Contacts of the strand formed by residues 13 - 17 (chain A) in PDB entry 4CQM


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 LEU 13 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ALA*     1.3    72.7    -      -       -      +
     14A  ALA*     1.3    66.9    +      -       -      +
     37A  THR*     3.3    32.1    -      -       +      +
     39A  ALA*     4.5     3.1    -      -       +      -
     89A  VAL*     3.7    19.5    -      -       +      -
     93A  PHE*     3.8    34.8    -      -       +      -
     95A  ARG*     3.3    48.8    -      -       -      +
     96A  PRO      4.0     8.3    -      -       -      +
     97A  PRO*     3.5    12.0    -      -       +      +
     98A  SER*     3.1    25.5    +      -       -      -
     99A  VAL*     3.1     9.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     1.3    74.1    -      -       -      +
     15A  LEU*     1.3    57.6    +      -       -      +
     16A  VAL*     4.0     1.3    +      -       +      -
     31A  LEU*     3.6    32.8    -      -       +      -
     36A  ALA*     4.6     7.0    -      -       +      -
     37A  THR      2.6    16.1    +      -       -      +
     38A  VAL*     4.2    12.1    -      -       +      -
     39A  ALA*     2.5    37.5    +      -       -      +
     97A  PRO*     4.5     1.3    -      -       -      -
     99A  VAL*     3.2    13.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ALA*     1.3    73.1    -      -       -      +
     16A  VAL*     1.3    57.4    +      -       -      +
     17A  THR*     4.1     5.6    +      -       +      -
     39A  ALA*     3.5    16.8    -      -       +      +
     41A  CYS*     4.3    16.6    -      -       +      -
     72A  PHE*     5.5     0.2    -      -       +      -
     85A  LEU*     4.5    11.9    -      -       +      -
     86A  LEU*     3.9    38.8    -      -       +      -
     89A  VAL*     4.2    21.3    -      -       +      -
     97A  PRO*     3.6    22.2    -      -       +      +
     99A  VAL      2.6    10.5    +      -       -      +
    100A  VAL*     3.3    18.3    -      -       +      +
    101A  VAL      2.7    33.1    +      -       -      +
    134A  VAL*     4.9     3.8    -      -       +      -
    138A  ALA*     5.3     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ALA*     4.0     0.6    -      -       +      -
     15A  LEU*     1.3    77.7    -      -       -      +
     17A  THR*     1.3    69.2    +      -       -      +
     19A  ALA*     3.3    10.3    -      -       +      +
     24A  GLY*     3.5    29.8    -      -       -      +
     27A  VAL*     3.7    23.3    -      -       +      -
     28A  SER*     4.0    12.3    -      -       -      +
     31A  LEU*     4.0    15.0    -      -       +      -
     38A  VAL*     4.7     7.2    -      -       +      -
     39A  ALA      3.4     9.1    +      -       -      +
     41A  CYS*     2.9    30.4    +      -       -      +
    101A  VAL*     3.3    13.7    -      -       +      +
    103A  CYS*     4.1     7.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 17 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     4.8     6.7    -      -       +      +
     16A  VAL*     1.3    71.8    -      -       -      +
     18A  GLY*     1.3    66.3    +      -       -      +
     19A  ALA      3.2     1.6    -      -       -      -
     41A  CYS*     3.4    10.1    -      -       +      -
     76A  VAL*     4.1    12.1    -      -       +      +
     85A  LEU*     4.4    15.5    -      -       +      -
    101A  VAL      3.1     6.0    +      -       -      +
    102A  SER*     3.2    21.3    -      -       -      -
    103A  CYS*     3.0    24.1    +      -       -      +
    104A  ALA*     3.2    17.5    +      -       -      +
    134A  VAL*     4.1    32.4    -      -       +      +
----------------------------------------------------------
 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