  TYR*     3.7    30.1    -      +       +      -
    273E  ALA      4.4     1.3    -      -       -      -
    274E  PHE*     3.8    41.1    -      +       +      -
    277E  GLY*     4.2     8.5    -      -       -      -
    278E  VAL*     4.2     6.3    -      -       +      -
    287E  SER*     3.6    32.0    +      -       -      -
    288E  ILE*     1.3    72.1    -      -       -      +
    290E  VAL*     1.3    56.9    +      -       -      +
    291E  TRP*     4.9     4.3    -      +       +      -
    313E  TYR      3.7    20.9    +      -       -      +
    314E  THR*     3.2    16.2    -      -       +      -
    315E  LEU*     2.8    34.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 290 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249E  ILE*     4.0    17.5    -      -       +      -
    250E  TYR      2.9    14.6    +      -       -      +
    251E  SER*     3.6     5.5    +      -       -      -
    252E  ALA*     2.9    28.9    +      -       -      +
    288E  ILE*     4.2     4.0    -      -       +      -
    289E  PHE*     1.3    74.4    -      -       -      +
    291E  TRP*     1.3    64.6    +      -       -      +
    315E  LEU*     3.7     5.4    -      -       +      +
    317E  ILE*     3.9    21.8    -      -       +      -
    371E  ALA*     3.5    31.1    -      -       +      +
    374E  ALA*     4.0     4.7    -      -       +      -
    375E  ALA*     4.1     5.4    -      -       +      -
    378E  ILE*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 291 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240E  LEU*     3.9    15.7    -      -       +      -
    250E  TYR*     6.6     0.2    -      -       +      -
    252E  ALA*     3.5    32.5    -      -       +      -
    254E  TRP*     2.8    49.3    +      +       -      -
    255E  GLY*     4.5     0.6    -      -       -      -
    274E  PHE*     3.6    21.1    -      +       -      -
    289E  PHE*     4.0     5.1    +      +       +      -
    290E  VAL*     1.3    78.3    -      -       -      +
    292E  ALA*     1.3    80.8    +      -       -      +
    308E  TYR*     3.5    42.7    -      +       +      +
    309E  THR*     3.7    17.0    -      -       +      -
    314E  THR*     3.9    31.0    -      -       +      +
    315E  LEU      3.0     9.1    +      -       -      +
    316E  SER*     3.5     4.2    -      -       -      -
    317E  ILE*     2.8    31.2    +      -       -      +
    371E  ALA*     3.9     4.9    -      -       -      -
      5L  00S      4.0     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 292 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252E  ALA      3.1    14.7    +      -       -      +
    253E  SER*     3.9     8.1    -      -       -      -
    291E  TRP*     1.3    76.9    -      -       -      +
    293E  SER*     1.3    59.4    +      -       -      +
    309E  THR*     3.4     0.6    -      -       -      +
    317E  ILE      3.9     4.9    -      -       -      -
    367E  THR*     3.4    30.1    -      -       -      +
    371E  ALA*     3.7    10.0    -      -       +      +
      5L  00S      2.9    44.7    +      -       +      -
----------------------------------------------------------
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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