Contacts of the helix formed by residues 1729 - 1747 (chain B) in PDB entry 4ASI
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 GLY1729 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1727B SER 3.8 0.8 - - - -
1728B PHE* 1.3 75.4 - - - +
1730B PRO* 1.3 71.4 - - - +
1732B GLU* 3.0 23.6 + - - -
1733B ASP* 2.8 33.4 + - - -
1760B ARG* 4.0 14.9 - - - -
1833B ASN* 3.3 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1729B GLY* 1.3 84.2 - - - +
1731B GLN* 1.3 68.5 + - + +
1732B GLU* 4.5 0.9 - - - +
1733B ASP* 3.4 11.5 + - + +
1734B LEU* 3.0 26.7 + - - +
1760B ARG* 5.3 1.3 - - - +
1827B GLU* 4.8 6.7 - - + +
1828B GLY* 3.6 19.7 - - - +
1832B GLU* 3.8 29.8 - - + +
1833B ASN* 3.2 16.1 - - - +
1836B GLY* 5.5 3.4 - - - -
1839B MET* 5.1 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1676B LEU* 3.7 23.6 - - - +
1680B GLY* 6.0 0.5 - - - -
1694B ILE* 3.8 31.7 - - + +
1729B GLY 3.3 0.4 - - - -
1730B PRO* 1.3 85.1 - - + +
1732B GLU* 1.3 71.1 + - - +
1734B LEU* 3.1 16.0 + - - +
1735B LEU 3.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1694B ILE* 3.7 12.5 - - + +
1695B GLY* 3.0 41.6 + - - +
1696B MET* 3.8 25.6 - - + +
1723B TYR* 4.0 2.6 - - - -
1727B SER 4.0 8.1 - - - +
1728B PHE* 4.3 6.7 - - - -
1729B GLY* 3.0 30.3 - - - +
1730B PRO* 4.5 0.3 - - - +
1731B GLN* 1.3 82.5 + - - +
1733B ASP* 1.3 64.3 + - - +
1735B LEU* 3.4 2.4 + - - +
1736B PHE* 3.2 21.8 + - - +
1760B ARG* 2.9 32.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1728B PHE* 3.2 34.1 - - - +
1729B GLY 2.8 30.2 + - - +
1730B PRO* 3.5 7.7 - - - +
1732B GLU* 1.3 78.2 - - - +
1734B LEU* 1.3 55.5 + - - +
1736B PHE* 3.5 0.7 + - - +
1737B LEU* 3.0 22.5 + - - +
1833B ASN* 3.8 7.4 - - - +
1836B GLY* 3.2 46.4 - - - +
1837B SER* 3.4 5.2 + - - -
1839B MET* 4.0 4.0 - - + -
1840B ILE* 3.1 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1676B LEU* 3.9 17.7 - - + -
1680B GLY* 4.3 13.7 - - - -
1730B PRO 3.0 16.4 + - - +
1731B GLN* 3.1 26.6 + - - +
1733B ASP* 1.3 75.8 - - - +
1735B LEU* 1.3 66.1 + - - +
1737B LEU* 3.1 10.6 + - + +
1738B ARG* 2.9 67.9 + - + +
1839B MET* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674B LEU 4.0 14.8 - - - +
1675B VAL* 4.7 0.4 - - - -
1676B LEU* 3.7 22.9 - - + +
1682B LEU* 3.5 29.6 - - + -
1694B ILE* 4.2 9.2 - - + -
1696B MET* 3.2 45.3 - - + +
1697B VAL* 3.7 12.3 - - - +
1698B ALA* 4.2 11.7 - - + +
1731B GLN 3.0 14.3 + - - +
1732B GLU 3.9 3.8 - - - +
1734B LEU* 1.3 74.9 - - - +
1736B PHE* 1.3 66.2 + - - +
1738B ARG* 3.1 2.1 + - - +
1739B ALA* 2.8 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1736 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1696B MET* 4.0 19.0 - - + +
1717B ILE* 3.7 34.0 - - + +
1732B GLU 3.2 10.6 + - - +
1733B ASP* 3.5 8.7 - - - +
1735B LEU* 1.3 79.9 - - - +
1737B LEU* 1.3 67.5 + - - +
1739B ALA* 3.4 1.4 + - - +
1740B SER* 3.0 23.1 + - - -
1750B ARG* 3.6 29.4 - - - -
1752B TYR* 3.9 29.8 - + - -
1840B ILE* 3.7 27.4 - - + -
1843B GLU* 5.1 1.6 - - + -
1844B SER* 3.5 20.9 - - - -
1868B LEU* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1737 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1733B ASP 3.0 14.9 + - - +
1734B LEU* 3.1 12.5 + - + +
1736B PHE* 1.3 80.2 - - - +
1738B ARG* 1.3 72.8 + - - +
1740B SER* 3.1 3.1 + - - -
1741B GLU* 2.9 55.1 + - + +
1839B MET* 3.6 39.7 - - + +
1840B ILE* 4.1 9.4 - - + -
1843B GLU* 3.8 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1738 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1676B LEU* 4.3 4.3 - - + -
1679B GLN 5.4 0.6 + - - -
1680B GLY* 2.9 23.8 + - - +
1681B GLN* 3.5 32.3 - - - +
1682B LEU* 3.3 33.7 - - + +
1734B LEU* 2.9 42.5 + - + +
1735B LEU* 3.8 2.9 - - - +
1737B LEU* 1.3 83.2 - - - +
1739B ALA* 1.3 65.6 + - - +
1741B GLU* 3.1 36.9 + - - +
1742B LEU* 3.1 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1739 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674B LEU* 5.1 1.1 - - + -
1682B LEU* 3.5 14.9 - - + +
1698B ALA* 3.9 17.7 - - + -
1715B ILE* 3.9 14.8 - - + +
1717B ILE* 3.8 26.9 - - + -
1735B LEU* 2.8 17.0 + - + +
1738B ARG* 1.3 75.6 - - - +
1740B SER* 1.3 63.4 + - - +
1742B LEU* 3.1 5.2 + - - +
1743B ALA* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1740 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1717B ILE* 4.2 0.8 - - - +
1736B PHE* 3.0 15.9 + - - -
1737B LEU 3.3 7.9 - - - -
1739B ALA* 1.3 75.3 - - - +
1741B GLU* 1.3 65.3 + - - +
1743B ALA* 3.0 5.9 + - - +
1744B ARG* 3.0 23.9 + - - +
1750B ARG* 3.1 43.8 + - - +
1843B GLU* 2.9 29.1 + - - +
1847B ALA* 4.0 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1741 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737B LEU* 2.9 42.5 + - + +
1738B ARG* 3.1 41.2 + - - +
1739B ALA 3.3 0.2 - - - -
1740B SER* 1.3 77.1 - - - +
1742B LEU* 1.3 57.0 + - - +
1744B ARG* 3.3 26.9 + - - +
1745B ALA* 2.9 27.3 + - - +
1843B GLU* 3.5 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1742 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674B LEU* 4.1 32.1 - - + -
1682B LEU* 4.1 13.5 - - + -
1684B HIS* 5.5 2.2 - - + -
1700B LYS* 5.4 5.2 - - + -
1715B ILE* 4.2 13.0 - - + -
1738B ARG 3.1 13.6 + - - +
1739B ALA 3.5 7.2 - - - +
1740B SER 3.1 0.2 - - - -
1741B GLU* 1.3 73.8 - - - +
1743B ALA* 1.3 67.7 + - - +
1745B ALA* 3.0 18.8 + - + +
1746B GLU* 3.1 40.3 + - + +
1748B ILE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1743 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1715B ILE* 3.8 23.5 - - + +
1739B ALA 3.0 12.4 + - - +
1740B SER* 3.3 10.1 - - - +
1742B LEU* 1.3 76.2 - - - +
1744B ARG* 1.3 57.2 + - - +
1746B GLU 3.3 0.5 + - - -
1747B GLY* 2.9 24.4 + - - -
1748B ILE* 3.1 23.6 + - - +
1750B ARG* 4.0 14.1 - - + -
1851B ILE* 3.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1744 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1740B SER 3.0 13.9 + - - +
1741B GLU* 3.6 23.3 + - - +
1743B ALA* 1.3 76.2 - - - +
1745B ALA* 1.3 63.3 + - - +
1747B GLY* 3.2 11.3 + - - -
1843B GLU* 2.8 38.7 + - - +
1846B LEU* 3.3 28.5 - - - +
1847B ALA* 3.9 19.5 - - + +
1850B GLU* 3.4 30.5 + - + +
1851B ILE* 3.8 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1745 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1741B GLU 2.9 14.2 + - - +
1742B LEU* 3.0 17.0 + - + +
1744B ARG* 1.3 79.5 - - - +
1746B GLU* 1.3 62.3 + - + +
1944B HIS* 5.0 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1700B LYS* 3.2 36.4 + - - +
1713B ASP* 4.7 2.4 - - - +
1742B LEU* 3.1 36.3 + - + +
1743B ALA 4.2 1.3 - - - +
1745B ALA* 1.3 79.3 - - + +
1747B GLY* 1.3 61.9 + - - +
1748B ILE* 3.4 28.4 + - + +
1942B SER* 4.3 1.9 - - - -
1944B HIS* 3.7 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1747 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1743B ALA 2.9 7.0 + - - -
1744B ARG 3.2 10.7 + - - -
1745B ALA 3.8 0.2 + - - -
1746B GLU* 1.3 78.8 - - - +
1748B ILE* 1.3 62.1 + - - +
1749B PRO* 4.8 0.2 - - - +
1851B ILE* 3.9 8.3 - - - +
1852B ILE 5.5 0.3 + - - -
1942B SER* 3.4 3.5 - - - -
1943B VAL* 3.0 52.6 + - - +
1944B HIS* 4.5 2.5 - - - -
----------------------------------------------------------
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