Contacts of the strand formed by residues 375 - 378 (chain B) in PDB entry 3N9Y


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 LEU 375 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  VAL*     3.9    12.6    -      -       +      -
     58B  GLU      3.8    12.3    +      -       -      +
     59B  SER*     3.3    23.1    -      -       -      +
     60B  VAL      2.9    24.3    +      -       -      -
     82B  PHE*     3.7    31.9    -      -       +      +
    356B  GLN*     3.8    22.9    -      -       +      -
    357B  ARG      3.8    11.2    -      -       -      +
    358B  TYR*     3.7    35.8    -      -       +      +
    373B  LYS      3.6     2.4    +      -       -      -
    374B  THR*     1.3    77.8    -      -       -      +
    376B  VAL*     1.3    62.3    +      -       -      +
    377B  GLN*     3.9    12.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 376 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  VAL*     3.3    23.3    -      -       +      +
     62B  VAL*     4.4    18.2    -      -       +      -
     71B  LEU*     3.8    31.8    -      -       +      +
    356B  GLN*     3.1     3.3    -      -       -      +
    357B  ARG      2.9    37.6    +      -       -      +
    359B  LEU*     4.0    31.4    -      -       +      -
    365B  LEU*     4.7     6.1    -      -       +      -
    370B  ILE*     4.4    11.0    -      -       +      -
    374B  THR      4.2     0.7    -      -       -      +
    375B  LEU*     1.3    77.7    -      -       -      +
    377B  GLN*     1.3    69.7    +      -       -      +
    378B  VAL      4.4     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 377 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  HIS*     5.4     0.2    -      -       -      -
     57B  VAL*     5.6     1.4    -      -       -      +
     59B  SER*     2.8    32.1    +      -       -      +
     60B  VAL      2.8     9.1    +      -       -      +
     61B  TYR*     3.4    35.1    +      -       +      +
     62B  VAL*     2.9    27.4    +      -       -      +
     82B  PHE*     5.4     3.8    -      -       -      -
    354B  THR*     3.0    30.0    +      -       -      +
    355B  LEU      3.1     6.5    -      -       -      +
    356B  GLN*     3.5    18.9    -      -       +      +
    375B  LEU*     3.9    11.0    -      -       +      +
    376B  VAL*     1.3    77.0    -      -       -      +
    378B  VAL*     1.3    63.5    +      -       -      +
    379B  ALA      3.8     0.5    +      -       -      -
    602B  CLR      4.3    13.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 378 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  VAL*     3.5    17.9    -      -       +      +
     63B  ILE      5.4     0.7    -      -       -      +
     68B  VAL*     3.6    35.7    -      -       +      -
     71B  LEU*     3.7    28.3    -      -       +      -
     72B  PHE*     4.3     6.7    -      -       +      -
    354B  THR*     3.1     4.7    -      -       -      -
    355B  LEU*     2.7    39.7    +      -       +      +
    377B  GLN*     1.3    72.5    -      -       -      +
    379B  ALA*     1.3    61.1    +      -       -      +
    380B  ILE*     2.9    28.9    +      -       +      +
    383B  LEU*     4.8     4.7    -      -       +      -
    414B  LEU*     4.3     5.8    -      -       +      -
----------------------------------------------------------
 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