Contacts of the helix formed by residues 185 - 194 (chain 3) in PDB entry 6Q8W
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.
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 LYS 185 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1981 ASN* 4.1 28.0 - - - +
3551 LYS* 4.3 18.0 - - + +
343 CYS* 4.9 1.4 + - - +
423 ILE* 3.6 21.6 - - + +
443 ALA* 5.7 1.1 - - + +
1843 CYS* 1.3 76.3 - - - +
1863 ARG* 1.3 56.5 + - - +
1873 CYS* 3.2 4.3 + - - -
1883 VAL* 3.3 26.4 - - + +
1893 ARG* 2.8 58.0 + - - +
2023 PHE* 4.4 9.6 - - + -
4393 GLU* 2.6 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323 LEU* 4.2 7.7 + - - +
333 PHE* 2.9 29.0 + - - +
343 CYS 4.0 9.8 + - - +
353 SER 2.7 24.4 + - - -
363 GLU* 3.0 31.1 + - - +
393 LEU* 3.7 23.3 - - + +
1293 GLU* 3.4 28.6 + - - -
1843 CYS* 3.4 21.7 - - - -
1853 LYS* 1.3 77.0 - - - +
1873 CYS* 1.3 58.4 + - - +
1893 ARG* 4.5 1.1 - - - +
1903 TYR* 2.9 31.9 + - - +
2263 ILE* 5.0 0.9 - - - -
2293 ILE* 3.1 45.3 + - + +
2303 CYS* 5.4 1.1 - - - +
2313 PRO* 4.0 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 187 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1843 CYS* 5.3 1.1 - - - -
1853 LYS* 5.3 1.1 - - - -
1863 ARG* 1.3 80.5 - - - +
1883 VAL* 1.3 65.7 + - - +
1903 TYR* 3.6 1.7 - - - +
1913 PHE* 3.0 37.1 + - - -
2003 LEU* 3.9 19.3 - - + -
2023 PHE* 6.0 0.9 - - - -
2113 ILE* 3.8 32.1 - - - -
2263 ILE* 3.4 28.7 - - + -
2303 CYS* 6.4 1.8 - - + -
2353 LEU* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 GLU* 5.8 0.2 - - - +
1853 LYS* 3.3 36.1 - - + +
1873 CYS* 1.3 75.3 - - - +
1893 ARG* 1.3 65.2 + - - +
1913 PHE* 3.4 3.1 + - - +
1923 GLU* 3.0 31.0 + - - +
1983 GLU* 5.6 0.5 - - - +
2003 LEU 3.3 27.9 - - - +
2013 ASP* 3.6 28.0 - - - +
2023 PHE* 4.4 9.9 - - + -
2113 ILE* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 189 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343 CYS 2.8 27.5 + - - -
353 SER* 4.0 7.5 - - - +
363 GLU 4.3 0.2 - - - +
393 LEU* 3.8 26.7 - - + +
403 SER* 2.6 40.5 + - - +
413 PRO* 4.8 0.8 - - - +
423 ILE* 3.2 23.3 - - - +
1853 LYS* 2.8 54.0 + - + +
1863 ARG* 3.9 3.9 - - - +
1883 VAL* 1.3 75.8 - - + +
1903 TYR* 1.3 59.9 + - - +
1923 GLU* 3.5 5.0 + - - +
1933 GLU* 2.9 61.4 + - - +
4393 GLU* 4.3 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393 LEU* 4.1 13.8 - - + +
1863 ARG 2.9 19.9 + - - +
1873 CYS 3.6 2.5 - - - +
1893 ARG* 1.3 75.4 - - - +
1913 PHE* 1.3 83.2 + + - +
1933 GLU 2.9 1.0 + - - -
1943 VAL* 2.7 63.8 + - + +
1953 PRO* 2.9 17.8 - - + +
2223 PHE* 2.2 46.5 + - - +
2233 SER* 4.8 0.4 - - - -
2253 ASN* 3.4 16.4 + - + -
2263 ILE* 3.6 27.4 - - + -
2293 ILE* 4.3 6.1 - - + -
2893 TRP* 3.9 28.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1873 CYS 3.0 24.6 + - - +
1883 VAL* 3.8 5.8 - - - +
1903 TYR* 1.3 84.9 - + - +
1923 GLU* 1.3 59.6 + - - +
1953 PRO* 3.7 10.5 - - + -
1963 GLY 3.4 4.2 + - - -
1973 ASP 3.0 52.6 + - - +
1983 GLU* 4.4 1.8 - - - -
1993 VAL* 3.5 16.4 - - + +
2003 LEU* 3.7 29.4 - - + +
2183 LEU* 3.6 22.2 - - + -
2203 SER* 3.0 28.3 - - - -
2233 SER* 4.0 9.9 - - - -
2263 ILE* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 GLU* 6.0 0.7 - - - +
1883 VAL 3.0 18.3 + - - +
1893 ARG* 3.9 4.2 - - - +
1913 PHE* 1.3 78.9 - - - +
1933 GLU* 1.3 77.4 + - - +
1963 GLY* 4.0 2.8 - - - -
1983 GLU* 3.3 37.1 - - + +
4393 GLU* 5.1 1.9 - - - +
4403 ARG* 3.7 49.1 + - - +
4413 MET 4.0 11.3 + - - +
4433 ARG* 2.5 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383 HIS 4.0 4.0 - - - +
393 LEU* 3.9 9.4 - - - +
403 SER* 3.0 43.8 + - - -
1893 ARG* 2.9 26.8 + - - +
1903 TYR* 2.9 3.6 + - - +
1923 GLU* 1.3 92.2 - - - +
1943 VAL* 1.3 57.6 + - + +
4143 SER* 2.7 8.5 + - - -
4183 ARG* 3.1 25.8 + - - +
4373 ILE* 3.8 12.3 - - - +
4383 LYS 4.1 6.6 - - - +
4393 GLU* 4.2 4.0 - - - +
4403 ARG 5.2 1.1 - - - +
4413 MET* 5.4 3.4 - - - +
4433 ARG* 2.3 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383 HIS 4.8 4.9 - - - +
393 LEU* 4.8 6.1 - - + -
1903 TYR* 2.7 47.6 + - + +
1933 GLU* 1.3 79.0 - - + +
1953 PRO* 1.4 66.3 - - + +
2893 TRP* 3.7 24.0 - - + +
4103 HIS* 3.8 4.7 + - - -
4113 LEU* 3.5 36.8 - - + +
4143 SER* 2.8 29.1 + - - -
4183 ARG* 4.4 7.4 - - - +
----------------------------------------------------------
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