Contacts of the strand formed by residues 377 - 381 (chain A) in PDB entry 5IYB


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 GLN 377 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  ASN      4.7     0.9    -      -       -      +
    373A  LEU*     3.6    23.9    -      -       +      +
    374A  SER*     2.7    47.0    +      -       -      +
    375A  ILE      3.0     8.4    +      -       -      +
    376A  ASP*     1.3    80.4    +      -       -      +
    378A  VAL*     1.3    61.5    +      -       -      +
    452A  ASP*     4.9     4.4    +      -       -      -
    472A  HIS*     3.4    12.7    +      -       -      -
    473A  ARG*     3.3    29.7    -      -       +      +
    474A  VAL      5.2     0.8    +      -       -      -
    475A  ARG*     3.5    26.6    -      -       +      +
    484A  LEU*     4.5     6.9    -      -       -      -
    485A  ASN      4.6     1.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 378 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373A  LEU*     4.0     3.1    -      -       -      -
    377A  GLN*     1.3    74.9    -      -       -      +
    379A  GLY*     1.3    60.2    +      -       -      +
    380A  VAL*     4.3     5.4    -      -       +      -
    456A  VAL*     4.1    15.5    -      -       +      -
    458A  PHE*     4.0    33.0    -      -       +      -
    472A  HIS*     3.8    23.1    -      -       +      +
    473A  ARG      2.7    17.6    +      -       -      +
    474A  VAL*     3.1    16.7    -      -       +      -
    475A  ARG*     2.5    33.3    +      -       -      +
    482A  PHE*     4.3     2.5    -      -       +      -
    483A  ARG      3.2    19.5    -      -       -      +
    484A  LEU*     4.5     2.7    -      -       +      -
    503A  LEU*     4.6     2.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    373A  LEU*     3.4    10.6    -      -       -      +
    378A  VAL*     1.3    73.7    -      -       -      +
    380A  VAL*     1.3    62.2    +      -       -      +
    381A  PRO*     4.6     0.7    -      -       -      -
    475A  ARG*     3.0    16.6    -      -       -      -
    477A  LEU*     4.8     9.4    -      -       -      -
    481A  THR      4.7     1.3    -      -       -      -
    482A  PHE*     3.4     8.5    -      -       -      -
    483A  ARG*     2.7    41.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    378A  VAL*     4.1     4.9    -      -       +      +
    379A  GLY*     1.3    77.7    -      -       -      +
    381A  PRO*     1.4    80.0    -      -       +      +
    384A  ILE*     3.9    20.9    -      -       +      -
    385A  ALA*     4.0    10.3    -      -       +      +
    450A  MET*     4.4     7.9    -      -       +      -
    474A  VAL*     3.6    35.7    -      -       +      -
    475A  ARG      2.9     7.8    +      -       -      +
    476A  ILE*     3.4    12.3    -      -       +      +
    477A  LEU*     3.3    21.7    +      -       -      +
    481A  THR      4.8     0.2    -      -       -      -
    482A  PHE*     4.3     5.8    -      -       +      -
    503A  LEU*     4.2    16.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380A  VAL*     1.4    92.0    -      -       +      +
    382A  ARG*     1.3    64.7    +      -       -      +
    383A  SER*     4.1    11.9    -      -       -      +
    384A  ILE*     3.1    18.6    +      -       +      +
    385A  ALA*     2.9    19.9    +      -       -      +
    477A  LEU*     3.8     8.9    -      -       -      +
    479A  TRP      3.8     3.4    -      -       -      +
    480A  SER*     3.6    24.7    -      -       -      +
    481A  THR      3.3    27.6    -      -       -      +
    482A  PHE*     4.2     7.9    -      -       +      -
   1059B  ILE*     4.5     0.2    -      -       +      -
      2K  ASN*     3.7    12.8    -      -       -      +
----------------------------------------------------------
 Back to top of page


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