Contacts of the strand formed by residues 381 - 385 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  ARG*     2.4    41.2    +      -       -      -
    302A  ASN*     5.9     0.2    +      -       -      -
    377A  ASN*     3.5     5.9    +      -       -      -
    378A  CYS      3.0    28.5    +      -       -      +
    380A  GLY*     1.3    79.1    -      -       -      +
    382A  PHE*     1.3    59.8    +      -       -      +
    383A  PHE*     3.3     6.1    +      -       +      -
    420A  ILE*     3.1    32.1    -      -       +      +
    421A  LYS      5.1     0.3    -      -       -      +
    422A  GLN*     5.3     6.4    +      -       -      +
    437A  PRO*     5.3     0.3    -      -       -      +
    438A  PRO*     3.4    33.3    -      -       +      +
    443A  ILE*     3.2    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112A  TRP*     3.8    30.5    -      +       -      -
    116A  LEU*     4.3     5.8    -      -       +      -
    376A  PHE      3.7     8.3    -      -       -      +
    377A  ASN*     3.9    13.7    -      -       +      -
    380A  GLY      4.1    13.5    -      -       -      -
    381A  GLU*     1.3    73.1    -      -       -      +
    383A  PHE*     1.3    59.9    +      -       -      +
    384A  TYR*     3.1    20.5    -      +       +      -
    420A  ILE*     3.4     4.9    -      -       -      +
    421A  LYS      3.0    43.0    +      -       -      +
    422A  GLN*     5.4     1.8    -      -       +      -
    424A  ILE*     3.4    30.1    -      -       +      -
    427A  TRP*     6.0     1.1    -      +       -      -
    435A  TYR*     3.6    48.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with PHE 383 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  CYS*     4.2     4.3    -      -       +      -
    297A  THR*     3.5    29.6    -      -       -      -
    298A  ARG*     3.6    24.5    -      -       +      -
    329A  ALA*     4.1     9.4    -      -       +      -
    330A  HIS      4.8     2.0    -      -       -      -
    375A  SER*     3.3     2.6    -      -       -      -
    376A  PHE*     2.9    64.1    +      +       +      +
    378A  CYS*     3.5    27.6    -      -       +      -
    381A  GLU*     3.3    11.2    +      -       +      -
    382A  PHE*     1.3    73.1    -      -       -      +
    384A  TYR*     1.3    65.5    +      -       -      +
    385A  CYS*     3.8    13.0    -      -       -      -
    418A  CYS*     4.3     7.0    -      -       +      -
    419A  ARG      3.7     3.4    -      -       -      -
    420A  ILE*     4.0     9.2    -      -       +      -
    443A  ILE*     3.5    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 384 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    369A  PRO*     4.1     7.0    -      -       +      -
    370A  GLU*     3.1    42.7    +      -       +      +
    373A  MET*     3.6    36.5    -      -       +      +
    374A  HIS      4.1     2.7    -      -       -      -
    375A  SER*     4.4    10.5    -      -       -      +
    382A  PHE*     3.1    34.5    -      +       +      -
    383A  PHE*     1.3    76.3    -      -       -      +
    385A  CYS*     1.3    64.5    +      -       -      +
    386A  ASN      4.0     0.2    +      -       -      -
    417A  PRO      4.3     0.2    -      -       -      +
    418A  CYS*     3.7     1.0    -      -       -      -
    419A  ARG*     2.9    39.1    +      -       +      +
    421A  LYS*     3.7    39.9    -      -       +      -
    424A  ILE*     3.0    34.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 385 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331A  CYS*     2.5    34.1    -      -       +      -
    373A  MET*     3.0     9.3    -      -       -      +
    374A  HIS*     2.8    48.8    +      -       +      +
    376A  PHE*     3.5    15.3    -      -       +      -
    383A  PHE*     4.1     4.3    -      -       -      -
    384A  TYR*     1.3    75.4    -      -       -      +
    386A  ASN*     1.3    58.5    +      -       -      +
    416A  LEU*     4.5     4.9    -      -       +      -
    417A  PRO      3.6     0.2    -      -       -      -
    418A  CYS*     2.0    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