Contacts of the strand formed by residues 387 - 396 (chain A) in PDB entry 5VZH


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 ARG 387 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347A  LEU*     3.5     2.4    -      -       -      +
    385A  PHE*     3.7     8.5    -      -       -      -
    386A  GLU*     1.3    90.3    +      -       +      +
    388A  SER*     1.3    61.3    +      -       -      +
    389A  PHE*     4.3    19.7    -      -       +      -
    419A  LEU      3.3     6.7    -      -       -      +
    420A  VAL*     4.1    20.0    -      -       +      +
    434A  HIS*     4.5    23.2    +      -       -      -
    458A  SER*     4.6    10.3    +      -       -      -
    459A  HIS*     4.4    13.1    -      -       -      -
      3P    T      5.1     2.2    +      -       -      -
      4P    A      5.3     1.6    -      -       -      +
      7T    A      3.4    37.0    +      -       -      -
      8T    C      3.2    47.2    +      -       -      +
      9T    G      3.1    34.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 388 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347A  LEU*     3.7     9.5    -      -       -      +
    351A  MET*     3.6    17.8    -      -       -      -
    363A  HIS*     5.5     3.4    -      -       -      -
    364A  GLN*     6.0     5.2    -      -       -      -
    385A  PHE*     4.3     8.7    -      -       -      -
    387A  ARG*     1.3    76.7    -      -       -      +
    389A  PHE*     1.3    66.3    +      -       -      +
    390A  CYS*     3.0    23.1    -      -       -      -
    417A  VAL      3.9     0.7    -      -       -      +
    418A  ASP*     3.4     5.4    -      -       -      +
    419A  LEU*     2.9    39.2    +      -       -      +
      9T    G      5.5     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 389 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  PHE*     3.8    17.2    -      -       +      -
    275A  GLN*     5.2     7.1    +      -       -      -
    362A  TYR*     3.7    20.6    -      -       -      -
    363A  HIS*     4.4     4.1    -      -       -      -
    364A  GLN*     4.7     5.9    +      -       -      +
    387A  ARG*     4.3    30.3    -      -       +      -
    388A  SER*     1.3    74.4    -      -       -      +
    390A  CYS*     1.3    60.1    +      -       -      +
    416A  ARG*     3.7     7.6    -      -       -      +
    418A  ASP*     3.4    28.3    -      -       +      +
    420A  VAL*     6.0     2.9    -      -       +      -
    507A  GOA      4.9     6.5    -      -       -      -
      2P    G      4.0     7.0    -      -       -      -
      3P    T      3.8    48.5    -      -       +      -
      8T    C      4.7     1.1    -      -       -      -
      9T    G      3.7    29.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 390 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  PHE*     5.5     0.2    -      -       -      -
    351A  MET*     3.5    25.1    -      -       +      -
    360A  ILE*     4.8     1.6    -      -       +      -
    362A  TYR      3.3    13.7    -      -       -      +
    363A  HIS*     4.0     5.4    -      -       +      -
    388A  SER*     3.0    34.5    -      -       -      -
    389A  PHE*     1.3    74.3    -      -       -      +
    391A  ILE*     1.3    65.1    +      -       -      +
    392A  PHE*     4.2    19.7    -      -       +      -
    416A  ARG*     3.0    22.7    +      -       -      -
    417A  VAL      2.9    26.5    +      -       -      +
    419A  LEU*     4.9     2.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 391 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  PHE*     4.1    15.5    -      -       +      -
    278A  ALA*     4.2     8.7    -      -       +      +
    282A  HIS*     4.1    19.5    -      -       +      -
    286A  LEU*     4.1    22.0    -      -       +      -
    360A  ILE*     3.7     3.3    -      -       -      +
    361A  LEU*     2.8    35.3    +      -       +      -
    362A  TYR*     2.9    34.6    +      -       +      +
    390A  CYS*     1.3    77.2    -      -       -      +
    392A  PHE*     1.3    63.9    +      -       -      +
    414A  ALA*     3.6    29.6    -      -       +      -
    415A  VAL      3.3    11.0    -      -       -      +
    416A  ARG*     4.0    13.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 392 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  LEU*     3.5    26.0    -      -       +      -
    301A  VAL*     4.1    13.5    -      -       +      -
    302A  VAL*     4.1    24.9    -      -       +      -
    354A  LEU*     3.4    33.2    -      -       +      -
    359A  LEU*     3.3    15.3    -      -       +      -
    360A  ILE*     3.4    20.6    -      -       +      -
    361A  LEU*     4.0     3.1    -      -       -      -
    390A  CYS*     4.2    14.1    -      -       +      -
    391A  ILE*     1.3    77.0    -      -       -      +
    393A  ARG*     1.3    61.8    +      -       -      +
    394A  LEU      3.6     0.7    +      -       -      -
    414A  ALA*     3.3     7.1    -      -       -      -
    415A  VAL*     2.6    39.0    +      -       +      +
    417A  VAL*     3.5    34.3    -      -       +      -
    419A  LEU*     4.9     3.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 393 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298A  LEU*     5.2     1.0    -      -       -      +
    358A  GLY      3.6    17.6    +      -       -      -
    359A  LEU*     2.8    39.9    +      -       +      +
    361A  LEU*     3.9    22.2    -      -       +      +
    392A  PHE*     1.3    76.2    -      -       -      +
    394A  LEU*     1.3    57.9    +      -       -      +
    395A  PRO*     3.4    10.6    -      -       +      +
    412A  TRP*     3.1    69.0    -      -       +      +
    413A  LYS      3.9     1.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 394 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ASP*     3.5    44.6    -      -       +      +
    297A  ALA*     4.2    20.9    -      -       +      -
    298A  LEU*     3.8    28.9    -      -       +      +
    301A  VAL*     6.4     1.1    -      -       +      -
    392A  PHE      3.6     0.6    +      -       -      -
    393A  ARG*     1.3    73.0    -      -       -      +
    395A  PRO*     1.3    84.5    -      -       +      +
    396A  GLN*     3.6     2.0    -      -       -      +
    412A  TRP*     3.1     3.0    -      -       -      -
    413A  LYS*     2.8    50.0    +      -       +      +
    415A  VAL*     3.9    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 395 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  VAL*     6.5     1.3    -      -       +      -
    359A  LEU*     5.1    10.1    -      -       +      -
    393A  ARG*     3.4    11.7    -      -       +      +
    394A  LEU*     1.3   106.9    -      -       +      +
    396A  GLN*     1.3    65.7    +      -       -      +
    411A  SER      3.8     8.7    -      -       -      +
    412A  TRP*     4.0     3.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 396 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ASP*     4.3    10.1    +      -       -      -
    394A  LEU*     3.6     2.6    -      -       -      +
    395A  PRO*     1.3    82.8    +      -       -      +
    397A  PRO*     1.3    82.1    -      -       +      +
    410A  GLY      2.9     5.0    +      -       -      -
    411A  SER*     3.0    15.5    +      -       -      +
    412A  TRP*     3.7    14.1    -      -       -      +
    413A  LYS*     3.6    54.7    +      -       +      +
----------------------------------------------------------
 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