Contacts of the helix formed by residues 224 - 230 (chain 3) in PDB entry 6Q8O
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 GLY 224 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1743 VAL* 4.8 1.3 - - - -
2233 SER* 1.3 68.9 + - - +
2253 ASN* 1.3 56.8 + - - +
2263 ILE 3.3 0.2 - - - -
2273 THR* 2.8 32.9 + - - -
2903 ILE 5.6 0.2 - - - -
2923 ASP* 2.3 26.6 + - - -
2953 ARG* 3.6 17.5 + - - -
2963 PHE* 3.6 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 225 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1903 TYR* 3.8 25.0 + - + +
2223 PHE* 3.6 2.4 + - - +
2233 SER 3.2 2.0 + - - -
2243 GLY* 1.3 72.7 - - - +
2263 ILE* 1.3 65.5 + - - +
2273 THR 3.0 1.6 - - - -
2283 ASP* 2.9 16.0 + - - +
2293 ILE* 3.0 17.8 - - - +
2883 ILE 4.9 0.9 - - - +
2893 TRP* 3.5 32.3 - - + +
2903 ILE 2.6 52.0 + - - +
2923 ASP* 4.4 0.2 + - - -
2953 ARG* 3.0 18.6 + - - +
4113 LEU* 4.4 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1743 VAL* 5.1 7.6 - - + -
1863 ARG 5.2 0.2 - - - -
1873 CYS* 3.7 28.9 - - + -
1903 TYR* 3.3 34.1 - - + -
1913 PHE* 3.6 23.3 - - + -
2003 LEU* 4.3 7.4 - - + -
2183 LEU* 5.7 1.3 - - + -
2233 SER* 3.3 13.7 + - - +
2253 ASN* 1.3 76.4 - - - +
2273 THR* 1.3 64.2 + - - +
2293 ILE* 4.0 9.4 - - + -
2303 CYS* 2.9 35.3 + - + +
2353 LEU* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 227 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243 LYS* 3.2 26.5 + - - +
1743 VAL* 4.3 15.9 - - - +
2243 GLY* 2.8 20.7 + - - -
2263 ILE* 1.3 83.0 - - - +
2283 ASP* 1.3 67.1 + - - +
2303 CYS* 4.3 1.9 + - - +
2353 LEU* 4.1 14.5 + - - +
2363 LEU* 4.0 15.0 + - - -
2373 ASP* 3.6 34.8 + - + +
2763 ARG* 6.0 3.4 - - - +
2953 ARG* 4.4 5.6 - - - +
2963 PHE* 5.2 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243 LYS* 5.0 6.5 - - - +
1293 GLU* 4.9 4.5 - - - +
2253 ASN* 2.9 8.3 + - - +
2273 THR* 1.3 81.9 - - - +
2293 ILE* 1.3 64.4 + - + +
2303 CYS 4.7 2.0 - - - +
2783 ARG* 4.3 12.4 - - - +
2793 ALA* 3.3 27.9 + - + +
2883 ILE 4.6 3.4 - - - +
2953 ARG* 2.3 50.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363 GLU* 3.4 28.5 - - + +
393 LEU* 4.7 9.0 - - + -
1293 GLU* 3.8 4.2 - - - +
1863 ARG* 3.1 47.9 + - + +
1903 TYR* 4.8 9.0 - - + -
2253 ASN* 3.0 22.9 - - + +
2263 ILE* 2.9 10.8 + - + +
2283 ASP* 1.3 83.4 - - + +
2303 CYS* 1.3 66.3 + - - +
2313 PRO* 2.9 5.4 - - - +
2883 ILE* 5.1 7.2 - - + +
2893 TRP* 3.4 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 230 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243 LYS* 3.9 14.2 - - - -
1293 GLU* 5.2 0.2 - - - +
1813 CYS* 6.0 0.7 - - - -
1843 CYS* 6.5 0.2 - - - -
1863 ARG* 5.1 3.1 - - - +
1873 CYS* 6.4 0.9 - - + -
2263 ILE* 2.9 16.1 + - + +
2273 THR 4.7 1.1 - - - +
2283 ASP 3.7 1.1 - - - +
2293 ILE* 1.3 73.0 - - - +
2313 PRO* 1.3 64.5 - - - +
2323 VAL* 2.9 49.6 + - - +
2343 ALA* 4.1 4.5 - - - -
2353 LEU* 3.9 41.3 - - + +
----------------------------------------------------------
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