Contacts of the helix formed by residues 200 - 211 (chain 3) in PDB entry 5IY6
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 SER 200 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333 LEU* 5.8 3.3 - - - +
1653 LYS* 2.8 28.7 + - - +
1673 ALA* 2.8 25.8 + - - +
1683 GLU* 3.9 5.7 - - - -
1693 ASP* 4.2 9.3 - - - +
1993 ASP* 1.3 71.1 - - - +
2013 GLY* 1.3 63.2 + - - +
2023 LEU 3.2 2.2 - - - +
2033 LEU* 3.5 27.0 - - - +
2043 GLN* 3.3 25.3 + - - +
2143 TYR* 4.7 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 201 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1693 ASP* 4.5 1.4 - - - +
1993 ASP* 3.6 6.2 + - - +
2003 SER* 1.3 70.0 - - - +
2023 LEU* 1.3 66.2 + - - +
2043 GLN* 2.9 18.7 + - - +
2053 GLN* 2.8 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1693 ASP* 2.9 50.5 - - + +
1743 TYR* 3.4 25.6 - - + -
1773 PHE* 3.6 21.4 - - + -
1783 MET* 2.9 37.2 - - + -
1813 ILE* 4.0 1.7 - - - +
2003 SER 3.2 0.6 - - - -
2013 GLY* 1.3 80.4 - - - +
2033 LEU* 1.3 52.6 + - + +
2053 GLN* 3.2 15.5 + - - +
2063 ALA* 2.7 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333 LEU* 4.8 14.1 - - + -
1633 VAL* 4.2 22.4 - - + -
1653 LYS* 3.0 47.3 - - + -
1773 PHE* 3.0 41.1 - - + -
1913 ILE* 5.5 2.7 - - + +
1933 ALA* 4.4 17.1 - - + +
2003 SER* 3.3 18.7 + - - +
2013 GLY 3.2 0.2 - - - -
2023 LEU* 1.3 74.0 - - + +
2043 GLN* 1.3 65.9 + - - +
2063 ALA* 3.1 6.7 + - + +
2073 CYS* 3.0 22.0 + - - +
2143 TYR* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 204 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1993 ASP* 5.4 7.7 + - - +
2003 SER 3.3 16.2 + - - +
2013 GLY* 2.9 16.1 + - - +
2033 LEU* 1.3 76.0 - - - +
2053 GLN* 1.3 61.7 + - + +
2073 CYS* 2.9 25.6 - - - -
2083 ASP* 3.3 10.9 + - - +
2143 TYR* 3.3 53.1 + - + -
2163 LYS* 5.1 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550 LEU* 1.2 93.0 - - + +
1000 PRO* 4.5 14.4 - - + -
1743 TYR* 5.0 0.4 - - - -
1783 MET* 3.7 6.3 - - + -
2013 GLY* 2.8 19.3 + - - +
2023 LEU* 3.4 27.3 - - - +
2043 GLN* 1.3 74.2 - - + +
2063 ALA* 1.3 54.7 + - - +
2083 ASP* 1.5 43.8 - - - +
2093 ILE* 3.3 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773 PHE* 3.8 11.9 - - + -
1813 ILE* 3.8 31.9 - - + -
1913 ILE* 4.7 17.0 - - + -
2023 LEU 2.7 14.7 + - - +
2033 LEU* 3.1 12.5 + - + +
2053 GLN* 1.3 78.0 - - - +
2073 CYS* 1.3 59.2 + - - +
2093 ILE* 4.1 0.9 - - - +
2103 THR* 2.6 32.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 207 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970 ASP* 4.7 0.2 - - - -
1913 ILE 3.6 22.4 + - - +
1933 ALA* 5.1 1.6 - - + +
2033 LEU 3.0 9.7 + - - +
2043 GLN* 2.9 23.1 - - - -
2053 GLN 3.2 0.4 - - - -
2063 ALA* 1.3 74.1 - - - +
2083 ASP* 1.3 75.7 + - - +
2113 GLY* 2.7 13.7 + - - -
2123 GLY 2.6 42.5 + - - +
2133 LEU 3.9 7.9 - - - +
2143 TYR* 3.1 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 208 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960 PHE 4.7 0.2 - - - +
970 ASP* 1.9 72.6 - - - +
1000 PRO* 3.7 18.7 - - + +
2043 GLN* 3.5 13.0 - - - +
2053 GLN* 1.5 41.3 + - - +
2063 ALA 3.1 0.7 - - - -
2073 CYS* 1.3 91.8 - - - +
2093 ILE* 1.3 56.5 + - - +
2113 GLY 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540 ARG* 1.5 95.8 - - + +
550 LEU* 3.0 5.8 - - + +
980 GLN* 2.5 37.0 + - - +
1783 MET* 4.5 7.0 - - - -
1813 ILE* 4.2 16.4 - - + -
1823 PHE* 3.7 14.1 - - + -
1853 GLN* 2.6 44.7 + - + +
2053 GLN* 3.3 13.0 - - + +
2063 ALA 4.1 2.7 - - - +
2073 CYS 3.5 0.4 + - - -
2083 ASP* 1.3 72.5 - - - +
2103 THR* 1.3 54.4 + - - +
2113 GLY* 3.2 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 210 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813 ILE* 3.9 11.8 + - - +
1853 GLN* 2.9 22.4 + - - +
1883 ASN 5.8 1.0 - - - -
1893 ILE 2.7 31.0 - - - +
1903 LEU* 2.9 21.8 + - - +
1913 ILE* 3.0 25.3 - - + +
2063 ALA 2.6 24.8 + - - -
2073 CYS 3.9 2.0 - - - -
2093 ILE* 1.3 73.5 - - - +
2113 GLY* 1.3 60.7 + - - +
2123 GLY 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970 ASP* 5.1 4.7 - - - -
980 GLN* 5.1 3.8 - - - -
1903 LEU* 4.3 7.6 - - - +
2073 CYS 2.7 6.6 + - - -
2083 ASP* 5.1 1.1 - - - -
2093 ILE 3.2 6.6 - - - +
2103 THR* 1.3 80.3 - - - +
2123 GLY* 1.3 64.9 + - - +
----------------------------------------------------------
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