Contacts of the helix formed by residues 1823 - 1841 (chain I) in PDB entry 2VKZ
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 SER1823 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1494I PRO* 3.7 31.2 - - - +
1495I THR* 4.3 4.2 - - - +
1693I ARG* 3.6 4.5 + - - -
1816I ALA* 5.9 0.2 - - - +
1822I MET* 1.3 78.1 - - - +
1824I ILE* 1.3 67.9 + - - +
1825I GLU* 2.9 29.3 + - - +
1826I SER* 3.8 19.3 + - - -
1827I LEU* 3.1 20.3 + - - +
2000I ASN* 5.8 0.4 - - - +
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Residues in contact with ILE1824 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494I PRO 4.6 1.0 + - - +
1496I LYS* 4.2 7.2 - - - +
1690I VAL* 3.4 42.6 - - + +
1693I ARG* 3.6 36.5 - - + +
1694I ALA* 4.1 16.4 - - + +
1783I LEU* 4.3 7.2 - - + -
1786I LYS* 3.4 44.6 - - + +
1822I MET 3.8 0.2 + - - -
1823I SER* 1.3 75.2 + - - +
1825I GLU* 1.3 60.8 + - - +
1827I LEU* 3.4 9.8 - - + +
1828I VAL* 3.3 22.2 + - - +
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Residues in contact with GLU1825 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1494I PRO* 5.3 0.4 - - + +
1693I ARG* 2.6 76.0 + - - +
1694I ALA* 5.5 0.7 - - - +
1697I HIS* 3.8 30.2 - - + +
1823I SER* 2.9 12.6 - - - +
1824I ILE* 1.3 71.9 - - - +
1826I SER* 1.3 64.4 + - - +
1827I LEU 3.0 1.8 - - - -
1828I VAL* 3.1 11.9 - - - +
1829I GLU* 3.0 26.7 + - - +
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Residues in contact with SER1826 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1822I MET* 3.8 13.9 - - - -
1823I SER* 3.3 29.3 + - - -
1825I GLU* 1.3 77.8 - - - +
1827I LEU* 1.3 57.3 + - - +
1829I GLU* 3.4 6.4 - - - +
1830I VAL* 2.9 35.3 + - - +
1995I ASN* 3.6 32.4 + - - +
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Residues in contact with LEU1827 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1782I THR* 3.2 37.0 - - + +
1783I LEU* 6.0 2.2 - - + -
1786I LYS* 4.4 19.7 - - + -
1812I TYR* 3.8 28.0 - - + +
1813I ALA* 4.7 0.4 - - - -
1816I ALA* 3.5 22.7 - - + -
1822I MET* 3.5 23.3 - - + -
1823I SER 3.1 11.8 + - - +
1824I ILE* 3.4 14.4 - - + +
1825I GLU 3.0 0.8 - - - -
1826I SER* 1.3 73.5 - - - +
1828I VAL* 1.3 71.2 + - + +
1829I GLU 2.9 1.8 + - - -
1830I VAL* 3.2 2.9 + - + +
1831I VAL* 2.8 28.0 + - + +
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Residues in contact with VAL1828 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1694I ALA* 3.7 13.5 - - + -
1697I HIS* 4.1 13.7 - - - +
1698I PHE* 3.5 27.1 - - + -
1779I PRO* 4.8 4.0 - - + +
1782I THR* 5.9 1.1 - - - -
1783I LEU* 3.6 39.3 - - + +
1824I ILE 3.3 13.7 + - - +
1825I GLU* 3.1 21.1 - - - +
1827I LEU* 1.3 79.4 - - + +
1829I GLU* 1.3 56.5 + - - +
1831I VAL* 4.2 7.8 - - - +
1832I PHE* 2.9 31.5 + - - +
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Residues in contact with GLU1829 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1697I HIS* 3.0 39.8 + - + +
1698I PHE* 5.4 1.6 - - + -
1701I THR* 4.2 2.8 + - - -
1702I TYR* 3.2 35.6 + - - -
1825I GLU 3.0 14.1 + - - +
1826I SER* 3.4 8.5 - - - +
1827I LEU 2.9 0.4 - - - -
1828I VAL* 1.3 76.0 - - + +
1830I VAL* 1.3 68.9 + - + +
1832I PHE* 3.0 15.3 + - - +
1833I TYR* 3.0 13.9 + - - +
1991I PHE* 4.3 13.5 - - + -
1995I ASN* 4.9 11.9 - - - +
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Residues in contact with VAL1830 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1812I TYR* 4.1 23.6 - - + -
1822I MET* 4.4 12.3 - - + -
1826I SER 2.9 18.5 + - - +
1827I LEU* 3.7 4.5 - - + +
1829I GLU* 1.3 80.0 - - - +
1831I VAL* 1.3 61.4 + - + +
1833I TYR* 3.1 2.4 + - - +
1834I ARG* 2.9 27.3 + - + +
1988I PHE* 4.4 8.0 - - + -
1991I PHE* 3.7 14.0 - - + -
1992I LEU* 3.5 30.5 - - + -
1995I ASN* 3.7 28.9 - - + -
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Residues in contact with VAL1831 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1778I GLN* 3.3 23.4 - - + +
1779I PRO* 3.2 39.0 - - + -
1782I THR* 3.4 20.4 - - + +
1809I LEU* 3.6 17.5 - - + -
1812I TYR* 4.1 26.9 - - + -
1827I LEU* 2.8 21.6 + - + +
1828I VAL* 4.3 2.0 - - - +
1830I VAL* 1.3 74.2 - - + +
1832I PHE* 1.3 62.1 + - - +
1834I ARG* 3.4 5.2 - - + +
1835I GLY 3.3 15.9 + - - -
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Residues in contact with PHE1832 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1698I PHE* 3.9 15.5 - + + -
1702I TYR* 3.8 47.6 - + + -
1704I PHE* 3.9 26.9 - + - -
1733I TYR* 5.0 6.3 - + - -
1736I MET* 4.7 7.2 - - - -
1752I PHE* 5.3 0.4 - + - -
1764I PHE* 5.0 2.5 - + - -
1775I GLN* 3.0 28.6 - - - +
1776I PHE* 4.1 7.6 - + - -
1779I PRO* 4.1 8.1 - - + -
1828I VAL 2.9 21.2 + - - +
1829I GLU* 3.0 6.6 + - - +
1831I VAL* 1.3 74.5 - - - +
1833I TYR* 1.3 64.2 + - + +
1835I GLY* 3.4 2.6 + - - -
1836I MET* 3.1 56.8 + - + +
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Residues in contact with TYR1833 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1736I MET* 3.5 34.3 - - + -
1737I ILE* 2.5 34.6 + - - +
1738I PHE* 4.5 3.3 - - - -
1739I GLU* 5.8 0.2 - - - +
1751I ILE* 4.3 9.9 - - + -
1829I GLU* 3.0 7.7 + - - +
1830I VAL 3.7 3.4 - - - +
1832I PHE* 1.3 76.5 - - + +
1834I ARG* 1.3 59.8 + - - +
1835I GLY 3.0 1.6 - - - -
1836I MET* 3.0 5.5 + - + +
1837I THR* 2.7 55.5 + - - -
1987I PRO* 4.3 14.6 + - - +
1988I PHE* 3.9 23.6 - + - -
1991I PHE* 3.7 52.2 - + + -
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Residues in contact with ARG1834 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLN* 3.9 12.9 - - - +
22C PHE* 4.3 18.3 - - + +
1778I GLN* 2.7 28.9 + - - +
1808I SER* 3.2 30.1 + - - -
1809I LEU* 3.6 19.4 - - - +
1812I TYR* 3.2 34.0 + - - -
1830I VAL* 2.9 17.5 + - - +
1831I VAL* 3.4 10.8 - - - +
1833I TYR* 1.3 78.3 - - - +
1835I GLY* 1.3 55.9 + - - +
1837I THR* 3.6 4.7 - - - -
1838I MET* 3.2 39.0 + - - +
1976I PHE* 5.8 1.8 - - - -
1977I HIS* 5.1 1.6 - - - -
1988I PHE* 3.6 31.2 - - + -
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Residues in contact with GLY1835 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1774I THR* 3.6 16.3 + - - -
1775I GLN* 4.3 11.0 - - - -
1778I GLN* 3.5 21.5 - - - +
1831I VAL 3.3 10.6 + - - -
1832I PHE 3.4 3.8 + - - -
1833I TYR 3.0 0.6 - - - -
1834I ARG* 1.3 75.2 - - - +
1836I MET* 1.3 63.8 + - - +
1837I THR 3.2 1.6 - - - -
1838I MET* 3.4 2.1 + - - +
1839I GLN* 3.1 21.8 + - - +
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Residues in contact with MET1836 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1736I MET* 4.7 7.9 - - - -
1751I ILE* 4.0 22.9 - - + +
1752I PHE* 3.5 26.9 - - + -
1764I PHE* 3.4 33.0 - - + -
1775I GLN* 3.3 36.8 - - + +
1832I PHE* 3.1 32.3 + - + +
1833I TYR* 3.0 10.0 + - - +
1835I GLY* 1.3 74.6 - - - +
1837I THR* 1.3 63.9 + - - +
1839I GLN* 3.3 16.5 + - - +
1840I VAL* 3.3 16.8 + - - +
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Residues in contact with THR1837 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PHE* 3.9 26.9 - - + -
1738I PHE* 3.4 29.6 - - + -
1751I ILE* 4.1 8.0 - - - +
1833I TYR* 2.7 52.0 + - + -
1834I ARG* 3.6 8.3 - - - -
1836I MET* 1.3 72.1 - - - +
1838I MET* 1.3 64.1 + - - +
1840I VAL* 3.0 13.5 + - - +
1841I ALA* 3.1 13.9 + - + +
1984I GLY 5.2 2.9 - - - +
1988I PHE* 4.6 3.1 - - + -
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Residues in contact with MET1838 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.8 27.4 - - + -
1669I GLN* 4.1 12.1 - - - +
1774I THR* 4.5 14.1 - - + +
1778I GLN* 3.7 23.1 - - - +
1834I ARG* 3.2 31.6 + - - +
1835I GLY 3.4 4.2 + - - +
1837I THR* 1.3 79.3 - - - +
1839I GLN* 1.3 62.4 + - - +
1840I VAL 3.1 1.0 + - - -
1841I ALA* 3.7 8.3 + - - -
1842I VAL 4.6 0.9 + - - -
1844I ARG* 4.6 0.2 + - - -
1974I VAL* 2.9 37.2 - - + +
1976I PHE* 4.0 42.8 - - + -
1981I LEU* 5.0 1.1 - - + -
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Residues in contact with GLN1839 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1773I ALA* 6.1 0.6 - - - +
1774I THR* 4.3 17.6 + - - +
1775I GLN* 4.0 29.5 + - + +
1835I GLY 3.1 15.0 + - - +
1836I MET* 3.5 15.5 - - - +
1837I THR 3.3 0.2 - - - -
1838I MET* 1.3 75.7 - - - +
1840I VAL* 1.3 60.8 + - + +
1844I ARG* 2.8 54.8 + - - +
1973I SER* 4.4 6.7 + - - -
1974I VAL* 5.6 1.4 - - - +
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Residues in contact with VAL1840 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1738I PHE* 3.8 23.1 - - + -
1749I GLU* 2.8 33.4 - - - +
1750I LYS 5.4 0.7 - - - +
1751I ILE* 3.8 38.6 - - + +
1753I LYS* 5.9 4.5 - - - -
1836I MET 3.3 8.7 + - - +
1837I THR 3.0 3.4 + - - +
1839I GLN* 1.3 83.6 - - + +
1841I ALA* 1.3 59.8 + - - +
1842I VAL 2.9 19.2 + - - +
1843I PRO* 5.3 0.3 - - - +
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Residues in contact with ALA1841 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1738I PHE* 3.4 33.7 - - + -
1837I THR* 3.1 13.9 + - + +
1838I MET* 3.7 7.0 + - - +
1840I VAL* 1.3 76.5 - - - +
1842I VAL* 1.3 64.7 + - - +
1843I PRO* 4.0 3.8 - - - +
1974I VAL* 4.8 9.0 - - + -
1980I TYR* 3.5 16.1 + - + -
1981I LEU* 5.1 12.6 - - + -
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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