Contacts of the helix formed by residues 1704 - 1720 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650B ILE 5.2 0.2 - - - +
1651B LEU 4.3 10.3 - - - +
1653B LEU* 5.3 4.3 - - + +
1654B SER* 5.2 18.2 - - - +
1660B GLN* 4.3 21.3 - - - +
1702B HIS 3.5 6.5 - - - +
1703B LEU* 1.3 104.2 - - + +
1705B GLY* 1.3 66.0 + - - +
1706B PRO* 4.4 2.0 - - + -
1707B LEU* 3.6 22.6 + - + +
1708B ARG* 3.1 22.1 + - - +
1832B GLY* 4.2 6.3 - - - +
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Residues in contact with GLY1705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1704B PRO* 1.3 71.3 - - - +
1706B PRO* 1.3 72.6 - - - +
1708B ARG* 3.2 5.2 + - - +
1709B ALA* 2.9 24.2 + - - +
1832B GLY* 3.6 14.5 + - - -
1837B PHE* 3.7 39.0 - - - +
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Residues in contact with PRO1706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660B GLN* 4.0 25.8 - - + +
1664B SER* 3.9 27.8 + - - +
1704B PRO* 3.9 1.3 - - + -
1705B GLY* 1.3 88.7 - - - +
1707B LEU* 1.3 59.9 + - + +
1709B ALA* 3.4 6.4 + - + +
1710B GLY* 2.9 26.7 + - - -
1832B GLY 5.4 0.2 - - - +
1837B PHE* 4.2 22.0 - - + -
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Residues in contact with LEU1707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650B ILE* 4.3 14.6 - - + +
1653B LEU* 5.2 11.2 - - + -
1660B GLN* 4.5 28.3 - - + +
1663B HIS* 3.8 34.8 - - + +
1664B SER* 4.9 5.2 - - - +
1667B LEU* 5.2 4.5 - - + +
1703B LEU* 4.2 16.4 - - + -
1704B PRO* 3.6 32.9 + - + +
1705B GLY 3.3 0.6 - - - -
1706B PRO* 1.3 83.3 - - + +
1708B ARG* 1.3 59.5 + - - +
1710B GLY* 3.3 1.7 + - - -
1711B TYR* 2.9 42.4 + - + +
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Residues in contact with ARG1708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1697B ALA 4.1 5.0 + - - +
1698B LEU* 3.3 26.2 + - + -
1700B ASP 3.6 15.6 + - - -
1703B LEU* 4.0 23.2 - - + +
1704B PRO 3.1 18.4 + - - +
1705B GLY* 3.7 4.3 - - - +
1707B LEU* 1.3 76.0 - - - +
1709B ALA* 1.3 57.6 + - - +
1711B TYR* 3.3 3.2 + - + +
1712B TYR* 2.8 77.6 + - + -
1815B MET* 4.6 11.9 - - - +
1831B VAL* 4.8 19.1 - - - +
1837B PHE 4.1 16.5 + - - +
1838B GLN* 4.9 10.7 + - - +
1841B PRO* 4.7 6.5 - - + +
1842B VAL* 4.7 7.5 - - - +
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Residues in contact with ALA1709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1705B GLY 2.9 17.8 + - - +
1706B PRO* 3.7 7.2 - - + +
1708B ARG* 1.3 77.7 - - - +
1710B GLY* 1.3 56.2 + - - +
1712B TYR* 3.3 3.4 + - - +
1713B ASP* 2.9 29.1 + - - +
1837B PHE* 5.6 7.9 - - + +
1841B PRO* 4.3 19.5 - - + +
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Residues in contact with GLY1710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1667B LEU* 4.0 24.5 - - - -
1668B ARG* 6.4 0.2 - - - -
1706B PRO 2.9 16.6 + - - -
1707B LEU 3.8 1.6 - - - -
1709B ALA* 1.3 76.7 - - - +
1711B TYR* 1.3 56.5 + - - +
1713B ASP* 3.3 5.6 + - - +
1714B LEU* 2.9 35.3 + - - +
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Residues in contact with TYR1711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635B THR* 4.0 19.5 - - + +
1650B ILE* 5.7 4.5 - - - +
1663B HIS* 3.4 21.4 + + - -
1667B LEU* 3.7 26.7 - - + -
1689B VAL* 5.7 13.2 - - + -
1694B LEU* 5.6 6.9 - - - +
1697B ALA* 3.6 33.0 - - + -
1698B LEU* 4.9 10.2 - - + +
1703B LEU* 3.6 23.8 - - + -
1707B LEU* 2.9 27.9 + - + +
1708B ARG* 3.7 4.9 - - - +
1709B ALA 3.3 0.2 - - - -
1710B GLY* 1.3 76.3 - - - +
1712B TYR* 1.3 58.3 + - - +
1714B LEU* 3.3 6.6 + - + +
1715B LEU* 2.9 28.6 + - - +
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Residues in contact with TYR1712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1698B LEU* 3.5 42.0 + - + +
1708B ARG* 2.8 74.3 + - + +
1709B ALA* 3.7 4.5 - - - +
1711B TYR* 1.3 76.0 - - - +
1713B ASP* 1.3 57.6 + - - +
1715B LEU* 3.3 10.6 + - + +
1716B ILE* 2.9 38.4 + - + +
1815B MET* 4.5 7.8 - - - +
1841B PRO* 3.4 46.0 - - + -
1842B VAL* 4.0 9.2 - - - +
1845B LEU* 3.8 19.7 - - + -
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Residues in contact with ASP1713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1671B ARG* 4.3 15.8 - - + +
1709B ALA 2.9 17.9 + - - +
1710B GLY* 3.6 7.9 - - - +
1712B TYR* 1.3 76.8 - - - +
1714B LEU* 1.3 57.5 + - - +
1716B ILE* 3.3 7.4 + - - +
1717B SER* 2.9 30.9 + - - -
1844B LYS* 6.0 4.9 - - - +
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Residues in contact with LEU1714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1667B LEU* 3.1 45.1 - - + +
1670B TYR* 3.7 33.9 - - + +
1671B ARG* 3.6 11.4 - - + +
1685B LEU* 5.7 7.2 - - + -
1689B VAL* 6.1 10.8 - - + -
1710B GLY 2.9 26.3 + - - +
1711B TYR* 3.7 8.5 - - + +
1713B ASP* 1.3 74.5 - - - +
1715B LEU* 1.3 59.6 + - - +
1717B SER* 3.3 4.9 + - - +
1718B ILE* 2.9 38.7 + - + +
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Residues in contact with LEU1715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1694B LEU* 4.0 26.9 - - + -
1695B LEU* 5.3 4.5 - - + -
1698B LEU* 4.0 28.0 - - + -
1711B TYR 2.9 15.3 + - - +
1712B TYR* 3.5 16.8 - - + +
1714B LEU* 1.3 74.6 - - - +
1716B ILE* 1.3 64.8 + - + +
1718B ILE* 3.3 6.8 - - + +
1719B HIS* 2.9 61.7 + - + +
1720B LEU* 4.8 3.5 - - + +
1808B LEU* 4.2 22.0 - - + -
1845B LEU* 5.5 5.6 - - + -
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Residues in contact with ILE1716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1712B TYR* 2.9 24.6 + - + +
1713B ASP* 3.7 6.7 - - - +
1715B LEU* 1.3 81.6 - - + +
1717B SER* 1.3 59.3 + - - +
1720B LEU* 2.9 56.1 + - + +
1721B GLU* 5.5 1.1 - - - -
1844B LYS* 5.8 9.0 - - + -
1845B LEU* 4.5 17.3 - - + +
1848B THR* 3.8 37.7 - - + +
1849B LEU* 6.0 0.7 - - + -
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Residues in contact with SER1717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1670B TYR 4.9 0.5 + - - -
1671B ARG* 3.5 18.0 + - - -
1674B CYS* 2.3 42.3 + - - +
1675B ALA* 5.5 2.0 - - - -
1682B ALA* 5.4 3.1 - - - +
1713B ASP 2.9 19.0 + - - -
1714B LEU* 4.0 6.3 - - - +
1716B ILE* 1.3 77.0 - - - +
1718B ILE* 1.3 60.4 + - - +
1721B GLU* 3.2 24.0 - - - +
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Residues in contact with ILE1718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1674B CYS* 5.5 2.9 - - + -
1682B ALA* 3.1 42.5 - - + +
1685B LEU* 4.6 7.0 - - + -
1686B CYS* 3.9 28.0 - - + +
1714B LEU* 2.9 23.4 + - + +
1715B LEU* 3.3 13.0 - - + +
1717B SER* 1.3 80.4 - - - +
1719B HIS* 1.3 89.7 + - + +
1721B GLU* 5.1 0.9 - - - -
1801B PRO* 3.8 25.1 - - + +
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Residues in contact with HIS1719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1686B CYS* 5.3 6.5 - - - -
1691B GLN* 4.5 12.2 - - + +
1694B LEU* 6.0 0.6 - - - +
1715B LEU* 2.9 39.5 + - + +
1718B ILE* 1.3 104.3 + - + +
1720B LEU* 1.3 76.3 + - + +
1721B GLU 3.7 1.3 - - - -
1723B ALA* 4.9 4.7 - - - +
1778B PHE* 4.7 15.6 - - - -
1800B SER* 5.6 2.6 + - - -
1801B PRO* 4.7 11.4 + - + +
1802B SER 3.7 12.8 + - - -
1803B ILE* 3.3 55.9 - - + +
1808B LEU* 5.8 1.1 - - + -
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Residues in contact with LEU1720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1715B LEU* 4.8 5.4 - - + +
1716B ILE* 2.9 32.2 + - + +
1719B HIS* 1.3 96.2 - - + +
1721B GLU* 1.3 59.4 + - - +
1722B SER 3.8 0.2 - - - -
1723B ALA* 4.5 9.9 - - + -
1724B CYS* 3.3 25.0 - - + +
1803B ILE* 5.8 2.7 - - + -
1805B LEU* 6.3 3.6 - - + -
1848B THR* 3.7 27.3 - - + +
1849B LEU* 3.7 24.9 - - + -
1852B MET* 3.7 32.1 - - + -
1854B ILE* 6.1 1.1 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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