Contacts of the strand formed by residues 381 - 385 (chain O) in PDB entry 4R2G


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 GLU 381 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298O  ARG*     3.1    41.8    +      -       -      +
    377O  ASN*     3.8     1.6    +      -       -      -
    378O  CYS      3.2    32.4    +      -       -      +
    379O  GLY      3.5     1.8    +      -       -      -
    380O  GLY*     1.3    79.3    -      -       -      +
    382O  PHE*     1.3    63.8    +      -       -      +
    383O  PHE*     3.5     8.7    +      -       +      -
    420O  ILE*     3.9    19.7    -      -       +      +
    421O  LYS      5.2     1.6    -      -       -      +
    422O  GLN*     6.4     1.6    -      -       +      -
    438O  PRO*     4.1    24.2    -      -       +      +
    443O  ILE*     2.4    39.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 382 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112O  TRP*     3.5    23.8    -      +       -      -
    116O  LEU*     4.4     5.6    -      -       +      -
    376O  PHE      3.7     6.1    -      -       -      +
    377O  ASN*     3.1    26.2    -      -       +      -
    380O  GLY      3.9    11.2    -      -       -      -
    381O  GLU*     1.3    74.8    -      -       -      +
    383O  PHE*     1.3    65.2    +      -       -      +
    384O  TYR*     3.7     7.1    -      -       +      -
    420O  ILE*     3.4     4.1    -      -       -      +
    421O  LYS      3.1    43.7    +      -       -      +
    422O  GLN*     5.0     2.2    -      -       +      -
    424O  ILE*     3.6    32.5    -      -       +      -
    435O  TYR*     3.5    53.6    -      +       +      -
    436O  ALA      5.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 383 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296O  CYS*     4.0     4.7    -      -       +      -
    297O  THR*     3.7    27.8    -      -       -      -
    298O  ARG      3.5    21.8    -      -       -      -
    329O  ALA*     4.4     3.4    -      -       +      -
    330O  HIS      4.7     2.0    -      -       -      -
    375O  SER*     3.5     4.5    -      -       -      -
    376O  PHE*     2.9    62.7    +      +       +      +
    378O  CYS*     3.6    21.8    -      -       +      -
    381O  GLU*     3.6    15.0    -      -       +      -
    382O  PHE*     1.3    75.2    -      -       -      +
    384O  TYR*     1.3    64.5    +      -       -      +
    385O  CYS*     3.8    12.1    -      -       -      -
    418O  CYS*     4.1     7.4    -      -       +      -
    419O  ARG      3.9     3.1    -      -       -      -
    420O  ILE*     3.7    18.2    -      -       +      -
    443O  ILE*     3.5    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 384 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369O  PRO*     3.4    22.2    -      -       +      -
    370O  GLU*     2.4    64.9    +      -       +      +
    373O  MET*     3.6    25.8    -      -       +      +
    374O  HIS      3.8     3.1    -      -       -      -
    375O  SER*     4.2     8.3    -      -       -      -
    382O  PHE*     3.7    13.9    -      -       +      -
    383O  PHE*     1.3    79.9    -      -       -      +
    385O  CYS*     1.3    63.6    +      -       -      +
    386O  ASN      4.0     0.2    +      -       -      -
    417O  PRO      4.3     0.3    -      -       -      +
    418O  CYS*     3.7     1.7    -      -       -      +
    419O  ARG*     2.8    40.7    +      -       +      +
    421O  LYS*     3.5    35.2    -      -       +      +
    424O  ILE*     3.7    21.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 385 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331O  CYS*     2.6    32.5    -      -       +      -
    373O  MET*     3.1     8.4    -      -       -      +
    374O  HIS*     2.9    48.8    +      -       +      +
    376O  PHE*     3.3    18.2    -      -       +      -
    383O  PHE*     4.1     2.0    -      -       -      -
    384O  TYR*     1.3    74.7    -      -       -      +
    386O  ASN*     1.3    59.8    +      -       -      +
    416O  LEU*     4.8     5.8    -      -       +      -
    417O  PRO      3.8     0.4    -      -       -      -
    418O  CYS*     2.1    43.7    -      -       -      -
----------------------------------------------------------
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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