Contacts of the strand formed by residues 51 - 55 (chain M) in PDB entry 5A0Q


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 51 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23M  VAL*     4.4    12.6    -      -       +      +
     43M  CYS*     3.8    28.9    -      -       +      +
     44M  TYR      3.5    14.8    -      -       -      +
     45M  LYS*     4.6     2.9    -      -       +      +
     50M  THR*     1.4    81.0    -      -       -      +
     52M  ILE*     1.3    66.0    +      -       -      +
     53M  GLY      4.3     0.4    -      -       -      -
    109M  ILE      4.1     0.3    -      -       -      +
    110M  ILE*     3.9     0.2    -      -       -      -
    111M  GLY      2.8    32.1    +      -       -      +
    196M  CYS*     3.9    15.3    -      -       +      -
    198M  VAL*     3.8    16.8    -      -       +      -
    203M  ILE*     3.7    33.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 52 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42M  LYS      3.0    13.5    -      -       -      +
     43M  CYS*     4.1     3.8    -      -       -      -
     44M  TYR*     3.0    15.8    +      -       +      +
     46M  LEU*     3.2    36.6    -      -       +      -
     50M  THR*     5.2     1.3    -      -       +      -
     51M  VAL*     1.3    74.8    -      -       -      +
     53M  GLY*     1.4    72.3    +      -       -      +
     54M  CYS*     4.9     1.0    -      -       -      +
     65M  THR*     4.2    19.7    -      -       +      +
     68M  ILE*     3.5    31.9    -      -       +      -
     92M  LEU*     4.2     4.5    -      -       +      -
    108M  ASN*     4.3     9.2    -      -       +      +
    109M  ILE      3.3     9.2    -      -       -      +
    110M  ILE*     3.5    25.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 53 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  ILE*     4.1    23.3    -      -       -      -
     23M  VAL*     4.1    10.8    -      -       -      +
     42M  LYS      3.3    11.0    -      -       -      -
     43M  CYS*     4.1     3.4    -      -       -      -
     52M  ILE*     1.4    79.3    -      -       -      +
     54M  CYS*     1.3    59.0    -      -       -      -
    108M  ASN*     3.2     4.6    -      -       -      -
    109M  ILE      2.9    32.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 54 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  ILE*     3.7     4.7    -      -       -      +
     42M  LYS*     3.3    31.5    +      -       -      +
     44M  TYR*     6.4     0.9    -      -       +      -
     52M  ILE*     4.9     1.1    -      -       +      +
     53M  GLY*     1.3    72.0    -      -       -      -
     55M  SER*     1.3    60.3    -      -       -      +
     58M  HIS*     5.8     0.7    -      -       -      -
     61M  CYS*     2.0    60.3    -      -       +      -
     64M  LEU*     5.1     0.4    -      -       -      -
     65M  THR*     4.8    11.4    -      -       +      -
    106M  VAL*     3.3    13.7    -      -       -      -
    107M  TYR      3.6     1.8    -      -       -      -
    108M  ASN*     2.6    33.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 55 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9M  GLY      5.0     1.8    -      -       -      -
     10M  GLY      3.2    26.9    -      -       -      -
     12M  ILE*     3.4    21.0    -      -       -      +
     42M  LYS*     5.2     3.1    -      -       -      -
     54M  CYS*     1.3    73.6    -      -       -      +
     56M  GLY*     1.3    54.8    +      -       -      +
     57M  PHE      3.9     1.8    -      -       -      -
     61M  CYS*     4.2     3.1    -      -       -      -
    106M  VAL*     3.3     2.3    -      -       -      +
    107M  TYR*     2.4    52.0    +      -       -      +
    138M  GLY*     4.1     0.3    -      -       -      -
    139M  GLY*     3.5    18.7    +      -       -      -
----------------------------------------------------------
 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