Contacts of the helix formed by residues 1803 - 1821 (chain B) in PDB entry 3RYT
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 ASP1803 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1377A ARG* 5.7 5.0 - - - +
1689B GLN* 2.9 29.4 + - - +
1799B LEU 5.3 1.0 - - - +
1800B TYR* 3.1 31.4 + - + +
1802B LYS* 1.3 88.3 - - - +
1804B ILE* 1.3 66.7 + - - +
1805B PRO* 3.2 3.1 - - - -
1806B ASN* 2.9 21.5 + - + +
1807B TYR* 3.1 35.8 + - + -
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Residues in contact with ILE1804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1777B THR* 3.5 30.1 - - + +
1780B ASP* 4.2 26.7 - - + +
1781B SER* 3.2 25.8 - - - +
1787B HIS* 5.4 12.6 - - + -
1796B ASN 5.9 0.7 - - - +
1797B LYS* 5.8 4.9 - - - +
1800B TYR* 3.0 24.0 + - + +
1801B ALA* 5.0 2.9 - - - +
1803B ASP* 1.3 76.7 - - - +
1805B PRO* 1.3 70.7 - - + +
1807B TYR* 3.1 6.0 + - + +
1808B LYS* 2.8 25.5 + - + +
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Residues in contact with PRO1805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1801B ALA 3.9 11.4 - - - +
1802B LYS* 3.7 17.5 - - - +
1803B ASP 3.3 4.0 - - - -
1804B ILE* 1.3 97.3 - - + +
1806B ASN* 1.3 64.7 + - - +
1808B LYS* 3.3 7.9 + - + +
1809B SER* 3.1 21.3 + - - -
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Residues in contact with ASN1806 (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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1377A ARG* 3.4 25.8 - - - +
1378A SER* 4.1 18.7 + - - +
1802B LYS 4.0 14.1 - - - +
1803B ASP* 2.9 11.7 + - - +
1805B PRO* 1.3 77.2 - - - +
1807B TYR* 1.3 61.9 + - + +
1809B SER* 2.6 26.1 + - - +
1810B TRP* 3.0 32.6 + - + +
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Residues in contact with TYR1807 (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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1689B GLN* 4.5 6.9 + - - -
1692B VAL* 3.5 16.2 - - + +
1693B ASP* 3.0 25.1 + - - -
1696B PHE* 3.4 44.9 - + + -
1700B PHE* 5.2 7.2 - + + -
1777B THR* 4.7 11.2 - - + -
1781B SER* 3.3 30.4 - - - +
1800B TYR* 5.0 4.3 - + - -
1803B ASP* 3.1 43.2 + - + -
1804B ILE* 3.1 10.8 + - + +
1806B ASN* 1.3 78.1 - - + +
1808B LYS* 1.3 61.6 + - - +
1810B TRP* 3.6 25.0 + + - +
1811B VAL* 3.5 20.8 + - - +
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Residues in contact with LYS1808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1781B SER* 3.8 21.5 - - - +
1783B SER 5.8 2.5 - - - +
1804B ILE* 2.8 19.1 + - + +
1805B PRO* 3.5 9.4 - - + +
1807B TYR* 1.3 78.4 - - - +
1809B SER* 1.3 57.5 + - - +
1811B VAL* 3.0 20.0 - - - +
1812B GLU* 3.2 18.4 - - - +
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Residues in contact with SER1809 (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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1805B PRO 3.1 10.0 + - - -
1806B ASN* 2.6 30.7 + - - -
1808B LYS* 1.3 74.7 - - - +
1810B TRP* 1.3 70.6 + - - +
1811B VAL 3.2 1.6 - - - -
1812B GLU* 3.2 16.9 + - - +
1813B ARG* 3.2 21.5 + - - +
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Residues in contact with TRP1810 (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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1377A ARG 5.5 2.9 - - - -
1378A SER 3.5 24.0 + - - -
1379A PHE* 5.0 0.4 - - - +
1380A SER* 3.7 33.1 + - - +
1382A ARG* 5.3 1.6 + - - -
1383A ASP* 5.9 0.2 + - - -
1693B ASP* 3.7 25.4 - - + -
1696B PHE* 3.3 46.2 - - + -
1697B GLU* 3.6 11.0 - - + -
1700B PHE* 4.3 15.6 - + + +
1806B ASN* 3.0 33.2 + - + +
1807B TYR* 3.8 21.3 - + - +
1808B LYS 3.5 0.4 - - - -
1809B SER* 1.3 83.4 + - - +
1811B VAL* 1.3 57.8 + - - +
1813B ARG* 3.4 5.4 + - - +
1814B TYR* 2.9 27.9 + - - +
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Residues in contact with VAL1811 (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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1700B PHE* 3.6 33.6 - - + -
1736B HIS* 3.6 18.6 - - + +
1740B SER* 5.0 2.0 - - - +
1781B SER 4.0 13.7 - - - +
1782B CYS* 5.2 5.8 - - - -
1807B TYR 3.5 8.1 + - - +
1808B LYS* 3.0 26.0 - - + +
1810B TRP* 1.3 76.2 - - - +
1812B GLU* 1.3 65.9 + - - +
1814B TYR* 3.6 5.5 - - - +
1815B TYR* 3.0 59.9 + - + +
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Residues in contact with GLU1812 (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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1736B HIS* 4.7 11.7 - - + +
1808B LYS* 3.2 20.6 - - - +
1809B SER* 3.2 14.8 + - - +
1811B VAL* 1.3 85.5 - - + +
1813B ARG* 1.3 57.5 + - - +
1815B TYR* 3.2 10.7 + - - +
1816B ALA* 2.9 28.3 + - - +
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Residues in contact with ARG1813 (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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1382A ARG* 3.3 35.1 - - - +
1383A ASP* 3.5 29.3 + - - -
1809B SER 3.2 8.7 + - - +
1810B TRP* 3.8 8.3 - - - +
1812B GLU* 1.3 79.8 - - - +
1814B TYR* 1.3 56.9 - - - +
1816B ALA* 3.8 6.2 - - + +
1817B ASP* 2.9 43.5 + - - +
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Residues in contact with TYR1814 (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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1382A ARG* 4.8 1.8 - - - +
1699B ILE* 3.6 19.3 + - + -
1700B PHE* 3.3 54.5 - + + +
1701B SER 3.9 16.2 - - - -
1702B THR* 4.4 4.3 - - - -
1709B LEU* 3.7 9.4 - - + +
1713B ILE* 3.4 30.5 - - - +
1717B PHE* 5.0 4.7 - + - -
1743B LEU* 4.5 5.7 - - + +
1744B PRO* 6.1 2.7 - - + -
1748B TRP* 5.7 0.9 + - - -
1810B TRP 2.9 19.0 + - - +
1811B VAL* 3.6 4.9 - - - +
1812B GLU 3.2 0.2 - - - -
1813B ARG* 1.3 76.0 - - - +
1815B TYR* 1.3 77.3 + + - +
1817B ASP* 3.9 6.5 + - - +
1818B ILE* 2.9 49.8 + - + +
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Residues in contact with TYR1815 (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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1717B PHE* 3.3 40.6 - + + -
1736B HIS* 3.4 39.9 - + - -
1739B LYS* 3.7 9.0 - - + -
1740B SER* 2.8 33.3 + - - -
1744B PRO* 3.8 10.2 - - + +
1811B VAL* 3.0 45.3 + - + +
1812B GLU* 3.4 6.5 - - - +
1814B TYR* 1.3 85.6 - + - +
1816B ALA* 1.3 66.8 + - - +
1818B ILE* 2.9 18.4 + - - +
1819B ALA* 3.2 11.0 + - - +
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Residues in contact with ALA1816 (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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1812B GLU 2.9 16.3 + - - +
1813B ARG* 3.8 9.0 - - + +
1815B TYR* 1.3 75.8 - - - +
1817B ASP* 1.3 59.5 + - - +
1819B ALA* 2.8 24.4 + - - +
1820B LYS* 3.0 34.8 + - - +
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Residues in contact with ASP1817 (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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1382A ARG* 2.7 39.7 + - - -
1702B THR* 4.5 21.7 - - - -
1813B ARG* 2.9 29.1 + - - +
1814B TYR* 3.9 6.3 - - - +
1815B TYR 3.2 0.2 - - - -
1816B ALA* 1.3 78.9 - - - +
1818B ILE* 1.3 58.8 + - + +
1820B LYS* 3.2 12.3 + - - +
1821B MET* 3.1 33.7 + - + +
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Residues in contact with ILE1818 (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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1702B THR* 5.8 1.6 - - - -
1709B LEU* 3.7 24.9 - - + -
1713B ILE* 3.8 17.3 - - + -
1714B LYS* 4.1 14.9 - - + +
1717B PHE* 4.0 35.7 - - + -
1718B ASP* 4.0 12.2 - - - +
1721B ASP* 5.6 0.4 - - - -
1814B TYR* 2.9 50.7 - - + +
1815B TYR* 2.9 8.9 + - - +
1817B ASP* 1.3 77.4 - - + +
1819B ALA* 1.3 59.0 + - - +
1820B LYS 3.4 0.2 - - - -
1821B MET* 4.0 18.5 + - - +
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Residues in contact with ALA1819 (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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1718B ASP* 5.1 3.0 - - - +
1721B ASP* 4.3 18.2 - - - +
1815B TYR 3.2 8.4 + - - +
1816B ALA* 2.8 13.9 + - - +
1818B ILE* 1.3 77.2 - - - +
1820B LYS* 1.3 65.2 - - + +
1821B MET 3.5 4.6 - - - +
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Residues in contact with LYS1820 (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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1816B ALA* 3.0 41.1 + - - +
1817B ASP* 3.2 12.9 + - - +
1819B ALA* 1.3 81.3 - - + +
1821B MET* 1.3 66.8 + - - +
1822B PRO* 3.6 2.8 - - - +
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Residues in contact with MET1821 (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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1702B THR* 3.4 41.3 - - - +
1703B ALA* 5.9 0.9 - - + -
1708B ALA* 6.5 0.4 - - + -
1709B LEU* 3.9 28.7 - - + -
1714B LYS* 5.6 5.6 - - + -
1718B ASP* 5.3 3.5 - - - +
1817B ASP* 3.1 23.0 + - + +
1818B ILE* 4.2 12.0 - - + +
1819B ALA 3.5 6.7 - - - +
1820B LYS* 1.3 80.3 - - - +
1822B PRO* 1.3 78.1 - - + +
1823B ALA* 3.7 1.7 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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