Contacts of the strand formed by residues 425 - 432 (chain D) in PDB entry 5UHF


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 SER 425 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1043C  ALA*     3.3     1.4    -      -       -      +
   1044C  ARG*     2.8    30.3    +      -       -      +
   1065C  GLY*     3.6     2.9    -      -       -      -
   1066C  GLN*     3.0    19.5    +      -       -      -
    422D  VAL*     3.0    24.7    +      -       -      -
    423D  ASP      4.0     0.2    -      -       -      -
    424D  TYR*     1.3    77.3    -      -       -      +
    426D  GLY*     1.3    57.8    +      -       -      +
    451D  LEU*     3.4     7.6    -      -       -      +
    543D  VAL      3.1    13.9    -      -       -      -
    544D  HIS*     3.4    25.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 426 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1042C  HIS      3.2    12.8    -      -       -      -
   1043C  ALA*     3.6     4.5    -      -       -      -
   1066C  GLN*     3.2    17.9    -      -       -      +
    425D  SER*     1.3    76.1    -      -       -      +
    427D  ARG*     1.3    58.7    +      -       -      +
    447D  MET*     3.7    12.6    -      -       -      -
    542D  ALA*     3.4     0.3    -      -       -      -
    543D  VAL*     2.6    41.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 427 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1040C  LYS      3.2     8.0    -      -       -      +
   1042C  HIS*     2.7    35.8    +      -       +      +
   1066C  GLN*     3.2    26.8    +      -       +      +
    426D  GLY*     1.3    75.5    -      -       -      +
    428D  SER*     1.3    62.9    +      -       -      +
    447D  MET*     3.9     4.2    -      -       -      +
    499D  ASN*     5.8     0.6    +      -       -      -
    501D  ALA*     4.7    13.1    -      -       -      +
    540D  GLN*     3.3    55.4    +      -       +      +
    541D  MET      3.2    15.5    -      -       -      +
    542D  ALA*     4.4    15.5    -      -       -      +
    543D  VAL*     5.0     0.7    -      -       -      -
     16G    C      3.9    48.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 428 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1037C  VAL*     4.7     0.7    -      -       -      +
   1040C  LYS      4.3     3.4    -      -       -      -
   1041C  ILE*     3.4    30.1    +      -       -      +
    427D  ARG*     1.3    80.6    -      -       -      +
    429D  VAL*     1.3    75.8    +      -       -      +
    430D  ILE*     3.7     0.5    +      -       -      +
    447D  MET*     4.0     2.7    -      -       -      -
    520D  LYS      3.0    23.0    +      -       -      -
    522D  ILE*     3.4    28.9    -      -       -      +
    540D  GLN*     4.3     6.5    -      -       -      -
    541D  MET      3.3    20.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 429 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    882C  GLY*     4.1    15.9    -      -       -      +
    894C  VAL*     4.1    10.3    -      -       +      -
   1035C  HIS      5.8     0.7    -      -       -      +
   1037C  VAL*     3.9    27.4    -      -       +      +
   1040C  LYS*     3.7    35.9    -      -       +      -
    428D  SER*     1.3    78.5    +      -       -      +
    430D  ILE*     1.3    71.3    +      -       -      +
    521D  ALA*     3.8     3.2    -      -       -      -
    522D  ILE*     2.9    25.5    +      -       -      +
    538D  GLY*     4.0    17.0    -      -       -      +
    539D  ASP      3.3    15.7    -      -       -      +
    540D  GLN*     4.3     3.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 430 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    894C  VAL*     3.8    10.0    -      -       -      +
    428D  SER      4.1     1.3    -      -       -      +
    429D  VAL*     1.3    79.9    -      -       -      +
    431D  VAL*     1.3    68.5    +      -       -      +
    522D  ILE*     3.2    14.8    -      -       +      +
    524D  LEU*     4.3    12.3    -      -       +      -
    534D  ALA*     4.0    19.3    -      -       +      -
    535D  ASP      3.8     7.2    -      -       -      +
    536D  PHE*     3.4    28.7    -      -       +      -
    539D  ASP*     3.1    39.2    +      -       +      +
    541D  MET*     3.6    43.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 431 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    881C  ASP*     4.5     2.9    -      -       +      -
    882C  GLY*     3.7    22.7    -      -       -      +
    894C  VAL*     4.6     5.8    -      -       +      -
    895C  ILE      3.8     4.7    -      -       -      +
    896C  GLY*     3.3    31.6    -      -       -      +
    430D  ILE*     1.3    82.4    -      -       -      +
    432D  VAL*     1.3    75.9    +      -       -      +
    521D  ALA*     3.6    25.6    -      -       +      -
    522D  ILE      2.7    12.0    +      -       -      +
    523D  GLN*     3.2    16.2    -      -       +      +
    524D  LEU      2.9    23.0    +      -       -      -
    536D  PHE*     3.4     7.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 432 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    728C  GLY      3.7    17.9    -      -       -      +
    729C  HIS*     3.5    36.2    +      -       -      +
    731C  TYR*     3.8    30.3    -      -       +      +
    734C  ALA*     4.1     9.8    -      -       +      +
    896C  GLY*     4.8     1.8    -      -       -      +
    431D  VAL*     1.3    90.0    -      -       +      +
    433D  GLY*     1.3    61.4    +      -       -      +
    434D  PRO*     4.0     3.8    -      -       +      +
    523D  GLN*     4.9     3.3    -      -       -      +
    524D  LEU      4.1     2.0    -      -       -      +
    526D  PRO*     4.1    15.7    -      -       +      -
    536D  PHE*     3.3    29.2    -      -       +      -
----------------------------------------------------------
 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