Contacts of the strand formed by residues 387 - 393 (chain C) in PDB entry 4ZZ7


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 VAL 387 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272C  ALA*     4.7     5.9    +      -       -      +
    273C  PHE*     4.1     2.8    -      -       -      -
    284C  SER*     4.0    19.3    -      -       -      +
    332C  VAL*     4.2     5.2    -      -       +      -
    336C  ILE*     4.0    16.8    -      -       +      -
    364C  VAL*     5.6     0.2    -      -       +      -
    367C  THR*     3.4    24.0    -      -       +      +
    369C  ILE*     3.5    26.9    -      -       +      -
    383C  ILE*     4.0    40.7    -      -       +      +
    385C  GLY      2.9     9.9    +      -       -      +
    386C  PRO*     1.3    84.2    -      -       +      +
    388C  LEU*     1.3    66.3    +      -       -      +
    389C  GLN*     4.4     1.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 388 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268C  LEU*     4.6    14.6    -      -       +      +
    272C  ALA*     4.1    15.0    -      -       +      -
    273C  PHE*     3.9    16.6    -      -       +      -
    283C  LEU*     3.5    23.6    -      -       +      +
    284C  SER      3.5    11.2    -      -       -      +
    285C  VAL      3.9     1.8    -      -       -      +
    286C  ALA*     4.0    18.4    -      -       +      +
    297C  LEU*     6.2     2.2    -      -       +      -
    301C  MET*     4.2    28.9    -      -       +      -
    367C  THR      3.0     7.5    +      -       -      +
    368C  LEU*     3.6    11.6    -      -       +      +
    369C  ILE*     2.9    27.2    +      -       -      +
    387C  VAL*     1.3    73.5    -      -       -      +
    389C  GLN*     1.3    78.8    +      -       -      +
    390C  VAL*     5.2     2.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 389 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250C  LYS*     3.3    32.6    +      -       -      -
    284C  SER      2.9    11.4    +      -       -      +
    285C  VAL*     3.3    10.7    -      -       +      +
    286C  ALA*     2.8    26.3    +      -       -      +
    339C  ALA*     5.0     0.8    -      -       -      +
    369C  ILE*     3.3    25.0    -      -       +      +
    372C  VAL*     4.0    23.3    -      -       +      +
    378C  SER*     3.4    38.1    +      -       -      -
    379C  TYR*     3.7     7.0    -      -       -      +
    383C  ILE*     3.9     8.9    -      -       +      +
    387C  VAL*     4.4     4.9    -      -       +      -
    388C  LEU*     1.3    79.3    -      -       -      +
    390C  VAL*     1.3    62.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 390 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286C  ALA*     3.2    16.2    -      -       +      +
    288C  ALA*     4.5     7.2    -      -       +      -
    294C  GLY      5.4     1.1    -      -       -      +
    297C  LEU*     3.9    25.6    -      -       +      -
    298C  VAL*     4.2    16.2    -      -       +      -
    368C  LEU*     3.6    29.2    -      -       +      -
    369C  ILE      2.9     7.2    +      -       -      +
    370C  ASP*     4.0    15.0    -      -       -      +
    371C  HIS      3.5     6.8    +      -       -      -
    372C  VAL*     3.0    25.9    +      -       -      +
    388C  LEU*     5.1     3.6    -      -       +      -
    389C  GLN*     1.3    78.3    -      -       -      +
    391C  VAL*     1.3    69.4    +      -       -      +
    392C  ARG*     4.9     3.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 391 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285C  VAL*     4.0    17.0    -      -       +      -
    286C  ALA      3.0     7.3    +      -       -      +
    287C  VAL*     3.5     5.7    -      -       -      -
    288C  ALA      2.8    25.3    +      -       -      -
    372C  VAL*     3.4    38.4    -      -       +      +
    373C  THR*     5.0     1.3    -      -       -      +
    374C  PRO*     5.5     6.5    -      -       +      -
    379C  TYR*     4.2    13.2    -      -       +      -
    390C  VAL*     1.3    74.5    -      -       -      +
    392C  ARG*     1.3    70.3    +      -       -      +
    393C  VAL*     3.9    13.5    -      -       +      -
    402C  LEU*     3.6    26.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 392 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288C  ALA*     3.4     6.3    -      -       +      +
    290C  GLY      4.9     0.7    -      -       -      +
    291C  ASP*     3.1    51.0    +      -       +      +
    294C  GLY*     3.5    30.0    +      -       -      -
    295C  ASP*     3.4    22.8    +      -       -      +
    298C  VAL*     3.9     4.4    -      -       -      +
    370C  ASP*     2.8    42.0    +      -       -      -
    371C  HIS*     3.6    30.2    +      -       -      +
    372C  VAL      4.9     1.4    +      -       -      +
    390C  VAL*     4.9     3.4    -      -       +      +
    391C  VAL*     1.3    82.1    -      -       -      +
    393C  VAL*     1.3    66.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 393 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287C  VAL*     3.8    27.6    -      -       +      -
    288C  ALA      2.9    14.0    +      -       -      +
    289C  VAL*     3.9     7.9    -      -       -      -
    290C  GLY*     2.8    27.4    +      -       -      +
    391C  VAL*     3.9    11.7    -      -       +      -
    392C  ARG*     1.3    80.3    -      -       -      +
    394C  ALA*     1.3    59.5    +      -       -      +
    395C  THR      3.5    21.5    -      -       -      +
    398C  ASP*     4.1    13.0    -      -       +      -
    399C  ALA*     3.9    12.6    -      -       +      +
    402C  LEU*     4.4     8.7    -      -       +      -
----------------------------------------------------------
 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