Contacts of the helix formed by residues 173 - 190 (chain 6) in PDB entry 5U8T
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 GLN 173 (chain 6).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3884 ARG* 5.9 0.4 - - - +
1686 MET 3.5 1.4 - - - +
1696 ALA* 3.1 34.9 + - + +
1726 GLU* 1.3 91.4 + - - +
1746 TYR* 1.3 64.2 + - - +
1756 TYR* 3.4 2.2 - - - -
1766 ARG* 3.0 45.9 + - - +
1776 PHE* 3.0 24.2 + - + -
2856 GLY* 3.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 174 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1696 ALA 3.9 0.2 + - - -
1706 ILE* 3.0 39.5 + - + +
1726 GLU 3.2 0.2 - - - -
1736 GLN* 1.3 75.5 - - - +
1756 TYR* 1.3 57.1 + - - +
1776 PHE* 2.7 24.8 + - - +
1786 LEU* 2.9 54.6 + - + +
1816 LEU* 4.6 10.3 - - + -
2656 ILE* 4.0 10.2 - - + +
2676 PHE* 4.0 17.0 - + - -
2856 GLY 2.8 14.6 + - - +
2866 SER* 4.3 2.9 - - - -
2876 LEU* 3.3 34.3 - - + -
4006 VAL* 3.6 26.9 - - + -
4576 CYS* 3.5 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3854 ILE* 4.6 18.0 - - + +
3874 ASN* 3.0 39.0 - - + +
3884 ARG* 4.7 11.4 - - + -
1746 TYR* 1.3 81.6 - - + +
1766 ARG* 1.3 67.1 + - + +
1776 PHE 3.3 0.2 + - - -
1786 LEU* 3.4 27.2 + - + +
1796 PRO* 4.1 4.2 - - - +
2856 GLY* 3.1 26.0 + - - -
3826 ARG* 5.7 6.5 - - - -
4006 VAL* 5.8 4.9 - - + -
4026 ILE* 4.6 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3884 ARG* 3.1 51.8 - - - +
1056 ASP 5.5 4.6 + - - -
1066 VAL* 6.2 2.2 - - - +
1076 THR* 5.5 6.5 - - - -
1736 GLN* 3.0 33.6 + - + +
1756 TYR* 1.3 84.5 - - + +
1776 PHE* 1.3 93.0 + - + +
1796 PRO* 3.7 13.9 - - - +
1806 PHE* 4.1 6.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056 ASP* 4.9 1.6 - - - -
1076 THR* 4.7 8.1 - - + -
1086 GLY* 3.5 29.2 - - - -
1116 VAL* 4.8 8.3 - - + -
1696 ALA* 3.1 45.1 - - + -
1706 ILE* 4.5 8.7 - - + -
1736 GLN* 3.0 15.4 + - + -
1746 TYR* 2.7 16.7 + - - +
1766 ARG* 1.3 114.5 - - + +
1786 LEU* 1.3 63.3 + - - +
1796 PRO* 3.4 2.9 - - - -
1806 PHE* 3.3 33.4 + + + -
1816 LEU* 3.0 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1746 TYR* 2.9 72.4 + - + +
1756 TYR* 3.4 23.3 - - + +
1766 ARG 3.6 0.4 - - - -
1776 PHE* 1.3 75.3 - - - +
1796 PRO* 1.4 73.1 - - + +
1806 PHE 2.8 2.4 + - - -
1816 LEU* 2.9 20.3 + - + +
1826 GLN* 3.3 35.2 - - + +
2656 ILE* 6.2 2.9 - - + -
3826 ARG* 6.2 1.8 - - - +
4006 VAL* 5.6 0.4 - - + -
4576 CYS* 6.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 179 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1756 TYR 4.1 4.7 - - - +
1766 ARG 3.7 10.5 - - - +
1776 PHE 3.4 1.8 - - - -
1786 LEU* 1.4 93.8 - - + +
1806 PHE* 1.3 80.0 + - + +
1826 GLN* 4.0 10.7 + - - +
1836 LYS* 3.1 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056 ASP* 3.2 42.2 - - + -
1086 GLY* 3.1 40.4 - - - +
1096 GLU* 5.1 2.9 - - - -
1126 ARG* 3.4 38.4 + - + +
1766 ARG* 4.1 11.0 - - + -
1776 PHE* 3.5 32.1 - + + +
1786 LEU 2.8 1.6 + - - -
1796 PRO* 1.3 91.6 - - + +
1816 LEU* 1.3 60.3 + - + +
1826 GLN 3.1 2.5 - - - -
1836 LYS* 5.1 4.9 - - + -
1846 GLY* 2.9 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116 VAL* 5.6 2.2 - - + -
1126 ARG* 6.3 0.2 - - - +
1156 PHE* 3.5 42.7 - - + -
1706 ILE* 4.1 24.5 - - + -
1746 TYR* 4.6 9.2 - - + -
1776 PHE* 3.0 38.1 - - + +
1786 LEU* 2.9 10.1 + - + +
1806 PHE* 1.3 80.2 - - + +
1826 GLN* 1.3 57.3 + - + +
1846 GLY 3.9 0.2 - - - -
1856 LEU* 3.0 28.8 + - - +
2656 ILE* 4.5 13.7 - - + +
2676 PHE* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1786 LEU* 3.3 45.2 + - + +
1796 PRO* 4.2 7.8 - - - +
1806 PHE 3.1 0.2 - - - -
1816 LEU* 1.3 74.4 - - + +
1836 LYS* 1.3 57.9 + - - +
1846 GLY 3.1 3.6 - - - -
1856 LEU* 3.0 7.5 + - - +
1866 ARG* 2.8 35.6 + - + +
2636 PHE* 4.4 19.0 + - + +
2646 GLN* 6.1 0.2 - - - +
2656 ILE* 3.6 29.0 - - + +
3056 TYR* 5.4 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126 ARG* 3.0 38.8 + - - +
1796 PRO* 3.1 26.7 + - - +
1806 PHE* 3.8 6.4 - - + +
1826 GLN* 1.3 77.5 - - - +
1846 GLY* 1.3 57.2 + - - +
1866 ARG* 3.6 33.7 - - - +
1876 ARG* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 184 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126 ARG* 3.5 20.2 - - - -
1156 PHE* 6.3 0.7 - - - -
1166 GLU* 4.0 8.7 - - - -
1196 LEU* 4.4 6.5 - - - -
1806 PHE 2.9 19.3 + - - -
1816 LEU* 4.0 0.9 - - - -
1836 LYS* 1.3 74.4 - - - +
1856 LEU* 1.3 67.6 + - - +
1876 ARG* 3.2 5.3 + - - +
1886 VAL* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156 PHE* 5.7 4.0 - - + -
1196 LEU* 3.9 25.6 - - + +
1406 ILE* 5.2 8.7 - - + -
1516 ILE* 4.3 35.9 - - + -
1816 LEU 3.0 17.1 + - - +
1826 GLN* 3.3 9.4 - - - +
1846 GLY* 1.3 75.9 - - - +
1866 ARG* 1.3 54.8 + - - +
1886 VAL* 3.0 4.5 + - - +
1896 VAL* 2.8 51.8 + - + +
2636 PHE* 3.3 32.3 - - + -
2656 ILE* 4.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1826 GLN* 2.8 21.2 + - - +
1836 LYS* 3.7 29.5 - - - +
1846 GLY 3.1 0.2 - - - -
1856 LEU* 1.3 71.6 - - - +
1876 ARG* 1.3 61.2 + - - +
1896 VAL* 4.5 0.7 - - - +
1906 ARG* 2.9 58.7 + - - +
2616 ARG* 4.9 18.8 + - - +
2626 VAL* 5.6 0.2 - - - +
2636 PHE* 3.6 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096 GLU* 4.9 4.0 + - - -
1126 ARG* 3.8 21.4 - - - +
1136 GLU* 3.3 22.0 + - - -
1166 GLU* 3.5 20.9 + - - +
1836 LYS 2.9 18.4 + - - +
1846 GLY 3.4 6.3 - - - +
1866 ARG* 1.3 78.8 - - - +
1886 VAL* 1.3 60.4 + - - +
1906 ARG* 3.3 23.9 + - + +
1916 LYS* 3.7 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166 GLU* 3.4 33.9 - - + +
1196 LEU* 3.5 26.9 - - + -
1206 GLU* 4.4 17.5 - - + +
1846 GLY 2.9 16.4 + - - +
1856 LEU 3.0 8.0 + - - +
1876 ARG* 1.3 74.9 - - - +
1896 VAL* 1.3 61.9 + - + +
1906 ARG 3.1 4.5 - - - -
1916 LYS* 3.0 33.3 + - - +
1926 TYR* 3.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196 LEU* 5.9 0.4 - - + -
1406 ILE* 3.7 32.8 - - + -
1856 LEU* 2.8 43.6 + - + +
1866 ARG 4.5 0.9 - - - +
1886 VAL* 1.3 75.9 - - + +
1906 ARG* 1.3 50.6 + - - +
1916 LYS 2.9 5.4 - - - -
1926 TYR* 2.6 14.3 + - + -
1936 ALA* 2.3 71.0 + - + +
2636 PHE* 4.4 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1866 ARG* 2.9 52.1 + - - +
1876 ARG* 3.3 16.6 - - - +
1896 VAL* 1.3 76.6 - - - +
1916 LYS* 1.3 57.6 + - - +
1926 TYR 3.2 1.5 + - - -
1936 ALA 3.9 8.0 - - - -
----------------------------------------------------------
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