Contacts of the helix formed by residues 1710 - 1718 (chain C) in PDB entry 5Y3R
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 LEU1710 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1640C GLU* 3.9 16.4 - - + +
1641C THR* 4.7 4.9 - - - +
1644C ALA* 3.4 28.0 - - + -
1648C LEU* 3.5 10.5 - - + -
1688C LEU* 3.5 31.8 - - + +
1691C GLN* 6.4 1.3 - - + -
1700C THR* 5.9 0.2 - - - -
1704C GLY* 4.2 11.2 - - - +
1707C LEU* 3.3 36.1 - - + +
1708C GLU 3.0 10.3 - - - +
1709C GLU* 1.3 85.2 - - - +
1711C ARG* 1.3 68.3 + - - +
1712C ARG 3.1 0.6 + - - +
1713C VAL* 3.6 8.1 + - - +
1714C LEU* 4.1 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1711 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700C THR* 4.9 7.8 + - - +
1704C GLY* 3.5 13.3 + - - +
1705C GLY* 2.2 41.6 + - - -
1706C SER 3.4 2.6 + - - -
1707C LEU 2.8 31.4 + - - +
1708C GLU* 3.1 28.1 + - - +
1709C GLU 4.9 0.4 - - - +
1710C LEU* 1.3 80.9 - - - +
1712C ARG* 1.3 64.5 + - + +
1714C LEU* 3.2 24.5 - - - +
1715C GLU* 2.6 24.4 - - - +
1734C PRO* 5.3 7.6 - - + -
1739C TYR* 3.2 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1712 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1709C GLU* 4.2 19.7 - - - +
1710C LEU 3.1 2.8 - - - +
1711C ARG* 1.3 83.9 - - + +
1713C VAL* 1.3 63.1 + - - +
1714C LEU 3.1 0.2 - - - -
1715C GLU* 2.7 45.4 - - - +
1716C GLN* 2.9 32.4 + - + +
1738C ASN* 3.2 37.0 + - - +
1739C TYR* 3.8 8.5 - - - +
1742C CYS* 3.5 23.8 - - - +
1746C PHE* 5.1 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1713 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648C LEU* 4.5 2.9 - - + -
1652C ILE* 3.4 20.6 - - + -
1684C LEU* 4.3 3.1 - - + -
1688C LEU* 4.5 12.6 - - + -
1709C GLU* 3.0 42.0 - - - +
1710C LEU* 3.6 5.4 + - - +
1711C ARG 3.4 0.8 - - - -
1712C ARG* 1.3 73.7 - - - +
1714C LEU* 1.3 69.9 + - - +
1716C GLN* 3.0 24.7 - - - +
1717C LEU* 3.0 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1714 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688C LEU* 4.4 15.9 - - + +
1700C THR* 5.7 2.7 - - - +
1710C LEU 4.1 5.9 + - - +
1711C ARG* 3.2 21.8 - - - +
1712C ARG 3.1 0.2 - - - -
1713C VAL* 1.3 79.5 - - - +
1715C GLU* 1.3 70.6 + - - +
1717C LEU 3.7 0.3 + - - -
1718C ILE* 3.1 5.0 - - - +
1728C GLU* 2.6 41.3 - - - +
1731C PRO* 3.5 34.3 - - + +
1732C GLY* 4.6 5.4 - - - -
1734C PRO* 3.6 39.3 - - + -
1743C MET* 5.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1715 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1711C ARG 2.6 25.8 - - - +
1712C ARG* 2.7 39.0 - - - +
1714C LEU* 1.3 85.7 - - - +
1716C GLN* 1.3 63.6 + - - +
1718C ILE* 3.1 17.9 - - - +
1734C PRO* 4.1 6.8 - - - +
1738C ASN 4.2 3.1 - - - +
1739C TYR* 3.0 35.9 - - + -
1743C MET* 4.5 17.6 - - + +
1746C PHE* 3.0 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1716 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1652C ILE* 2.9 16.6 - - - +
1653C LEU* 4.4 9.2 - - + +
1656C ASP* 3.3 21.2 - - - +
1709C GLU* 2.3 46.8 + - - +
1712C ARG* 2.9 28.7 + - + +
1713C VAL* 3.0 18.5 + - - +
1715C GLU* 1.3 80.1 - - - +
1717C LEU* 1.3 57.3 + - + +
1718C ILE 2.7 13.1 + - - -
1719C VAL* 3.7 14.4 + - - +
1746C PHE* 5.3 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1717 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1652C ILE* 3.3 30.5 - - + +
1655C ILE* 4.1 16.9 - - + +
1656C ASP* 3.1 32.2 - - - +
1681C ASP* 4.3 9.9 - - + +
1684C LEU* 3.5 35.0 - - + -
1685C ASP* 6.0 0.9 - - - +
1688C LEU* 5.6 2.2 - - + -
1713C VAL* 3.0 24.9 + - + +
1714C LEU 3.7 0.4 + - - -
1715C GLU 3.6 0.2 - - - -
1716C GLN* 1.3 71.3 - - - +
1718C ILE* 1.3 56.0 + - - +
1719C VAL 2.8 16.1 + - - +
1721C HIS* 4.3 9.7 - - - +
1728C GLU* 3.1 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1718 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1714C LEU 3.1 24.0 - - - +
1715C GLU* 3.1 9.6 - - - +
1716C GLN 2.7 2.8 + - - -
1717C LEU* 1.3 76.2 - - - +
1719C VAL* 1.3 62.2 + - - +
1720C ALA 3.2 2.9 + - - -
1721C HIS 4.0 11.8 + - - +
1725C GLN* 4.8 7.8 - - + +
1728C GLU* 3.1 25.6 - - + +
1729C PHE* 4.8 4.5 - - + -
1743C MET* 3.4 30.1 - - + -
1746C PHE* 3.4 39.0 - - + +
1750C LEU* 3.5 25.9 - - + +
1754C GLN* 4.8 1.7 + - - -
----------------------------------------------------------
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