Contacts of the helix formed by residues 1764 - 1783 (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 ASN1764 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1467B LYS* 3.2 30.3 + - - +
1471B GLU* 5.5 0.7 - - - +
1475B ILE* 6.0 0.2 - - - +
1762B HIS* 3.2 27.3 + - + +
1763B LYS* 1.3 78.0 - - - +
1765B SER* 1.3 72.6 + - - +
1766B ILE* 3.3 25.3 - - - +
1767B THR* 2.8 33.1 + - - -
1768B ASP* 3.6 6.2 + - - +
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Residues in contact with SER1765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1480B GLY* 4.0 22.0 + - - -
1764B ASN* 1.3 80.8 - - - +
1766B ILE* 1.3 66.6 + - - +
1767B THR 2.9 2.0 + - - -
1768B ASP* 3.1 4.2 + - - +
1769B ALA* 3.1 19.2 + - - +
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Residues in contact with ILE1766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467B LYS* 6.1 0.7 - - - -
1470B MET* 3.6 44.1 - - + +
1475B ILE* 4.4 15.3 - - + -
1480B GLY 3.5 23.3 - - - +
1482B ALA* 4.3 9.0 - - + -
1485B SER* 3.8 25.1 - - - +
1490B LYS* 3.9 9.6 - - + +
1764B ASN* 3.3 15.0 - - - +
1765B SER* 1.3 79.4 + - - +
1767B THR* 1.3 65.6 + - - +
1769B ALA* 3.1 15.6 + - + +
1770B CYS* 3.1 24.6 + - - -
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Residues in contact with THR1767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1463B TYR* 3.8 24.5 - - + +
1466B ILE* 4.9 13.8 - - + +
1467B LYS* 4.6 11.8 - - - +
1763B LYS* 3.4 22.2 - - + -
1764B ASN* 2.8 37.1 + - - -
1765B SER 2.9 1.6 + - - -
1766B ILE* 1.3 83.5 - - - +
1768B ASP* 1.3 57.7 + - - -
1769B ALA 3.2 0.2 + - - -
1770B CYS* 3.3 1.9 + - - +
1771B LEU* 3.0 46.6 + - + +
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Residues in contact with ASP1768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1753B LYS* 2.9 26.7 - - - +
1754B ASN* 4.4 1.1 - - - +
1763B LYS* 3.3 33.4 + - - -
1764B ASN 3.6 3.9 + - - +
1765B SER 3.1 7.7 + - - +
1767B THR* 1.3 78.0 - - - +
1769B ALA* 1.3 59.4 + - - +
1770B CYS 3.3 0.2 - - - -
1771B LEU* 4.1 6.3 - - - +
1772B SER* 2.8 35.9 + - - -
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Residues in contact with ALA1769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1480B GLY 5.6 0.2 - - - +
1487B SER* 3.2 20.8 + - - -
1490B LYS* 4.3 14.4 - - + -
1765B SER* 3.1 15.0 + - - +
1766B ILE* 3.2 29.8 - - + +
1767B THR 3.0 0.2 - - - -
1768B ASP* 1.3 80.1 - - - +
1770B CYS* 1.3 57.3 + - - +
1772B SER* 4.3 6.7 - - - -
1773B VAL* 4.1 2.9 - - - +
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Residues in contact with CYS1770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1466B ILE* 4.2 15.3 - - + -
1470B MET* 4.2 10.5 - - - -
1485B SER* 4.1 3.6 - - - -
1486B LEU* 3.3 43.2 - - + +
1487B SER 4.0 2.9 - - - -
1766B ILE* 3.1 32.5 + - - +
1767B THR 4.1 1.8 - - - +
1769B ALA* 1.3 79.8 - - - +
1771B LEU* 1.3 57.1 + - - +
1772B SER 2.9 2.2 - - - -
1773B VAL* 2.7 39.2 + - - +
1774B VAL* 3.4 6.8 + - - +
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Residues in contact with LEU1771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462B LEU* 4.5 26.7 - - + -
1463B TYR* 4.9 6.3 - - + -
1466B ILE* 4.8 12.6 - - + -
1752B ILE* 3.5 30.3 - - + +
1753B LYS* 4.5 2.9 - - - +
1755B PRO* 3.7 26.9 - - + -
1763B LYS* 4.3 4.0 - - + -
1767B THR* 3.0 40.2 + - + +
1768B ASP* 4.3 8.3 - - - +
1770B CYS* 1.3 76.4 - - - +
1772B SER* 1.3 56.4 + - - +
1774B VAL* 3.2 12.5 + - + +
1775B ALA* 2.8 31.2 + - - +
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Residues in contact with SER1772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1753B LYS* 5.4 3.8 - - - +
1768B ASP* 2.8 30.2 + - - -
1769B ALA* 4.3 7.4 - - - -
1770B CYS 2.9 0.4 - - - -
1771B LEU* 1.3 79.3 - - - +
1773B VAL* 1.3 63.1 + - - +
1775B ALA* 3.7 7.5 - - - +
1776B GLN* 2.9 26.5 + - - +
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Residues in contact with VAL1773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1486B LEU* 4.2 20.6 - - + +
1487B SER* 3.6 42.8 - - - +
1769B ALA 4.1 2.0 - - - +
1770B CYS* 2.7 20.4 + - - +
1772B SER* 1.3 73.3 - - - +
1774B VAL* 1.3 57.6 + - - +
1776B GLN* 3.5 4.4 + - - +
1777B THR* 3.1 25.9 + - - -
1796B ASN* 3.6 30.3 - - + +
1799B LEU* 5.2 3.1 - - + -
1800B TYR* 4.3 13.5 - - + -
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Residues in contact with VAL1774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1462B LEU* 4.8 13.7 - - + -
1466B ILE* 6.1 3.1 - - + -
1486B LEU* 4.2 18.4 - - + -
1692B VAL* 4.9 14.8 - - + -
1696B PHE* 3.9 28.0 - - + -
1752B ILE* 4.1 16.2 - - + -
1770B CYS 3.4 9.6 + - - +
1771B LEU* 3.2 16.9 + - + +
1773B VAL* 1.3 74.4 - - - +
1775B ALA* 1.3 60.0 + - - +
1777B THR* 3.0 9.6 + - - -
1778B PHE* 2.9 27.7 + - - +
1800B TYR* 4.8 7.2 - - + +
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Residues in contact with ALA1775 (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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1749B VAL* 3.4 31.4 - - + +
1752B ILE* 4.4 11.0 - - + +
1753B LYS* 4.2 15.3 - - + -
1771B LEU 2.8 19.1 + - - +
1772B SER* 3.7 6.5 - - - +
1774B VAL* 1.3 73.6 - - - +
1776B GLN* 1.3 60.8 + - - +
1778B PHE* 3.4 5.4 + - - +
1779B MET* 3.1 27.9 + - - +
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Residues in contact with GLN1776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772B SER 2.9 17.5 + - - +
1773B VAL* 3.8 4.9 - - - +
1775B ALA* 1.3 74.8 - - - +
1777B THR* 1.3 63.3 + - - +
1779B MET* 3.2 27.9 + - - +
1780B ASP* 3.0 48.5 + - - +
1796B ASN* 3.4 29.2 - - - +
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Residues in contact with THR1777 (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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1692B VAL* 6.3 1.1 - - + -
1696B PHE* 4.8 7.4 - - + -
1773B VAL 3.1 14.2 + - - -
1774B VAL* 3.0 11.8 + - - -
1776B GLN* 1.3 77.3 - - - +
1778B PHE* 1.3 61.4 + - - +
1780B ASP* 3.4 8.1 + - - -
1781B SER* 2.8 29.6 + - - +
1796B ASN* 3.9 9.3 + - - +
1800B TYR* 3.3 40.6 - - + -
1804B ILE* 3.5 22.4 - - + +
1807B TYR* 4.7 10.5 - - + -
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Residues in contact with PHE1778 (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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1696B PHE* 3.8 30.0 - + + -
1699B ILE* 4.0 22.2 - - + -
1700B PHE* 4.0 25.8 - + - -
1744B PRO* 3.2 46.2 - - + -
1745B LEU* 5.0 0.4 - - + -
1748B TRP* 3.8 17.3 - + + -
1749B VAL* 4.2 12.6 - - + -
1752B ILE* 3.7 18.2 - - + -
1774B VAL 2.9 12.4 + - - +
1775B ALA* 3.4 12.3 - - - +
1776B GLN 3.2 0.2 - - - -
1777B THR* 1.3 77.8 - - - +
1779B MET* 1.3 63.9 + - - +
1781B SER* 3.3 11.9 + - - -
1782B CYS* 3.4 19.4 + - - -
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Residues in contact with MET1779 (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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1430B ARG* 3.2 26.7 - - - +
1745B LEU* 3.7 22.1 - - + +
1749B VAL* 3.6 23.8 - - + -
1775B ALA* 3.1 15.3 + - - +
1776B GLN* 3.2 30.7 + - - +
1778B PHE* 1.3 77.2 - - - +
1780B ASP* 1.3 65.9 + - - +
1782B CYS* 3.2 12.8 + - - +
1783B SER* 3.2 14.0 + - - -
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Residues in contact with ASP1780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1776B GLN* 3.0 38.1 + - - +
1777B THR* 3.8 7.3 - - - +
1778B PHE 3.3 0.2 - - - -
1779B MET* 1.3 78.3 - - - +
1781B SER* 1.3 60.9 + - - +
1783B SER* 3.7 20.6 + - - +
1785B SER 5.0 2.6 - - - +
1796B ASN* 3.4 21.3 + - - -
1797B LYS* 4.7 8.8 - - - +
1804B ILE* 4.2 21.9 - - + +
1808B LYS* 5.9 0.2 - - - +
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Residues in contact with SER1781 (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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1696B PHE* 5.1 2.3 - - - -
1700B PHE* 6.2 4.0 - - - -
1736B HIS* 5.0 0.9 - - - -
1777B THR 2.8 15.0 + - - -
1778B PHE* 3.7 10.4 - - - -
1779B MET 3.1 0.6 - - - -
1780B ASP* 1.3 75.8 - - - +
1782B CYS* 1.3 63.8 + - - +
1783B SER 4.2 2.6 - - - +
1804B ILE* 3.2 22.9 - - - +
1807B TYR* 3.3 35.0 - - - +
1808B LYS* 3.8 22.1 - - - +
1811B VAL* 4.0 9.0 - - - +
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Residues in contact with CYS1782 (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* 4.6 11.7 - - - -
1736B HIS* 3.0 28.0 + - - -
1737B THR* 5.5 0.7 - - - -
1740B SER* 3.2 27.6 + - - +
1744B PRO* 3.5 32.1 - - - -
1745B LEU* 4.1 11.7 - - + -
1778B PHE* 3.4 27.6 - - - -
1779B MET 3.2 7.7 + - - +
1781B SER* 1.3 77.3 - - - +
1783B SER* 1.3 60.8 + - - +
1784B THR 3.4 0.5 + - - -
1811B VAL* 5.1 6.7 - - - -
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Residues in contact with SER1783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1736B HIS* 4.6 1.0 - - - -
1737B THR* 6.5 1.3 - - - -
1740B SER* 5.8 0.2 - - - -
1745B LEU* 5.7 2.9 - - - +
1779B MET 3.2 15.3 + - - -
1780B ASP* 3.8 16.6 - - - +
1781B SER 3.3 4.2 - - - +
1782B CYS* 1.3 77.9 - - - +
1784B THR* 1.3 62.4 + - - +
1785B SER* 3.0 34.1 + - - +
1808B LYS* 5.8 2.4 - - - +
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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