Contacts of the helix formed by residues 1704 - 1720 (chain D) in PDB entry 6X34
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 PRO1704 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1650D ILE 5.2 0.2 - - - +
1651D LEU 4.3 11.0 - - - +
1653D LEU* 5.3 4.3 - - + +
1654D SER* 5.2 18.6 - - - +
1660D GLN* 4.3 20.9 - - - +
1702D HIS 3.5 7.4 - - - +
1703D LEU* 1.3 104.3 - - + +
1705D GLY* 1.3 66.3 + - - +
1706D PRO* 3.6 1.8 - - + -
1707D LEU* 3.6 22.8 + - + +
1708D ARG* 3.1 21.0 + - - +
1832D GLY* 4.1 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1705 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1704D PRO* 1.3 71.2 - - - +
1706D PRO* 1.3 73.5 - - - +
1708D ARG* 3.2 4.8 + - - +
1709D ALA* 2.9 23.8 + - - +
1832D GLY* 3.6 14.8 + - - -
1837D PHE* 3.7 39.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1706 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1660D GLN* 4.0 26.7 - - + +
1664D SER* 3.9 28.4 + - - +
1667D LEU* 5.9 0.2 - - - +
1704D PRO* 3.9 1.1 - - + -
1705D GLY* 1.3 88.7 - - - +
1707D LEU* 1.3 60.9 + - + +
1709D ALA* 3.4 6.1 + - + +
1710D GLY* 2.9 26.5 + - - -
1832D GLY 5.4 0.7 - - - +
1837D PHE* 4.2 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1707 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1650D ILE* 4.3 15.3 - - + +
1653D LEU* 5.2 11.4 - - + -
1660D GLN* 4.5 27.8 - - + +
1663D HIS* 3.8 36.6 - - + +
1664D SER* 4.9 4.9 - - - +
1667D LEU* 5.2 3.7 - - + +
1703D LEU* 4.2 17.0 - - + -
1704D PRO* 3.6 33.5 + - + +
1705D GLY 3.3 0.8 - - - -
1706D PRO* 1.3 83.1 - - + +
1708D ARG* 1.3 58.7 + - - +
1710D GLY* 3.3 1.9 + - - -
1711D TYR* 2.9 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1708 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1697D ALA 4.1 4.8 + - - +
1698D LEU* 3.3 27.0 + - + -
1700D ASP 3.6 15.4 + - - -
1703D LEU* 4.0 23.0 - - + +
1704D PRO 3.1 19.2 + - - +
1705D GLY* 3.7 4.5 - - - +
1707D LEU* 1.3 75.7 - - - +
1709D ALA* 1.3 58.6 + - - +
1711D TYR* 3.3 3.6 + - + +
1712D TYR* 2.8 76.6 + - + -
1815D MET* 4.6 12.1 - - - +
1831D VAL* 4.8 19.1 - - - +
1837D PHE 4.1 16.8 + - - +
1838D GLN* 4.9 10.5 + - - +
1841D PRO* 4.7 6.8 - - + +
1842D VAL* 4.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1709 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1705D GLY 2.9 17.0 + - - +
1706D PRO* 3.7 7.9 - - + +
1708D ARG* 1.3 78.2 - - - +
1710D GLY* 1.3 56.2 + - - +
1712D TYR* 3.3 3.7 + - - +
1713D ASP* 2.9 29.6 + - - +
1837D PHE* 5.6 7.9 - - + +
1841D PRO* 4.3 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1710 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1667D LEU* 4.0 25.6 - - - -
1668D ARG* 6.4 0.2 - - - -
1706D PRO 2.9 16.2 + - - -
1707D LEU 3.8 1.3 - - - -
1709D ALA* 1.3 75.2 - - - +
1711D TYR* 1.3 57.5 + - - +
1713D ASP* 3.3 6.6 + - - +
1714D LEU* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1711 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635D THR* 4.0 20.1 - - + +
1650D ILE* 5.7 4.5 - - - +
1663D HIS* 3.4 21.5 + + - -
1667D LEU* 3.7 26.9 - - + -
1689D VAL* 5.7 12.8 - - + -
1694D LEU* 5.6 7.5 - - + +
1697D ALA* 3.6 32.5 - - + -
1698D LEU* 4.9 10.6 - - + +
1703D LEU* 3.6 24.2 - - + -
1707D LEU* 2.9 28.3 + - + +
1708D ARG* 3.7 5.4 - - - +
1710D GLY* 1.3 74.8 - - - +
1712D TYR* 1.3 58.3 + - - +
1714D LEU* 3.3 6.8 + - + +
1715D LEU* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1712 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698D LEU* 3.5 42.2 + - + +
1708D ARG* 2.8 74.2 + - + +
1709D ALA 3.7 4.3 - - - +
1711D TYR* 1.3 75.1 - - - +
1713D ASP* 1.3 58.3 + - - +
1715D LEU* 3.3 9.7 + - + +
1716D ILE* 2.9 37.7 + - + +
1815D MET* 4.5 8.1 - - - +
1841D PRO* 3.4 45.3 - - + -
1842D VAL* 4.0 9.2 - - - +
1845D LEU* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1713 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1671D ARG* 4.3 16.4 - - + +
1709D ALA 2.9 17.4 + - - +
1710D GLY* 3.6 7.6 - - - +
1712D TYR* 1.3 77.4 - - - +
1714D LEU* 1.3 57.1 + - - +
1716D ILE* 3.3 6.4 + - - +
1717D SER* 2.9 31.1 + - - -
1844D LYS* 6.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1714 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1667D LEU* 3.1 46.4 - - + +
1670D TYR* 3.7 33.4 - - + +
1671D ARG* 3.6 10.3 - - + +
1685D LEU* 5.7 6.5 - - + -
1689D VAL* 6.1 10.1 - - + -
1710D GLY* 2.9 27.4 + - - +
1711D TYR* 3.7 9.0 - - + +
1713D ASP* 1.3 74.5 - - - +
1715D LEU* 1.3 60.6 + - - +
1717D SER* 3.3 5.5 + - - +
1718D ILE* 2.9 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1715 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1694D LEU* 4.0 26.0 - - + -
1695D LEU* 5.3 3.6 - - + -
1698D LEU* 4.0 27.6 - - + -
1711D TYR 2.9 14.4 + - - +
1712D TYR* 3.5 17.9 - - + +
1714D LEU* 1.3 75.9 - - - +
1716D ILE* 1.3 65.8 + - + +
1718D ILE* 3.3 7.9 - - + +
1719D HIS* 2.9 60.6 + - + +
1720D LEU* 4.8 3.5 - - + +
1808D LEU* 4.2 23.1 - - + -
1845D LEU* 5.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1716 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1712D TYR* 2.9 24.6 + - + +
1713D ASP* 3.7 6.7 - - - +
1714D LEU 3.3 0.2 - - - -
1715D LEU* 1.3 81.6 - - + +
1717D SER* 1.3 58.3 + - - +
1720D LEU* 2.9 57.2 + - + +
1721D GLU* 3.7 0.8 - - - -
1844D LYS* 5.0 9.2 - - + +
1845D LEU* 4.5 17.5 - - + +
1848D THR* 3.8 37.0 - - + +
1849D LEU* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1717 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1670D TYR 4.9 0.2 + - - -
1671D ARG* 3.5 17.3 + - - -
1674D CYS* 2.3 43.5 + - - +
1675D ALA* 5.5 2.0 - - - -
1682D ALA* 5.4 2.9 - - - +
1713D ASP 2.9 16.0 + - - -
1714D LEU* 4.0 6.7 - - - +
1715D LEU 3.3 0.2 - - - -
1716D ILE* 1.3 78.4 - - - +
1718D ILE* 1.3 58.3 + - - +
1721D GLU* 3.2 24.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1718 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674D CYS* 5.5 2.9 - - + -
1682D ALA* 3.1 42.7 - - + +
1685D LEU* 4.6 7.4 - - + -
1686D CYS* 3.9 28.0 - - + +
1714D LEU* 2.9 23.5 + - + +
1715D LEU* 3.3 12.3 - - + +
1717D SER* 1.3 78.4 - - - +
1719D HIS* 1.3 89.8 + - + +
1721D GLU* 5.1 0.9 - - - -
1801D PRO* 3.8 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1719 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1686D CYS* 5.3 7.4 - - - -
1691D GLN* 4.5 11.7 - - + +
1694D LEU* 6.0 0.4 - - - +
1715D LEU* 2.9 39.0 + - + +
1718D ILE* 1.3 105.2 + - + +
1720D LEU* 1.3 76.7 + - + +
1721D GLU 3.7 1.3 - - - -
1723D ALA* 4.9 4.5 - - - +
1778D PHE* 4.7 15.8 - - - -
1800D SER* 5.6 2.6 + - - -
1801D PRO* 4.7 13.0 + - + +
1802D SER 3.7 12.4 + - - -
1803D ILE* 3.3 56.8 - - + +
1808D LEU* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1720 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1715D LEU* 4.8 5.2 - - + +
1716D ILE* 2.9 32.5 + - + +
1719D HIS* 1.3 95.3 - - + +
1721D GLU* 1.3 59.8 + - - +
1722D SER 3.8 0.4 - - - -
1723D ALA* 4.8 9.9 - - + -
1724D CYS* 3.3 24.2 - - + +
1803D ILE* 5.8 2.5 - - + -
1805D LEU* 6.3 3.1 - - + -
1848D THR* 3.7 27.3 - - + +
1849D LEU* 3.7 26.0 - - + -
1852D MET* 3.7 31.0 - - + -
1854D ILE* 6.1 0.9 - - + -
----------------------------------------------------------
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