Contacts of the strand formed by residues 646 - 653 (chain C) in PDB entry 1UEX


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 646 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    601C  THR*     5.0     0.2    -      -       +      -
    606C  PHE*     3.7    46.0    -      -       +      -
    609C  ILE*     5.1     0.4    -      -       +      -
    616C  ARG*     3.5    15.3    -      -       +      +
    618C  ALA*     4.4    11.9    -      -       +      -
    641C  LEU*     2.8    38.2    +      -       +      +
    642C  LYS*     4.4     2.5    +      -       -      -
    644C  LYS*     3.7    26.0    -      -       +      +
    645C  LYS*     1.3    76.1    -      -       -      +
    647C  ILE*     1.3    70.6    +      -       -      +
    648C  VAL*     3.4    11.2    -      -       +      +
    672C  ASN*     4.9     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 647 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    615C  SER*     5.0     6.1    -      -       -      -
    616C  ARG      2.6    18.5    +      -       -      +
    617C  ILE*     3.2     9.0    -      -       +      -
    618C  ALA      2.7    30.9    +      -       -      -
    645C  LYS      4.3     6.7    -      -       -      +
    646C  VAL*     1.3    77.4    -      -       -      +
    648C  VAL*     1.3    56.9    +      -       -      +
    649C  ILE*     3.6    13.5    -      -       +      -
    671C  GLU*     3.6    37.0    -      -       +      +
    672C  ASN*     3.4    14.6    -      -       -      +
    697C  LEU*     4.0    41.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 648 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598C  LEU*     4.6    10.5    -      -       +      -
    618C  ALA*     3.5    18.2    -      -       +      +
    620C  LEU*     4.5    11.7    -      -       +      -
    638C  VAL*     5.4     6.3    -      -       +      +
    641C  LEU*     3.4    29.4    -      -       +      -
    646C  VAL*     3.4    16.4    -      -       +      +
    647C  ILE*     1.3    73.2    -      -       -      +
    649C  ILE*     1.3    62.5    +      -       -      +
    650C  PRO*     3.0     5.5    -      -       -      +
    665C  ILE*     3.4    32.7    -      -       +      +
    672C  ASN*     2.9    38.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 649 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    617C  ILE*     3.7    23.8    -      -       +      -
    618C  ALA      2.8    12.0    +      -       -      +
    619C  LEU*     3.7    20.3    -      -       +      -
    620C  LEU*     3.1    20.0    +      -       -      -
    647C  ILE*     3.6    11.9    -      -       +      -
    648C  VAL*     1.3    71.4    -      -       -      +
    650C  PRO*     1.3    61.1    -      -       -      +
    651C  VAL*     3.3     6.3    +      -       +      +
    671C  GLU      3.1    28.3    -      -       -      +
    673C  LYS      3.2    23.1    -      -       -      +
    675C  PHE*     3.7    23.6    -      -       +      -
    693C  TYR*     3.8    10.3    -      -       +      -
    694C  LEU*     3.9    12.6    -      -       +      -
    697C  LEU*     4.5     0.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 650 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    620C  LEU*     4.0    11.2    -      -       +      +
    622C  MET*     4.9     3.1    -      -       -      -
    648C  VAL      3.0    13.6    -      -       -      +
    649C  ILE*     1.3    81.2    -      -       -      +
    651C  VAL*     1.3    62.2    +      -       -      +
    652C  GLY      4.0     0.8    +      -       -      -
    662C  ILE*     4.1    25.3    -      -       +      +
    665C  ILE*     3.6    35.2    -      -       +      -
    672C  ASN      3.9     5.2    -      -       -      +
    673C  LYS      3.7     8.4    -      -       -      +
    674C  ALA*     3.4    22.7    -      -       +      +
    675C  PHE      3.1    21.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 651 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536C  PHE*     6.0     0.4    -      -       +      -
    619C  LEU*     4.0    20.4    -      -       +      -
    620C  LEU      3.1    10.6    +      -       -      +
    621C  LEU*     3.7    27.3    -      -       +      -
    622C  MET*     2.9    33.2    +      -       -      +
    649C  ILE*     3.7    15.3    -      -       +      +
    650C  PRO*     1.3    76.8    -      -       -      +
    652C  GLY*     1.3    59.8    +      -       -      +
    653C  ILE*     3.8    14.6    +      -       +      +
    675C  PHE*     3.4    20.0    -      -       +      +
    677C  LEU*     4.1    17.9    -      -       +      -
    683C  LEU*     4.6     2.5    -      -       +      -
    690C  ILE*     5.0     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 652 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    622C  MET      3.5     4.5    -      -       -      -
    650C  PRO      4.0     1.2    -      -       -      -
    651C  VAL*     1.3    73.5    -      -       -      +
    653C  ILE*     1.3    61.7    +      -       -      +
    654C  GLY      5.1     0.2    -      -       -      -
    657C  ALA*     3.9     6.3    -      -       -      -
    662C  ILE*     3.7    24.6    -      -       -      +
    675C  PHE      2.6    14.4    +      -       -      +
    676C  VAL*     4.4     5.4    -      -       -      -
    677C  LEU*     2.7    34.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 653 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525C  LEU*     4.9     1.3    -      -       +      -
    533C  LEU*     3.6    30.7    -      -       +      -
    621C  LEU*     4.3    15.3    -      -       +      -
    622C  MET      2.9    11.9    +      -       -      +
    623C  ALA*     3.3    31.9    -      -       +      +
    651C  VAL*     4.0    13.9    -      -       +      +
    652C  GLY*     1.3    79.7    -      -       -      +
    654C  GLY*     1.3    71.6    +      -       -      +
    657C  ALA*     3.9     5.9    +      -       -      +
    677C  LEU*     3.7     8.1    -      -       +      -
    679C  SER      3.5     5.4    -      -       -      +
    680C  VAL*     3.4    39.9    -      -       +      +
    683C  LEU*     4.1    16.6    -      -       +      -
----------------------------------------------------------
 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