Contacts of the strand formed by residues 38 - 48 (chain P) in PDB entry 3QUM


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 38 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  LEU*     4.2     1.2    -      -       -      +
     28A  TYR*     4.1     8.1    -      -       -      +
     93A  GLU*     4.1    17.6    +      -       -      -
     34P  ALA*     3.6     6.8    -      -       -      +
     35P  SER      3.0    28.5    +      -       -      +
     36P  ARG*     3.8    19.0    +      -       +      +
     37P  GLY*     1.3    82.9    +      -       -      +
     39P  ALA*     1.3    71.0    +      -       -      +
     41P  VAL*     3.4     3.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 39 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  TYR*     3.2    31.0    +      -       +      +
     32P  LEU*     4.8     9.9    -      -       +      -
     33P  VAL      4.6     4.7    -      -       -      -
     34P  ALA*     4.9     0.4    -      -       -      -
     38P  ARG*     1.3    80.1    -      -       -      +
     41P  VAL*     1.3    63.7    +      -       -      +
    144P  ILE*     5.7     5.4    -      -       +      +
    149P  PHE*     3.9    23.3    -      -       +      -
    194P  ASP*     4.5     9.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 41 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33P  VAL*     3.6    13.7    +      -       +      -
     34P  ALA*     4.2    10.3    -      -       -      -
     35P  SER*     3.8    21.3    -      -       -      +
     38P  ARG*     3.4     8.8    +      -       +      +
     39P  ALA*     1.3    79.0    -      -       -      +
     42P  CYS*     1.3    78.4    +      -       +      +
     58P  CYS*     3.6    26.0    -      -       +      +
     60P  ARG*     3.6    36.1    +      -       +      +
    144P  ILE*     5.1     8.4    -      -       -      +
    194P  ASP*     5.2     3.0    -      -       -      +
    195P  SER*     5.3     1.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 42 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32P  LEU*     3.6     9.8    -      -       -      +
     33P  VAL*     2.7    39.3    +      -       +      +
     39P  ALA*     5.2     0.2    -      -       -      +
     41P  VAL*     1.3    88.3    -      -       +      +
     43P  GLY*     1.3    57.4    +      -       -      +
     54P  THR*     4.2     6.7    -      -       +      -
     57P  HIS*     5.3     0.2    -      -       -      -
     58P  CYS*     2.1    56.5    -      -       +      -
    194P  ASP*     4.6     9.1    +      -       -      +
    195P  SER*     3.3    25.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 43 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30P  GLN*     4.5     8.5    -      -       -      -
     31P  VAL      3.3    11.2    -      -       -      -
     32P  LEU*     4.4     4.3    -      -       -      -
     42P  CYS*     1.3    74.1    -      -       -      +
     44P  GLY*     1.3    54.0    +      -       -      -
     54P  THR*     2.8    12.4    -      -       -      +
    141P  TRP*     4.8     3.6    -      -       -      -
    194P  ASP*     4.4     9.2    -      -       -      +
    195P  SER      2.9     9.4    +      -       -      +
    196P  GLY      2.7    28.5    -      -       -      +
    197P  GLY*     4.5     3.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 44 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30P  GLN*     3.9     6.8    +      -       -      +
     31P  VAL*     3.0    41.3    +      -       -      +
     33P  VAL*     4.7     1.5    -      -       -      +
     42P  CYS      4.2     0.2    +      -       -      -
     43P  GLY*     1.3    73.9    -      -       -      -
     45P  VAL*     1.3    68.3    +      -       -      +
     52P  VAL*     4.2     2.9    -      -       -      -
     53P  LEU      3.2    13.5    -      -       -      -
     54P  THR*     3.4     7.0    -      -       -      -
    196P  GLY      3.9     2.9    -      -       -      -
    198P  PRO*     4.6     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 45 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29P  TRP*     4.0    22.7    -      -       +      -
     44P  GLY*     1.3    74.9    -      -       -      +
     46P  LEU*     1.3    61.3    +      -       -      +
     47P  VAL*     3.2    13.7    +      -       +      +
     52P  VAL*     3.4     5.7    -      -       -      +
     53P  LEU*     2.7    45.8    +      -       +      +
    121P  MET*     4.1    21.3    -      -       +      -
    196P  GLY      4.9     2.2    -      -       -      +
    198P  PRO*     3.2    43.3    -      -       +      -
    209P  LEU*     4.6    14.1    -      -       +      -
    212P  ILE*     5.4     5.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 46 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28P  PRO      4.9     1.6    -      -       -      +
     29P  TRP*     3.5    18.1    +      -       -      +
     31P  VAL*     4.4     3.9    -      -       +      +
     45P  VAL*     1.3    71.8    -      -       -      +
     47P  VAL*     1.3    58.8    +      -       -      +
     48P  HIS      3.4    23.3    -      -       -      +
     49P  PRO*     4.3    12.3    -      -       +      +
     51P  TRP      3.6    10.3    -      -       -      +
     52P  VAL*     3.9    15.0    -      -       +      -
     67P  LEU*     3.3    32.1    -      -       +      -
    108P  LEU*     4.6     3.1    -      -       +      -
    112P  ALA*     5.4     2.5    -      -       +      -
    114P  LEU*     6.4     1.3    -      -       +      -
    118P  VAL*     3.7    12.8    -      -       +      -
    119P  LYS      3.4    23.8    -      -       -      +
    120P  VAL*     3.3    10.2    -      -       +      +
    121P  MET*     3.2    23.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 47 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45P  VAL*     3.2    20.4    +      -       +      +
     46P  LEU*     1.3    72.6    -      -       -      +
     48P  HIS*     1.3    63.9    +      -       +      +
     51P  TRP*     3.1    32.8    +      -       +      +
     52P  VAL*     4.6     0.7    -      -       -      +
     53P  LEU*     4.0    24.9    -      -       +      -
    105P  LEU*     4.7     9.0    -      -       +      -
    120P  VAL*     4.2     8.2    -      -       -      +
    121P  MET      4.1    12.6    -      -       -      +
    122P  ASP*     5.8     0.2    -      -       -      -
    123P  LEU*     4.3    24.3    -      -       +      +
    209P  LEU*     5.5     2.0    -      -       +      -
    238P  ILE*     5.3     3.1    -      -       +      -
    242P  ILE*     4.3    12.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 48 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46P  LEU*     3.4    11.0    +      -       -      +
     47P  VAL*     1.3    84.8    -      -       +      +
     49P  PRO*     1.4    88.1    -      -       +      +
     50P  GLN*     2.8    36.4    +      -       +      -
     51P  TRP*     3.2    42.8    +      +       +      +
    111P  PRO*     6.2     1.1    -      -       +      -
    120P  VAL*     4.1     9.6    -      -       -      +
    242P  ILE*     4.5    14.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 49 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46P  LEU*     4.3     8.7    -      -       +      +
     48P  HIS*     1.4   100.5    -      -       +      +
     50P  GLN*     1.3    56.3    +      -       -      +
    108P  LEU*     4.2     6.1    -      -       -      +
    111P  PRO*     3.9    10.9    -      -       +      +
    112P  ALA*     3.3    42.7    +      -       +      +
    114P  LEU*     4.0    26.7    -      -       +      -
    120P  VAL*     4.8     8.1    -      -       +      -
----------------------------------------------------------
 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