Contacts of the strand formed by residues 378 - 383 (chain A) in PDB entry 4RRO


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 ASP 378 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330A  CYS*     4.0    22.3    -      -       +      +
    331A  TRP      3.4    15.8    -      -       -      +
    332A  GLN*     3.2    27.4    +      -       -      +
    371A  GLU*     5.7     3.6    -      -       -      +
    372A  ASP      5.4     3.8    +      -       -      -
    375A  THR*     3.1    34.7    +      -       +      +
    376A  SER*     4.1     6.1    -      -       -      +
    377A  GLN*     1.3    81.5    -      -       -      +
    379A  ASP*     1.3    65.7    +      -       -      +
    380A  CYS*     3.8     8.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330A  CYS*     3.2     1.7    -      -       -      -
    331A  TRP      2.8    34.8    +      -       -      +
    333A  ALA*     3.8    16.0    -      -       -      +
    334A  GLY*     2.9    25.3    +      -       -      +
    336A  THR*     4.0     7.1    +      -       -      +
    378A  ASP*     1.3    74.8    -      -       -      +
    380A  CYS*     1.3    59.7    +      -       -      +
    381A  TYR*     3.7    32.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328A  LEU*     4.1    12.8    -      -       +      -
    329A  VAL      3.4     3.4    -      -       -      +
    330A  CYS*     2.0    46.9    -      -       -      -
    369A  PRO*     3.4     6.6    -      -       -      +
    370A  VAL*     2.9    42.5    +      -       -      +
    371A  GLU*     5.9     0.8    -      -       -      +
    372A  ASP*     4.2    20.9    -      -       +      -
    375A  THR*     4.6     2.2    -      -       -      -
    378A  ASP*     3.8    14.2    +      -       -      +
    379A  ASP*     1.3    74.5    -      -       -      +
    381A  TYR*     1.3    65.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  PHE*     4.0     6.5    -      -       +      -
    328A  LEU*     3.3    10.4    -      -       -      +
    329A  VAL*     2.9    35.7    +      -       +      +
    331A  TRP*     3.7    20.4    -      +       +      -
    336A  THR*     3.2    33.7    +      -       +      -
    338A  TRP*     3.4    29.8    -      +       -      -
    367A  LEU*     3.8    34.3    -      -       +      -
    368A  ARG      3.2     4.5    -      -       -      +
    369A  PRO*     3.7    27.4    -      -       +      -
    370A  VAL      4.6     0.2    -      -       -      +
    379A  ASP*     3.7    31.8    +      -       +      +
    380A  CYS*     1.3    79.3    -      -       -      +
    382A  LYS*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 382 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ASN*     3.8    25.3    +      -       -      +
    322A  PHE*     4.4     1.6    -      -       -      -
    325A  GLY*     3.2    31.9    +      -       -      +
    327A  GLN      4.8     4.3    -      -       -      +
    328A  LEU*     3.8    18.5    -      -       +      +
    367A  LEU*     3.4     4.2    -      -       -      -
    368A  ARG*     2.8    49.9    +      -       +      +
    370A  VAL*     4.2     8.7    -      -       +      -
    381A  TYR*     1.3    73.9    -      -       -      +
    383A  PHE*     1.3    82.2    +      -       -      +
    384A  ALA*     3.3     2.6    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    294A  ASN*     4.7     0.3    +      -       -      -
    302A  PHE*     4.3     0.2    -      +       -      -
    306A  VAL*     4.2    15.5    -      -       +      -
    309A  ILE*     4.2    12.1    -      -       +      -
    322A  PHE*     3.2    41.3    +      +       +      +
    323A  TRP*     3.5    53.6    -      +       -      -
    325A  GLY*     3.9     7.1    -      -       -      -
    327A  GLN      5.1     0.2    +      -       -      -
    366A  TYR*     3.9    12.3    -      +       -      -
    367A  LEU*     3.9    17.0    -      -       +      -
    382A  LYS*     1.3    86.8    +      -       -      +
    384A  ALA*     1.3    60.2    +      -       -      +
    385A  ILE*     3.3    63.9    +      -       +      +
----------------------------------------------------------
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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